Starting phenix.real_space_refine on Fri Sep 11 09:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nsj_0498/09_2026/6nsj_0498.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 6234 2.51 5 N 1332 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "C" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "D" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "E" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1449 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'XP4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'XP4:plan-1': 1, 'XP4:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.93, per 1000 atoms: 0.21 Number of scatterers: 9096 At special positions: 0 Unit cell: (101.65, 95.23, 59.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1494 8.00 N 1332 7.00 C 6234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.82 Conformation dependent library (CDL) restraints added in 325.7 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 3.806A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 54 removed outlier: 3.651A pdb=" N THR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N MET A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.541A pdb=" N ALA A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 125 removed outlier: 4.771A pdb=" N VAL A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.530A pdb=" N SER A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 161 removed outlier: 3.885A pdb=" N TRP A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.748A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 4.069A pdb=" N TRP A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 removed outlier: 3.581A pdb=" N LEU B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 23 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 54 removed outlier: 3.734A pdb=" N THR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N MET B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 98 removed outlier: 3.517A pdb=" N ALA B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 125 removed outlier: 4.734A pdb=" N VAL B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix removed outlier: 3.582A pdb=" N SER B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 161 removed outlier: 3.874A pdb=" N TRP B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TRP B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 157 " --> pdb=" O TRP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.700A pdb=" N TRP B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 4.030A pdb=" N TRP B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 23 removed outlier: 3.978A pdb=" N LEU C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 23 " --> pdb=" O CYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 54 removed outlier: 3.699A pdb=" N THR C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N MET C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 3.537A pdb=" N ALA C 79 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 125 removed outlier: 4.765A pdb=" N VAL C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.612A pdb=" N SER C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 161 removed outlier: 3.904A pdb=" N TRP C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 157 " --> pdb=" O TRP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.694A pdb=" N TRP C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 54 removed outlier: 3.651A pdb=" N THR D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N MET D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 97 removed outlier: 3.542A pdb=" N ALA D 79 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 125 removed outlier: 4.772A pdb=" N VAL D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Proline residue: D 117 - end of helix removed outlier: 3.530A pdb=" N SER D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 161 removed outlier: 3.891A pdb=" N TRP D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE D 157 " --> pdb=" O TRP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.747A pdb=" N TRP D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 4.067A pdb=" N TRP D 187 " --> pdb=" O TRP D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 23 removed outlier: 3.578A pdb=" N LEU E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 23 " --> pdb=" O CYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 54 removed outlier: 3.732A pdb=" N THR E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N MET E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL E 47 " --> pdb=" O CYS E 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 98 removed outlier: 3.518A pdb=" N ALA E 79 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 125 removed outlier: 4.736A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Proline residue: E 117 - end of helix removed outlier: 3.576A pdb=" N SER E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 161 removed outlier: 3.868A pdb=" N TRP E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP E 142 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 157 " --> pdb=" O TRP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.700A pdb=" N TRP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 4.030A pdb=" N TRP E 187 " --> pdb=" O TRP E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 23 removed outlier: 3.978A pdb=" N LEU F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS F 23 " --> pdb=" O CYS F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 54 removed outlier: 3.708A pdb=" N THR F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL F 47 " --> pdb=" O CYS F 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 98 removed outlier: 3.538A pdb=" N ALA F 79 " --> pdb=" O PHE F 75 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 125 removed outlier: 4.768A pdb=" N VAL F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.617A pdb=" N SER F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 161 removed outlier: 3.907A pdb=" N TRP F 141 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE F 157 " --> pdb=" O TRP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.695A pdb=" N TRP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 192 578 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1266 1.31 - 1.43: 2834 1.43 - 1.56: 5242 1.56 - 1.68: 6 1.68 - 1.80: 48 Bond restraints: 9396 Sorted by residual: bond pdb=" C18 XP4 D 201 " pdb=" O7 XP4 D 201 " ideal model delta sigma weight residual 1.328 1.403 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C18 XP4 E 201 " pdb=" O7 XP4 E 201 " ideal model delta sigma weight residual 1.328 1.403 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C18 XP4 A 201 " pdb=" O7 XP4 A 201 " ideal model delta sigma weight residual 1.328 1.402 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C18 XP4 B 201 " pdb=" O7 XP4 B 201 " ideal model delta sigma weight residual 1.328 1.402 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C18 XP4 C 201 " pdb=" O7 XP4 C 201 " ideal model delta sigma weight residual 1.328 1.401 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11914 2.05 - 4.10: 666 4.10 - 6.15: 143 6.15 - 8.21: 47 8.21 - 10.26: 34 Bond angle restraints: 12804 Sorted by residual: angle pdb=" N MET A 127 " pdb=" CA MET A 127 " pdb=" C MET A 127 " ideal model delta sigma weight residual 108.96 99.52 9.44 1.59e+00 3.96e-01 3.53e+01 angle pdb=" N MET D 127 " pdb=" CA MET D 127 " pdb=" C MET D 127 " ideal model delta sigma weight residual 108.96 99.68 9.28 1.59e+00 3.96e-01 3.41e+01 angle pdb=" C MET A 127 " pdb=" CA MET A 127 " pdb=" CB MET A 127 " ideal model delta sigma weight residual 110.22 117.20 -6.98 1.67e+00 3.59e-01 1.74e+01 angle pdb=" N TRP F 153 " pdb=" CA TRP F 153 " pdb=" C TRP F 153 " ideal model delta sigma weight residual 113.18 108.60 4.58 1.21e+00 6.83e-01 1.44e+01 angle pdb=" C MET D 127 " pdb=" CA MET D 127 " pdb=" CB MET D 127 " ideal model delta sigma weight residual 110.22 116.54 -6.32 1.67e+00 3.59e-01 1.43e+01 ... (remaining 12799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 4466 11.99 - 23.98: 435 23.98 - 35.97: 147 35.97 - 47.96: 70 47.96 - 59.95: 60 Dihedral angle restraints: 5178 sinusoidal: 2046 harmonic: 3132 Sorted by residual: dihedral pdb=" CA MET F 127 " pdb=" C MET F 127 " pdb=" N LEU F 128 " pdb=" CA LEU F 128 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 127 " pdb=" C MET C 127 " pdb=" N LEU C 128 " pdb=" CA LEU C 128 " ideal model delta harmonic sigma weight residual -180.00 -150.62 -29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA MET E 127 " pdb=" C MET E 127 " pdb=" N LEU E 128 " pdb=" CA LEU E 128 " ideal model delta harmonic sigma weight residual 180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 754 0.041 - 0.082: 479 0.082 - 0.122: 135 0.122 - 0.163: 43 0.163 - 0.204: 29 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB VAL C 12 " pdb=" CA VAL C 12 " pdb=" CG1 VAL C 12 " pdb=" CG2 VAL C 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL F 12 " pdb=" CA VAL F 12 " pdb=" CG1 VAL F 12 " pdb=" CG2 VAL F 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA ARG F 102 " pdb=" N ARG F 102 " pdb=" C ARG F 102 " pdb=" CB ARG F 102 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.47e-01 ... (remaining 1437 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 182 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.38e+00 pdb=" C ALA B 182 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA B 182 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP B 183 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 182 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C ALA E 182 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA E 182 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP E 183 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 182 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ALA D 182 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA D 182 " 0.015 2.00e-02 2.50e+03 pdb=" N TRP D 183 " 0.014 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2826 2.85 - 3.36: 8734 3.36 - 3.88: 14628 3.88 - 4.39: 17459 4.39 - 4.90: 29691 Nonbonded interactions: 73338 Sorted by model distance: nonbonded pdb=" O ARG D 102 " pdb=" OG SER D 105 " model vdw 2.340 3.040 nonbonded pdb=" O ARG A 102 " pdb=" OG SER A 105 " model vdw 2.340 3.040 nonbonded pdb=" O GLU E 177 " pdb=" OG1 THR E 181 " model vdw 2.360 3.040 nonbonded pdb=" O GLU B 177 " pdb=" OG1 THR B 181 " model vdw 2.360 3.040 nonbonded pdb=" O GLU C 177 " pdb=" OG1 THR C 181 " model vdw 2.364 3.040 ... (remaining 73333 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 201 or (resid 203 and (name C10 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O5 or name \ O6 )))) selection = (chain 'B' and (resid 1 through 201 or (resid 203 and (name C10 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O5 or name \ O6 )))) selection = (chain 'C' and (resid 1 through 201 or (resid 203 and (name C10 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O5 or name \ O6 )))) selection = (chain 'D' and (resid 1 through 201 or (resid 203 and (name C10 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O5 or name \ O6 )))) selection = (chain 'E' and (resid 1 through 201 or (resid 203 and (name C10 or name C3 or na \ me C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O5 or name \ O6 )))) selection = (chain 'F' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 7 or name O8 )) or resid 203)) } 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: 0.260 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.009 0.075 9396 Z= 0.399 Angle : 1.212 10.256 12804 Z= 0.610 Chirality : 0.060 0.204 1440 Planarity : 0.008 0.051 1470 Dihedral : 14.232 59.945 3174 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.18 % Allowed : 5.66 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.17), residues: 1068 helix: -2.78 (0.11), residues: 804 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG E 102 TYR 0.022 0.003 TYR A 88 PHE 0.025 0.004 PHE C 86 TRP 0.018 0.002 TRP D 142 HIS 0.009 0.002 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00861 / 0.40 ( 9396) covalent geometry : angle 1.21194 / 0.61 (12804) hydrogen bonds : bond 0.13471 / 9.11 ( 578) hydrogen bonds : angle 8.95768 / 6.43 ( 1734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.7946 (m) cc_final: 0.7698 (t) REVERT: A 146 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: B 75 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6299 (t80) REVERT: B 125 SER cc_start: 0.7684 (m) cc_final: 0.7412 (t) REVERT: B 134 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3984 (tt) REVERT: B 177 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 124 TYR cc_start: 0.6483 (m-80) cc_final: 0.5883 (m-10) REVERT: D 125 SER cc_start: 0.7927 (m) cc_final: 0.7700 (t) REVERT: D 146 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: E 75 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6282 (t80) REVERT: E 125 SER cc_start: 0.7614 (m) cc_final: 0.7333 (t) REVERT: E 177 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7535 (mt-10) REVERT: F 124 TYR cc_start: 0.6458 (m-80) cc_final: 0.5861 (m-10) outliers start: 20 outliers final: 4 residues processed: 153 average time/residue: 0.4400 time to fit residues: 73.2123 Evaluate side-chains 108 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 HIS B 131 HIS C 131 HIS E 95 HIS E 131 HIS F 131 HIS F 160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.124992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085889 restraints weight = 12877.927| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.89 r_work: 0.3133 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9396 Z= 0.157 Angle : 0.597 5.788 12804 Z= 0.307 Chirality : 0.042 0.136 1440 Planarity : 0.004 0.030 1470 Dihedral : 15.185 60.000 1428 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.18 % Allowed : 13.62 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1068 helix: -0.04 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -2.11 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 102 TYR 0.016 0.001 TYR C 8 PHE 0.016 0.002 PHE C 110 TRP 0.017 0.001 TRP E 142 HIS 0.003 0.001 HIS E 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9396) covalent geometry : angle 0.59658 / 0.31 (12804) hydrogen bonds : bond 0.04745 / 3.04 ( 578) hydrogen bonds : angle 4.34049 / 3.14 ( 1734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.245 Fit side-chains REVERT: A 125 SER cc_start: 0.6975 (m) cc_final: 0.6770 (t) REVERT: A 146 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: B 125 SER cc_start: 0.7025 (m) cc_final: 0.6753 (t) REVERT: B 126 ASP cc_start: 0.4621 (p0) cc_final: 0.3854 (t0) REVERT: B 134 LEU cc_start: 0.3784 (OUTLIER) cc_final: 0.3538 (tt) REVERT: B 146 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6657 (m-10) REVERT: C 22 THR cc_start: 0.7956 (m) cc_final: 0.7636 (p) REVERT: C 23 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8493 (mttm) REVERT: C 126 ASP cc_start: 0.4563 (p0) cc_final: 0.3653 (t0) REVERT: C 127 MET cc_start: 0.2184 (OUTLIER) cc_final: 0.1229 (ttm) REVERT: C 146 TRP cc_start: 0.7452 (OUTLIER) cc_final: 0.6970 (m-90) REVERT: C 153 TRP cc_start: 0.8508 (m-90) cc_final: 0.8303 (m-90) REVERT: D 125 SER cc_start: 0.6969 (m) cc_final: 0.6763 (t) REVERT: D 146 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: E 125 SER cc_start: 0.7033 (m) cc_final: 0.6747 (t) REVERT: E 126 ASP cc_start: 0.4597 (p0) cc_final: 0.3839 (t0) REVERT: E 146 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: F 22 THR cc_start: 0.7954 (m) cc_final: 0.7635 (p) REVERT: F 23 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8492 (mttm) REVERT: F 126 ASP cc_start: 0.4562 (p0) cc_final: 0.3649 (t0) REVERT: F 127 MET cc_start: 0.2271 (OUTLIER) cc_final: 0.1337 (ttm) REVERT: F 146 TRP cc_start: 0.7440 (OUTLIER) cc_final: 0.6946 (m-90) REVERT: F 153 TRP cc_start: 0.8501 (m-90) cc_final: 0.8298 (m-90) outliers start: 20 outliers final: 1 residues processed: 126 average time/residue: 0.4293 time to fit residues: 59.1193 Evaluate side-chains 110 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.125484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086108 restraints weight = 12760.822| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.86 r_work: 0.3140 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9396 Z= 0.140 Angle : 0.547 7.595 12804 Z= 0.279 Chirality : 0.041 0.133 1440 Planarity : 0.003 0.029 1470 Dihedral : 14.249 59.224 1424 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.94 % Allowed : 13.62 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1068 helix: 0.96 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.05 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 102 TYR 0.017 0.002 TYR D 8 PHE 0.015 0.002 PHE C 110 TRP 0.010 0.001 TRP C 142 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9396) covalent geometry : angle 0.54695 / 0.28 (12804) hydrogen bonds : bond 0.04194 / 2.68 ( 578) hydrogen bonds : angle 3.81815 / 2.77 ( 1734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.324 Fit side-chains REVERT: A 22 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7724 (p) REVERT: A 75 PHE cc_start: 0.6329 (OUTLIER) cc_final: 0.5785 (t80) REVERT: B 75 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6565 (t80) REVERT: B 125 SER cc_start: 0.6956 (m) cc_final: 0.6628 (t) REVERT: B 126 ASP cc_start: 0.4406 (p0) cc_final: 0.3774 (t0) REVERT: B 127 MET cc_start: 0.3092 (OUTLIER) cc_final: 0.2059 (ttm) REVERT: B 134 LEU cc_start: 0.3745 (OUTLIER) cc_final: 0.3497 (tt) REVERT: B 146 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: C 22 THR cc_start: 0.7941 (m) cc_final: 0.7643 (p) REVERT: C 23 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8458 (mttm) REVERT: C 75 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5920 (t80) REVERT: C 126 ASP cc_start: 0.4504 (p0) cc_final: 0.3613 (t0) REVERT: D 75 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5795 (t80) REVERT: E 75 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6624 (t80) REVERT: E 125 SER cc_start: 0.6899 (m) cc_final: 0.6570 (t) REVERT: E 126 ASP cc_start: 0.4359 (p0) cc_final: 0.3710 (t0) REVERT: E 127 MET cc_start: 0.3074 (OUTLIER) cc_final: 0.2036 (ttm) REVERT: E 146 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: F 22 THR cc_start: 0.7932 (m) cc_final: 0.7636 (p) REVERT: F 23 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8450 (mttm) REVERT: F 75 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.5985 (t80) REVERT: F 126 ASP cc_start: 0.4502 (p0) cc_final: 0.3609 (t0) outliers start: 27 outliers final: 9 residues processed: 126 average time/residue: 0.4161 time to fit residues: 57.4072 Evaluate side-chains 127 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.125761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086085 restraints weight = 12904.511| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.90 r_work: 0.3135 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9396 Z= 0.128 Angle : 0.526 6.469 12804 Z= 0.266 Chirality : 0.040 0.136 1440 Planarity : 0.003 0.030 1470 Dihedral : 13.626 59.722 1424 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.03 % Allowed : 13.40 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1068 helix: 1.44 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 102 TYR 0.020 0.001 TYR F 8 PHE 0.015 0.001 PHE F 110 TRP 0.009 0.001 TRP E 142 HIS 0.002 0.001 HIS E 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9396) covalent geometry : angle 0.52578 / 0.27 (12804) hydrogen bonds : bond 0.03911 / 2.50 ( 578) hydrogen bonds : angle 3.62949 / 2.63 ( 1734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.338 Fit side-chains REVERT: A 22 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7726 (p) REVERT: A 75 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.5790 (t80) REVERT: B 4 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8058 (mm) REVERT: B 75 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6497 (t80) REVERT: B 125 SER cc_start: 0.6871 (m) cc_final: 0.6561 (t) REVERT: B 126 ASP cc_start: 0.4444 (p0) cc_final: 0.3782 (t0) REVERT: B 134 LEU cc_start: 0.3837 (OUTLIER) cc_final: 0.3579 (tt) REVERT: B 146 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6822 (m-10) REVERT: C 22 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7685 (p) REVERT: C 23 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8339 (mppt) REVERT: C 126 ASP cc_start: 0.4421 (p0) cc_final: 0.3657 (t0) REVERT: D 22 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7734 (p) REVERT: D 75 PHE cc_start: 0.6335 (OUTLIER) cc_final: 0.5793 (t80) REVERT: E 4 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8018 (mm) REVERT: E 75 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6484 (t80) REVERT: E 125 SER cc_start: 0.6834 (m) cc_final: 0.6592 (t) REVERT: E 126 ASP cc_start: 0.4430 (p0) cc_final: 0.3776 (t0) REVERT: E 146 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: F 22 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7684 (p) REVERT: F 23 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8337 (mppt) REVERT: F 126 ASP cc_start: 0.4424 (p0) cc_final: 0.3657 (t0) outliers start: 37 outliers final: 9 residues processed: 133 average time/residue: 0.4369 time to fit residues: 63.4418 Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.127490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087750 restraints weight = 12742.586| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.90 r_work: 0.3160 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9396 Z= 0.105 Angle : 0.500 5.748 12804 Z= 0.252 Chirality : 0.039 0.145 1440 Planarity : 0.003 0.028 1470 Dihedral : 12.878 59.384 1424 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.14 % Allowed : 13.83 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1068 helix: 1.72 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.48 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG D 102 TYR 0.019 0.001 TYR F 8 PHE 0.014 0.001 PHE C 110 TRP 0.008 0.001 TRP E 142 HIS 0.001 0.000 HIS D 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9396) covalent geometry : angle 0.49971 / 0.25 (12804) hydrogen bonds : bond 0.03380 / 2.15 ( 578) hydrogen bonds : angle 3.44415 / 2.50 ( 1734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.366 Fit side-chains REVERT: A 22 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7812 (p) REVERT: B 75 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 125 SER cc_start: 0.6702 (m) cc_final: 0.6353 (t) REVERT: B 126 ASP cc_start: 0.4405 (p0) cc_final: 0.3692 (t0) REVERT: B 134 LEU cc_start: 0.3923 (OUTLIER) cc_final: 0.3686 (tt) REVERT: B 146 TRP cc_start: 0.7335 (OUTLIER) cc_final: 0.6761 (m-10) REVERT: C 22 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 23 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8360 (mppt) REVERT: C 126 ASP cc_start: 0.4471 (p0) cc_final: 0.3778 (t0) REVERT: C 168 LYS cc_start: 0.8259 (tptt) cc_final: 0.8041 (mtpp) REVERT: E 75 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6318 (t80) REVERT: E 125 SER cc_start: 0.6833 (m) cc_final: 0.6528 (t) REVERT: E 126 ASP cc_start: 0.4388 (p0) cc_final: 0.3681 (t0) REVERT: E 146 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.6762 (m-10) REVERT: F 22 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7553 (p) REVERT: F 23 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8359 (mppt) REVERT: F 126 ASP cc_start: 0.4476 (p0) cc_final: 0.3778 (t0) REVERT: F 168 LYS cc_start: 0.8250 (tptt) cc_final: 0.8035 (mtpp) outliers start: 38 outliers final: 15 residues processed: 137 average time/residue: 0.3963 time to fit residues: 59.5331 Evaluate side-chains 134 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083521 restraints weight = 12988.555| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.90 r_work: 0.3101 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9396 Z= 0.194 Angle : 0.563 6.334 12804 Z= 0.287 Chirality : 0.043 0.147 1440 Planarity : 0.003 0.028 1470 Dihedral : 12.820 57.801 1424 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.05 % Allowed : 15.36 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1068 helix: 1.75 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 102 TYR 0.021 0.002 TYR D 8 PHE 0.018 0.002 PHE C 75 TRP 0.008 0.001 TRP C 172 HIS 0.003 0.001 HIS C 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 9396) covalent geometry : angle 0.56305 / 0.29 (12804) hydrogen bonds : bond 0.04546 / 2.90 ( 578) hydrogen bonds : angle 3.68057 / 2.66 ( 1734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.371 Fit side-chains REVERT: A 22 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 32 MET cc_start: 0.8173 (tpt) cc_final: 0.7855 (tpt) REVERT: B 75 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6358 (t80) REVERT: B 125 SER cc_start: 0.7016 (m) cc_final: 0.6689 (t) REVERT: B 126 ASP cc_start: 0.4420 (p0) cc_final: 0.3717 (t0) REVERT: B 134 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3808 (tt) REVERT: B 146 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: C 22 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7702 (p) REVERT: C 23 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8266 (mppt) REVERT: C 126 ASP cc_start: 0.4565 (p0) cc_final: 0.3855 (t0) REVERT: D 22 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7863 (p) REVERT: D 32 MET cc_start: 0.8180 (tpt) cc_final: 0.7860 (tpt) REVERT: E 75 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.6434 (t80) REVERT: E 125 SER cc_start: 0.6927 (m) cc_final: 0.6643 (t) REVERT: E 126 ASP cc_start: 0.4417 (p0) cc_final: 0.3717 (t0) REVERT: E 146 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6861 (m-10) REVERT: F 22 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7699 (p) REVERT: F 23 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8264 (mppt) REVERT: F 126 ASP cc_start: 0.4628 (p0) cc_final: 0.3864 (t0) outliers start: 28 outliers final: 12 residues processed: 127 average time/residue: 0.4188 time to fit residues: 58.1428 Evaluate side-chains 130 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 75 PHE Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.127130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087387 restraints weight = 12748.170| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.90 r_work: 0.3160 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9396 Z= 0.101 Angle : 0.505 9.070 12804 Z= 0.254 Chirality : 0.039 0.133 1440 Planarity : 0.003 0.026 1470 Dihedral : 12.486 56.610 1424 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.94 % Allowed : 15.03 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.26), residues: 1068 helix: 2.02 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.39 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 102 TYR 0.016 0.001 TYR C 8 PHE 0.013 0.001 PHE C 110 TRP 0.009 0.001 TRP B 142 HIS 0.001 0.000 HIS C 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 9396) covalent geometry : angle 0.50518 / 0.25 (12804) hydrogen bonds : bond 0.03453 / 2.20 ( 578) hydrogen bonds : angle 3.47531 / 2.52 ( 1734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.379 Fit side-chains REVERT: A 22 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7873 (p) REVERT: A 32 MET cc_start: 0.8163 (tpt) cc_final: 0.7853 (tpt) REVERT: B 125 SER cc_start: 0.6913 (m) cc_final: 0.6569 (t) REVERT: B 126 ASP cc_start: 0.4350 (p0) cc_final: 0.3657 (t0) REVERT: B 146 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.6813 (m-10) REVERT: C 22 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7581 (p) REVERT: C 23 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8283 (mppt) REVERT: C 126 ASP cc_start: 0.4721 (p0) cc_final: 0.4015 (t0) REVERT: D 22 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7881 (p) REVERT: D 32 MET cc_start: 0.8174 (tpt) cc_final: 0.7871 (tpt) REVERT: E 125 SER cc_start: 0.6820 (m) cc_final: 0.6516 (t) REVERT: E 126 ASP cc_start: 0.4340 (p0) cc_final: 0.3647 (t0) REVERT: E 146 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: F 22 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7583 (p) REVERT: F 23 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8280 (mppt) REVERT: F 126 ASP cc_start: 0.4749 (p0) cc_final: 0.4066 (t0) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.3983 time to fit residues: 58.3432 Evaluate side-chains 139 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086774 restraints weight = 12747.854| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.89 r_work: 0.3148 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9396 Z= 0.117 Angle : 0.511 6.962 12804 Z= 0.259 Chirality : 0.040 0.144 1440 Planarity : 0.003 0.026 1470 Dihedral : 12.272 56.128 1422 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.40 % Allowed : 15.90 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1068 helix: 2.22 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG D 102 TYR 0.019 0.001 TYR D 8 PHE 0.024 0.001 PHE D 75 TRP 0.008 0.001 TRP A 153 HIS 0.001 0.000 HIS E 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9396) covalent geometry : angle 0.51079 / 0.26 (12804) hydrogen bonds : bond 0.03631 / 2.31 ( 578) hydrogen bonds : angle 3.48651 / 2.53 ( 1734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.322 Fit side-chains REVERT: A 22 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 32 MET cc_start: 0.8226 (tpt) cc_final: 0.7922 (tpt) REVERT: B 125 SER cc_start: 0.6910 (m) cc_final: 0.6564 (t) REVERT: B 126 ASP cc_start: 0.4344 (p0) cc_final: 0.3764 (t0) REVERT: B 146 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.6816 (m-10) REVERT: C 22 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 23 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8320 (mtpt) REVERT: C 126 ASP cc_start: 0.4825 (p0) cc_final: 0.4111 (t0) REVERT: D 22 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7875 (p) REVERT: D 32 MET cc_start: 0.8230 (tpt) cc_final: 0.7925 (tpt) REVERT: E 125 SER cc_start: 0.6902 (m) cc_final: 0.6545 (t) REVERT: E 126 ASP cc_start: 0.4461 (p0) cc_final: 0.3849 (t0) REVERT: E 146 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.6847 (m-10) REVERT: F 22 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (p) REVERT: F 23 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8320 (mtpt) REVERT: F 126 ASP cc_start: 0.4835 (p0) cc_final: 0.4113 (t0) outliers start: 22 outliers final: 12 residues processed: 131 average time/residue: 0.4163 time to fit residues: 59.7923 Evaluate side-chains 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088860 restraints weight = 12587.781| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.88 r_work: 0.3177 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9396 Z= 0.098 Angle : 0.500 9.185 12804 Z= 0.250 Chirality : 0.039 0.141 1440 Planarity : 0.003 0.024 1470 Dihedral : 11.999 57.962 1422 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 15.90 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.26), residues: 1068 helix: 2.33 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG D 102 TYR 0.016 0.001 TYR C 8 PHE 0.014 0.001 PHE C 110 TRP 0.008 0.001 TRP C 153 HIS 0.001 0.000 HIS F 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 9396) covalent geometry : angle 0.50027 / 0.25 (12804) hydrogen bonds : bond 0.03188 / 2.03 ( 578) hydrogen bonds : angle 3.39440 / 2.46 ( 1734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.322 Fit side-chains REVERT: A 32 MET cc_start: 0.8206 (tpt) cc_final: 0.7912 (tpt) REVERT: B 125 SER cc_start: 0.6889 (m) cc_final: 0.6528 (t) REVERT: B 126 ASP cc_start: 0.4422 (p0) cc_final: 0.3939 (t0) REVERT: B 146 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: C 22 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7601 (p) REVERT: C 23 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8379 (mtpt) REVERT: C 126 ASP cc_start: 0.4956 (p0) cc_final: 0.4229 (t0) REVERT: D 32 MET cc_start: 0.8218 (tpt) cc_final: 0.7914 (tpt) REVERT: E 125 SER cc_start: 0.6877 (m) cc_final: 0.6511 (t) REVERT: E 126 ASP cc_start: 0.4410 (p0) cc_final: 0.3931 (t0) REVERT: E 146 TRP cc_start: 0.7412 (OUTLIER) cc_final: 0.6836 (m-10) REVERT: F 22 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7605 (p) REVERT: F 23 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8379 (mtpt) REVERT: F 126 ASP cc_start: 0.4963 (p0) cc_final: 0.4230 (t0) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.4140 time to fit residues: 59.5151 Evaluate side-chains 134 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.129439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089479 restraints weight = 12579.303| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.88 r_work: 0.3200 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9396 Z= 0.096 Angle : 0.497 7.214 12804 Z= 0.249 Chirality : 0.039 0.140 1440 Planarity : 0.003 0.024 1470 Dihedral : 11.922 59.073 1422 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.74 % Allowed : 16.88 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1068 helix: 2.39 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG D 102 TYR 0.021 0.001 TYR C 8 PHE 0.014 0.001 PHE F 110 TRP 0.009 0.001 TRP D 153 HIS 0.001 0.000 HIS D 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 9396) covalent geometry : angle 0.49747 / 0.25 (12804) hydrogen bonds : bond 0.03141 / 1.99 ( 578) hydrogen bonds : angle 3.37712 / 2.45 ( 1734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.391 Fit side-chains REVERT: A 32 MET cc_start: 0.8193 (tpt) cc_final: 0.7886 (tpt) REVERT: B 125 SER cc_start: 0.6816 (m) cc_final: 0.6436 (t) REVERT: B 126 ASP cc_start: 0.4348 (p0) cc_final: 0.3940 (t0) REVERT: B 146 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.6641 (m-90) REVERT: C 22 THR cc_start: 0.7899 (m) cc_final: 0.7618 (p) REVERT: C 23 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8370 (mtpt) REVERT: C 126 ASP cc_start: 0.5029 (p0) cc_final: 0.4306 (t0) REVERT: E 125 SER cc_start: 0.6801 (m) cc_final: 0.6418 (t) REVERT: E 126 ASP cc_start: 0.4332 (p0) cc_final: 0.3928 (t0) REVERT: E 146 TRP cc_start: 0.7418 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: F 22 THR cc_start: 0.7898 (m) cc_final: 0.7615 (p) REVERT: F 23 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8364 (mtpt) REVERT: F 126 ASP cc_start: 0.5045 (p0) cc_final: 0.4311 (t0) outliers start: 16 outliers final: 14 residues processed: 126 average time/residue: 0.4038 time to fit residues: 55.9146 Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 146 TRP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 146 TRP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 TRP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 146 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086001 restraints weight = 12665.892| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.88 r_work: 0.3135 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9396 Z= 0.156 Angle : 0.547 9.295 12804 Z= 0.274 Chirality : 0.042 0.137 1440 Planarity : 0.003 0.024 1470 Dihedral : 11.914 59.232 1422 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 16.23 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.26), residues: 1068 helix: 2.27 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -1.25 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 102 TYR 0.021 0.002 TYR C 8 PHE 0.022 0.002 PHE D 75 TRP 0.008 0.001 TRP D 153 HIS 0.003 0.001 HIS D 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9396) covalent geometry : angle 0.54668 / 0.27 (12804) hydrogen bonds : bond 0.03910 / 2.50 ( 578) hydrogen bonds : angle 3.52821 / 2.56 ( 1734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2386.68 seconds wall clock time: 41 minutes 38.67 seconds (2498.67 seconds total)