Starting phenix.real_space_refine on Sat Jun 14 05:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.map" model { file = "/net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7h_19772/06_2025/8s7h_19772.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 10290 2.51 5 N 2720 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16120 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "B" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "H" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "I" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "J" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Time building chain proxies: 10.34, per 1000 atoms: 0.64 Number of scatterers: 16120 At special positions: 0 Unit cell: (120.35, 123.67, 80.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3020 8.00 N 2720 7.00 C 10290 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: 4.53 Conformation dependent library (CDL) restraints added in 2.3 seconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 63.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.971A pdb=" N ARG A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 38 through 50 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.734A pdb=" N ALA A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'B' and resid 9 through 18 removed outlier: 4.001A pdb=" N ARG B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 38 through 50 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 64 through 79 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 113 through 123 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.886A pdb=" N ALA B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 197 through 216 Processing helix chain 'C' and resid 9 through 18 removed outlier: 4.160A pdb=" N ARG C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 38 through 50 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'C' and resid 89 through 103 Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 141 through 157 Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.750A pdb=" N ALA C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 197 through 216 Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.941A pdb=" N ARG D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 38 through 50 Proline residue: D 44 - end of helix Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 89 through 103 Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 141 through 157 Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.768A pdb=" N ALA D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 197 through 216 Processing helix chain 'E' and resid 9 through 18 removed outlier: 4.071A pdb=" N ARG E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 36 Processing helix chain 'E' and resid 38 through 50 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 64 through 79 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 141 through 157 Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.845A pdb=" N ALA E 173 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.503A pdb=" N ILE E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 216 Processing helix chain 'F' and resid 9 through 18 removed outlier: 4.350A pdb=" N ARG F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 36 Processing helix chain 'F' and resid 38 through 50 Proline residue: F 44 - end of helix Processing helix chain 'F' and resid 64 through 79 Processing helix chain 'F' and resid 89 through 103 Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 141 through 157 Processing helix chain 'F' and resid 169 through 179 removed outlier: 3.743A pdb=" N ALA F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 195 Processing helix chain 'F' and resid 197 through 216 Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.937A pdb=" N ARG G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 38 through 51 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 64 through 79 Processing helix chain 'G' and resid 89 through 103 Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 131 through 138 Processing helix chain 'G' and resid 141 through 157 Processing helix chain 'G' and resid 169 through 179 removed outlier: 3.762A pdb=" N ALA G 173 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 195 Processing helix chain 'G' and resid 197 through 216 Processing helix chain 'H' and resid 9 through 18 removed outlier: 4.099A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 36 Processing helix chain 'H' and resid 38 through 50 Proline residue: H 44 - end of helix Processing helix chain 'H' and resid 64 through 79 Processing helix chain 'H' and resid 89 through 102 Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 131 through 138 Processing helix chain 'H' and resid 141 through 157 Processing helix chain 'H' and resid 169 through 179 removed outlier: 3.784A pdb=" N ALA H 173 " --> pdb=" O THR H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 195 Processing helix chain 'H' and resid 197 through 216 Processing helix chain 'I' and resid 9 through 18 removed outlier: 4.091A pdb=" N ARG I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 Processing helix chain 'I' and resid 38 through 50 Proline residue: I 44 - end of helix Processing helix chain 'I' and resid 64 through 79 Processing helix chain 'I' and resid 89 through 103 Processing helix chain 'I' and resid 113 through 124 Processing helix chain 'I' and resid 131 through 138 Processing helix chain 'I' and resid 141 through 157 Processing helix chain 'I' and resid 169 through 179 removed outlier: 3.870A pdb=" N ALA I 173 " --> pdb=" O THR I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 195 Processing helix chain 'I' and resid 197 through 216 Processing helix chain 'J' and resid 9 through 18 removed outlier: 4.044A pdb=" N ARG J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 36 Processing helix chain 'J' and resid 38 through 50 Proline residue: J 44 - end of helix Processing helix chain 'J' and resid 64 through 79 Processing helix chain 'J' and resid 89 through 103 Processing helix chain 'J' and resid 113 through 124 Processing helix chain 'J' and resid 131 through 138 Processing helix chain 'J' and resid 141 through 157 Processing helix chain 'J' and resid 169 through 179 removed outlier: 3.798A pdb=" N ALA J 173 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 195 Processing helix chain 'J' and resid 197 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 6.645A pdb=" N LEU A 3 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR A 26 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 5 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 57 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 56 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LYS A 85 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA A 58 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR A 106 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ALA A 129 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 108 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL A 128 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU A 2 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU A 186 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR A 4 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 6 removed outlier: 6.539A pdb=" N LEU B 3 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR B 26 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 5 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 56 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS B 85 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 58 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR B 106 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA B 129 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY B 108 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL B 128 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU B 2 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 186 " --> pdb=" O GLU B 2 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 4 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.563A pdb=" N LEU C 3 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR C 26 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU C 5 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 57 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 56 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS C 85 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA C 58 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C 106 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ALA C 129 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 108 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL C 128 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU C 2 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU C 186 " --> pdb=" O GLU C 2 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR C 4 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 6.503A pdb=" N LEU D 3 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR D 26 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU D 5 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 57 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 56 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LYS D 85 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA D 58 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 84 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 109 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 86 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL D 111 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR D 106 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA D 129 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY D 108 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL D 128 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU D 2 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU D 186 " --> pdb=" O GLU D 2 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR D 4 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.599A pdb=" N LEU E 3 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR E 26 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU E 5 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 57 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 56 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS E 85 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA E 58 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL E 84 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR E 109 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 86 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 111 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR E 106 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ALA E 129 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY E 108 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL E 128 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP E 6 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 6.619A pdb=" N LEU F 3 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 26 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU F 5 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE F 57 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 56 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS F 85 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA F 58 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 109 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR F 106 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA F 129 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY F 108 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL F 128 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 6 removed outlier: 6.541A pdb=" N LEU G 3 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR G 26 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU G 5 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 57 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU G 56 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LYS G 85 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA G 58 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL G 84 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR G 109 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL G 86 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL G 111 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR G 106 " --> pdb=" O TYR G 127 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ALA G 129 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY G 108 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL G 128 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU G 2 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LEU G 186 " --> pdb=" O GLU G 2 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR G 4 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.537A pdb=" N LEU H 3 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR H 26 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU H 5 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 56 " --> pdb=" O VAL H 83 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LYS H 85 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA H 58 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR H 106 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA H 129 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY H 108 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL H 128 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL H 162 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR H 185 " --> pdb=" O VAL H 162 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA H 164 " --> pdb=" O THR H 185 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU H 2 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU H 186 " --> pdb=" O GLU H 2 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR H 4 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 removed outlier: 6.485A pdb=" N LEU I 3 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR I 26 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU I 5 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE I 57 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU I 56 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS I 85 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA I 58 " --> pdb=" O LYS I 85 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR I 106 " --> pdb=" O TYR I 127 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ALA I 129 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY I 108 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL I 128 " --> pdb=" O LEU I 163 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL I 162 " --> pdb=" O SER I 183 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR I 185 " --> pdb=" O VAL I 162 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA I 164 " --> pdb=" O THR I 185 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP I 6 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 6 removed outlier: 6.482A pdb=" N LEU J 3 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR J 26 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU J 5 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE J 57 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU J 56 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LYS J 85 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA J 58 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR J 106 " --> pdb=" O TYR J 127 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA J 129 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY J 108 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL J 128 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU J 2 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU J 186 " --> pdb=" O GLU J 2 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR J 4 " --> pdb=" O LEU J 186 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2892 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: 5.18 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5330 1.34 - 1.46: 3122 1.46 - 1.58: 7758 1.58 - 1.70: 0 1.70 - 1.82: 160 Bond restraints: 16370 Sorted by residual: bond pdb=" CA ILE A 104 " pdb=" C ILE A 104 " ideal model delta sigma weight residual 1.525 1.541 -0.016 8.80e-03 1.29e+04 3.12e+00 bond pdb=" CB LYS A 206 " pdb=" CG LYS A 206 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB LYS G 206 " pdb=" CG LYS G 206 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB LYS I 206 " pdb=" CG LYS I 206 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CD GLU B 208 " pdb=" OE1 GLU B 208 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.53e+00 ... (remaining 16365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 21902 3.47 - 6.94: 291 6.94 - 10.40: 54 10.40 - 13.87: 21 13.87 - 17.34: 2 Bond angle restraints: 22270 Sorted by residual: angle pdb=" CA LEU E 43 " pdb=" CB LEU E 43 " pdb=" CG LEU E 43 " ideal model delta sigma weight residual 116.30 133.64 -17.34 3.50e+00 8.16e-02 2.45e+01 angle pdb=" N GLY C 51 " pdb=" CA GLY C 51 " pdb=" C GLY C 51 " ideal model delta sigma weight residual 115.64 108.89 6.75 1.46e+00 4.69e-01 2.14e+01 angle pdb=" CA MET H 194 " pdb=" CB MET H 194 " pdb=" CG MET H 194 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" CA LEU H 43 " pdb=" CB LEU H 43 " pdb=" CG LEU H 43 " ideal model delta sigma weight residual 116.30 130.89 -14.59 3.50e+00 8.16e-02 1.74e+01 angle pdb=" CB MET H 1 " pdb=" CG MET H 1 " pdb=" SD MET H 1 " ideal model delta sigma weight residual 112.70 125.05 -12.35 3.00e+00 1.11e-01 1.70e+01 ... (remaining 22265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 8960 17.45 - 34.89: 760 34.89 - 52.34: 164 52.34 - 69.78: 65 69.78 - 87.23: 11 Dihedral angle restraints: 9960 sinusoidal: 3680 harmonic: 6280 Sorted by residual: dihedral pdb=" CA MET I 50 " pdb=" C MET I 50 " pdb=" N GLY I 51 " pdb=" CA GLY I 51 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA MET H 50 " pdb=" C MET H 50 " pdb=" N GLY H 51 " pdb=" CA GLY H 51 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA MET D 50 " pdb=" C MET D 50 " pdb=" N GLY D 51 " pdb=" CA GLY D 51 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 9957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2272 0.059 - 0.119: 387 0.119 - 0.178: 58 0.178 - 0.237: 11 0.237 - 0.296: 2 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CG LEU G 99 " pdb=" CB LEU G 99 " pdb=" CD1 LEU G 99 " pdb=" CD2 LEU G 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CG LEU A 99 " pdb=" CB LEU A 99 " pdb=" CD1 LEU A 99 " pdb=" CD2 LEU A 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU D 43 " pdb=" CB LEU D 43 " pdb=" CD1 LEU D 43 " pdb=" CD2 LEU D 43 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2727 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 211 " 0.017 2.00e-02 2.50e+03 1.30e-02 4.23e+00 pdb=" CG TRP A 211 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 211 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 211 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 211 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 211 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 211 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 211 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 211 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 211 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 28 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO A 29 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 28 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO G 29 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 29 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 29 " 0.027 5.00e-02 4.00e+02 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 661 2.71 - 3.26: 18041 3.26 - 3.81: 29493 3.81 - 4.35: 33540 4.35 - 4.90: 55747 Nonbonded interactions: 137482 Sorted by model distance: nonbonded pdb=" N GLU J 126 " pdb=" OE1 GLU J 126 " model vdw 2.167 3.120 nonbonded pdb=" N GLU B 126 " pdb=" OE1 GLU B 126 " model vdw 2.182 3.120 nonbonded pdb=" OD2 ASP D 136 " pdb=" OG1 THR I 169 " model vdw 2.204 3.040 nonbonded pdb=" N GLU H 66 " pdb=" OE1 GLU H 66 " model vdw 2.206 3.120 nonbonded pdb=" NH1 ARG H 76 " pdb=" O ALA H 80 " model vdw 2.207 3.120 ... (remaining 137477 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.750 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: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 39.930 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16370 Z= 0.187 Angle : 1.034 17.340 22270 Z= 0.501 Chirality : 0.047 0.296 2730 Planarity : 0.005 0.070 2850 Dihedral : 14.767 87.227 5920 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.84 % Allowed : 22.57 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2180 helix: 0.97 (0.14), residues: 1400 sheet: -0.24 (0.27), residues: 350 loop : -1.12 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 211 HIS 0.009 0.001 HIS B 156 PHE 0.017 0.002 PHE A 207 TYR 0.008 0.001 TYR J 127 ARG 0.014 0.001 ARG H 217 Details of bonding type rmsd hydrogen bonds : bond 0.09532 ( 972) hydrogen bonds : angle 5.96156 ( 2892) covalent geometry : bond 0.00389 (16370) covalent geometry : angle 1.03405 (22270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 475 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LEU cc_start: 0.3819 (mt) cc_final: 0.3564 (tp) REVERT: A 91 GLU cc_start: 0.6768 (mm-30) cc_final: 0.5688 (pp20) REVERT: A 112 TYR cc_start: 0.5307 (m-80) cc_final: 0.5092 (m-80) REVERT: A 126 GLU cc_start: 0.5751 (tt0) cc_final: 0.5377 (tp30) REVERT: A 127 TYR cc_start: 0.4235 (m-80) cc_final: 0.3793 (m-10) REVERT: A 128 VAL cc_start: 0.5271 (t) cc_final: 0.5065 (t) REVERT: A 217 ARG cc_start: 0.6413 (mpp-170) cc_final: 0.5987 (mmp80) REVERT: B 91 GLU cc_start: 0.5910 (mm-30) cc_final: 0.4788 (pp20) REVERT: B 112 TYR cc_start: 0.5645 (m-80) cc_final: 0.5299 (m-80) REVERT: B 127 TYR cc_start: 0.3652 (m-80) cc_final: 0.2897 (m-10) REVERT: B 153 LEU cc_start: 0.6008 (mt) cc_final: 0.5747 (mt) REVERT: C 75 LEU cc_start: 0.5196 (mm) cc_final: 0.4931 (mm) REVERT: C 112 TYR cc_start: 0.5934 (m-80) cc_final: 0.5695 (m-80) REVERT: C 126 GLU cc_start: 0.6010 (tt0) cc_final: 0.5380 (mm-30) REVERT: C 127 TYR cc_start: 0.3911 (m-80) cc_final: 0.2606 (m-10) REVERT: C 128 VAL cc_start: 0.5552 (t) cc_final: 0.5347 (t) REVERT: D 91 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5374 (pp20) REVERT: D 116 GLN cc_start: 0.3900 (tt0) cc_final: 0.3487 (tm-30) REVERT: D 126 GLU cc_start: 0.5939 (tt0) cc_final: 0.5531 (mm-30) REVERT: D 127 TYR cc_start: 0.4541 (m-80) cc_final: 0.4187 (m-10) REVERT: D 207 PHE cc_start: 0.4103 (t80) cc_final: 0.3795 (t80) REVERT: E 112 TYR cc_start: 0.5575 (m-80) cc_final: 0.5282 (m-80) REVERT: E 127 TYR cc_start: 0.3755 (m-80) cc_final: 0.2981 (m-10) REVERT: F 5 LEU cc_start: 0.4720 (mt) cc_final: 0.4500 (tp) REVERT: F 6 ASP cc_start: 0.4092 (t0) cc_final: 0.3533 (p0) REVERT: F 7 THR cc_start: 0.5750 (t) cc_final: 0.5433 (t) REVERT: F 61 MET cc_start: 0.1543 (ppp) cc_final: 0.0939 (pp-130) REVERT: F 91 GLU cc_start: 0.6605 (mm-30) cc_final: 0.5707 (pp20) REVERT: F 112 TYR cc_start: 0.5629 (m-80) cc_final: 0.5272 (m-80) REVERT: F 126 GLU cc_start: 0.5923 (tt0) cc_final: 0.5457 (mm-30) REVERT: F 127 TYR cc_start: 0.4019 (m-80) cc_final: 0.3090 (m-10) REVERT: F 131 TYR cc_start: 0.3718 (m-10) cc_final: 0.3187 (m-10) REVERT: F 207 PHE cc_start: 0.3786 (t80) cc_final: 0.3543 (t80) REVERT: G 50 MET cc_start: 0.2343 (mmt) cc_final: 0.2131 (mmm) REVERT: G 91 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5462 (pp20) REVERT: G 112 TYR cc_start: 0.5626 (m-80) cc_final: 0.5212 (m-80) REVERT: G 126 GLU cc_start: 0.5848 (tt0) cc_final: 0.5031 (mm-30) REVERT: G 127 TYR cc_start: 0.4701 (m-80) cc_final: 0.2526 (m-10) REVERT: G 128 VAL cc_start: 0.5200 (t) cc_final: 0.4924 (t) REVERT: G 177 LEU cc_start: 0.5058 (mt) cc_final: 0.4850 (mp) REVERT: H 50 MET cc_start: 0.2955 (mmt) cc_final: 0.2729 (mmm) REVERT: H 61 MET cc_start: 0.1095 (ppp) cc_final: 0.0745 (pp-130) REVERT: H 126 GLU cc_start: 0.5823 (tt0) cc_final: 0.5428 (tt0) REVERT: H 127 TYR cc_start: 0.4784 (m-80) cc_final: 0.4186 (m-10) REVERT: I 75 LEU cc_start: 0.5123 (mm) cc_final: 0.4868 (mm) REVERT: I 126 GLU cc_start: 0.5919 (tt0) cc_final: 0.5624 (mm-30) REVERT: I 127 TYR cc_start: 0.4126 (m-80) cc_final: 0.3657 (m-10) REVERT: J 29 PRO cc_start: 0.4622 (Cg_exo) cc_final: 0.4363 (Cg_endo) REVERT: J 61 MET cc_start: 0.0999 (ppp) cc_final: 0.0791 (pp-130) REVERT: J 91 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5220 (pp20) REVERT: J 127 TYR cc_start: 0.3590 (m-80) cc_final: 0.2556 (m-10) REVERT: J 128 VAL cc_start: 0.5331 (t) cc_final: 0.5056 (t) REVERT: J 194 MET cc_start: 0.4645 (tpp) cc_final: 0.4222 (mmt) outliers start: 14 outliers final: 2 residues processed: 480 average time/residue: 1.0723 time to fit residues: 578.1644 Evaluate side-chains 274 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 208 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 1.9990 chunk 166 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.263303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.261845 restraints weight = 19618.562| |-----------------------------------------------------------------------------| r_work (start): 0.4974 rms_B_bonded: 0.23 r_work: 0.4971 rms_B_bonded: 0.30 restraints_weight: 0.5000 r_work: 0.4954 rms_B_bonded: 0.61 restraints_weight: 0.2500 r_work: 0.4844 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4141 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16370 Z= 0.165 Angle : 0.821 15.869 22270 Z= 0.379 Chirality : 0.045 0.219 2730 Planarity : 0.006 0.058 2850 Dihedral : 5.303 56.552 2306 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.35 % Allowed : 23.35 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2180 helix: 0.99 (0.14), residues: 1400 sheet: -0.20 (0.27), residues: 370 loop : -1.02 (0.26), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.011 0.002 HIS C 156 PHE 0.025 0.002 PHE A 207 TYR 0.013 0.002 TYR B 127 ARG 0.010 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 972) hydrogen bonds : angle 5.00559 ( 2892) covalent geometry : bond 0.00380 (16370) covalent geometry : angle 0.82088 (22270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 290 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3261 (pmm) cc_final: 0.2628 (pp-130) REVERT: A 207 PHE cc_start: 0.5564 (OUTLIER) cc_final: 0.4837 (m-80) REVERT: C 75 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5807 (mm) REVERT: E 196 SER cc_start: 0.4080 (OUTLIER) cc_final: 0.3680 (m) REVERT: E 197 TYR cc_start: 0.4972 (m-80) cc_final: 0.4119 (m-80) REVERT: F 1 MET cc_start: 0.4374 (tmt) cc_final: 0.4033 (tmt) REVERT: G 26 THR cc_start: 0.4084 (OUTLIER) cc_final: 0.3876 (t) REVERT: G 61 MET cc_start: 0.3358 (pmm) cc_final: 0.2650 (pp-130) REVERT: G 197 TYR cc_start: 0.5624 (m-80) cc_final: 0.5394 (m-80) REVERT: H 26 THR cc_start: 0.3869 (OUTLIER) cc_final: 0.3553 (t) REVERT: H 186 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5229 (pp) REVERT: I 61 MET cc_start: 0.1829 (pp-130) cc_final: 0.1239 (pmm) REVERT: J 138 GLN cc_start: 0.5297 (tt0) cc_final: 0.4912 (tt0) outliers start: 106 outliers final: 23 residues processed: 365 average time/residue: 1.0569 time to fit residues: 433.3258 Evaluate side-chains 263 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 196 SER Chi-restraints excluded: chain J residue 204 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 44 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN B 116 GLN C 116 GLN C 138 GLN C 144 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN I 138 GLN J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.264348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.262590 restraints weight = 19545.507| |-----------------------------------------------------------------------------| r_work (start): 0.4975 rms_B_bonded: 0.28 r_work: 0.4968 rms_B_bonded: 0.41 restraints_weight: 0.5000 r_work: 0.4943 rms_B_bonded: 0.94 restraints_weight: 0.2500 r_work (final): 0.4943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4022 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16370 Z= 0.134 Angle : 0.743 13.702 22270 Z= 0.342 Chirality : 0.044 0.268 2730 Planarity : 0.005 0.048 2850 Dihedral : 4.616 23.660 2300 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.63 % Allowed : 25.21 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2180 helix: 1.08 (0.14), residues: 1400 sheet: 0.05 (0.27), residues: 360 loop : -1.38 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 211 HIS 0.005 0.001 HIS F 156 PHE 0.025 0.001 PHE A 207 TYR 0.016 0.001 TYR D 197 ARG 0.008 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 972) hydrogen bonds : angle 4.74528 ( 2892) covalent geometry : bond 0.00310 (16370) covalent geometry : angle 0.74307 (22270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3596 (pmm) cc_final: 0.2838 (pp-130) REVERT: A 127 TYR cc_start: 0.4601 (m-10) cc_final: 0.4128 (m-10) REVERT: A 207 PHE cc_start: 0.5477 (OUTLIER) cc_final: 0.4700 (m-80) REVERT: B 1 MET cc_start: 0.4509 (tmt) cc_final: 0.4069 (tmt) REVERT: B 131 TYR cc_start: 0.4295 (m-10) cc_final: 0.4077 (m-10) REVERT: D 1 MET cc_start: 0.4358 (tmt) cc_final: 0.3852 (tmt) REVERT: E 126 GLU cc_start: 0.4375 (OUTLIER) cc_final: 0.3555 (mm-30) REVERT: E 197 TYR cc_start: 0.4718 (m-80) cc_final: 0.4038 (m-80) REVERT: F 207 PHE cc_start: 0.5023 (m-80) cc_final: 0.4601 (m-10) REVERT: G 61 MET cc_start: 0.3270 (pmm) cc_final: 0.2615 (pp-130) REVERT: G 71 ASP cc_start: 0.3472 (m-30) cc_final: 0.3107 (m-30) REVERT: H 186 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4971 (pp) outliers start: 94 outliers final: 22 residues processed: 326 average time/residue: 1.0412 time to fit residues: 381.9172 Evaluate side-chains 243 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 219 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN C 138 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 156 HIS ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN I 138 GLN J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.262425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.261052 restraints weight = 19729.049| |-----------------------------------------------------------------------------| r_work (start): 0.4965 rms_B_bonded: 0.20 r_work: 0.4962 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.4943 rms_B_bonded: 0.63 restraints_weight: 0.2500 r_work: 0.4836 rms_B_bonded: 3.35 restraints_weight: 0.1250 r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4398 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16370 Z= 0.171 Angle : 0.776 10.396 22270 Z= 0.366 Chirality : 0.045 0.290 2730 Planarity : 0.005 0.047 2850 Dihedral : 5.098 25.610 2300 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.11 % Allowed : 25.69 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2180 helix: 0.75 (0.14), residues: 1400 sheet: -0.35 (0.26), residues: 360 loop : -1.56 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 211 HIS 0.004 0.001 HIS C 150 PHE 0.026 0.002 PHE A 207 TYR 0.018 0.002 TYR F 127 ARG 0.008 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 972) hydrogen bonds : angle 4.90036 ( 2892) covalent geometry : bond 0.00407 (16370) covalent geometry : angle 0.77633 (22270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 249 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.4042 (pmm) cc_final: 0.3220 (pp-130) REVERT: A 127 TYR cc_start: 0.4819 (m-10) cc_final: 0.4230 (m-10) REVERT: A 207 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.4851 (m-80) REVERT: B 1 MET cc_start: 0.4764 (tmt) cc_final: 0.4406 (tmt) REVERT: B 131 TYR cc_start: 0.4579 (m-10) cc_final: 0.4352 (m-10) REVERT: B 138 GLN cc_start: 0.5228 (OUTLIER) cc_final: 0.4924 (tt0) REVERT: B 155 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.3459 (ppp) REVERT: C 118 LEU cc_start: 0.3767 (OUTLIER) cc_final: 0.3054 (tt) REVERT: D 6 ASP cc_start: 0.3409 (p0) cc_final: 0.3201 (p0) REVERT: D 14 LYS cc_start: 0.4455 (OUTLIER) cc_final: 0.4189 (ttpp) REVERT: D 61 MET cc_start: 0.3685 (pmm) cc_final: 0.2499 (pp-130) REVERT: E 126 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.3646 (mm-30) REVERT: E 197 TYR cc_start: 0.4944 (m-80) cc_final: 0.4144 (m-80) REVERT: F 153 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.4975 (mm) REVERT: G 61 MET cc_start: 0.3628 (pmm) cc_final: 0.3013 (pp-130) REVERT: G 197 TYR cc_start: 0.5885 (m-80) cc_final: 0.5672 (m-80) REVERT: G 201 ASP cc_start: 0.5787 (m-30) cc_final: 0.5026 (m-30) REVERT: H 186 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5745 (pp) REVERT: I 6 ASP cc_start: 0.3637 (p0) cc_final: 0.3420 (p0) REVERT: I 50 MET cc_start: 0.2889 (mmt) cc_final: 0.2666 (mmm) outliers start: 102 outliers final: 25 residues processed: 324 average time/residue: 1.1361 time to fit residues: 410.9165 Evaluate side-chains 236 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 156 optimal weight: 0.0050 chunk 147 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS B 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN I 116 GLN J 116 GLN J 138 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.262273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.261778 restraints weight = 19843.046| |-----------------------------------------------------------------------------| r_work (start): 0.4980 rms_B_bonded: 0.08 r_work: 0.4978 rms_B_bonded: 0.12 restraints_weight: 0.5000 r_work: 0.4971 rms_B_bonded: 0.25 restraints_weight: 0.2500 r_work: 0.4912 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4165 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16370 Z= 0.130 Angle : 0.739 11.210 22270 Z= 0.344 Chirality : 0.044 0.283 2730 Planarity : 0.005 0.049 2850 Dihedral : 4.731 25.131 2300 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.03 % Allowed : 27.90 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2180 helix: 0.99 (0.14), residues: 1400 sheet: -0.30 (0.26), residues: 360 loop : -1.60 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 211 HIS 0.004 0.001 HIS A 156 PHE 0.019 0.001 PHE A 207 TYR 0.015 0.001 TYR H 127 ARG 0.005 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 972) hydrogen bonds : angle 4.68534 ( 2892) covalent geometry : bond 0.00299 (16370) covalent geometry : angle 0.73893 (22270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 230 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3927 (pmm) cc_final: 0.3311 (pp-130) REVERT: A 127 TYR cc_start: 0.4567 (m-10) cc_final: 0.4163 (m-10) REVERT: A 186 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5554 (pp) REVERT: A 207 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4482 (m-80) REVERT: B 131 TYR cc_start: 0.4401 (m-10) cc_final: 0.4137 (m-10) REVERT: B 155 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.3274 (ppp) REVERT: D 14 LYS cc_start: 0.4424 (OUTLIER) cc_final: 0.4213 (ttpp) REVERT: D 61 MET cc_start: 0.3562 (pmm) cc_final: 0.2453 (pp-130) REVERT: E 197 TYR cc_start: 0.4707 (m-80) cc_final: 0.3993 (m-80) REVERT: G 61 MET cc_start: 0.3528 (pmm) cc_final: 0.3016 (pp-130) REVERT: G 138 GLN cc_start: 0.5120 (OUTLIER) cc_final: 0.4578 (tt0) REVERT: H 186 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5252 (pp) outliers start: 84 outliers final: 19 residues processed: 298 average time/residue: 1.0907 time to fit residues: 365.3814 Evaluate side-chains 225 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 HIS I 116 GLN J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.259548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.257539 restraints weight = 19794.398| |-----------------------------------------------------------------------------| r_work (start): 0.4949 rms_B_bonded: 0.30 r_work: 0.4938 rms_B_bonded: 0.51 restraints_weight: 0.5000 r_work: 0.4908 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4469 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16370 Z= 0.189 Angle : 0.836 14.992 22270 Z= 0.397 Chirality : 0.047 0.389 2730 Planarity : 0.005 0.049 2850 Dihedral : 5.410 27.551 2300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.45 % Allowed : 27.43 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2180 helix: 0.34 (0.13), residues: 1400 sheet: -0.68 (0.25), residues: 360 loop : -1.71 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 211 HIS 0.006 0.001 HIS B 156 PHE 0.027 0.002 PHE A 207 TYR 0.025 0.002 TYR E 127 ARG 0.007 0.001 ARG D 55 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 972) hydrogen bonds : angle 5.08118 ( 2892) covalent geometry : bond 0.00457 (16370) covalent geometry : angle 0.83638 (22270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 244 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.4170 (pmm) cc_final: 0.3189 (pp-130) REVERT: A 127 TYR cc_start: 0.4847 (m-10) cc_final: 0.4477 (m-10) REVERT: A 207 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4367 (m-80) REVERT: C 138 GLN cc_start: 0.5151 (OUTLIER) cc_final: 0.4743 (tt0) REVERT: C 215 PHE cc_start: 0.3682 (OUTLIER) cc_final: 0.2353 (m-10) REVERT: D 61 MET cc_start: 0.3793 (pmm) cc_final: 0.2654 (pp-130) REVERT: E 138 GLN cc_start: 0.5225 (OUTLIER) cc_final: 0.4856 (tt0) REVERT: E 197 TYR cc_start: 0.4896 (m-80) cc_final: 0.4025 (m-80) REVERT: F 47 HIS cc_start: 0.4232 (t-170) cc_final: 0.3924 (t-90) REVERT: G 61 MET cc_start: 0.4170 (pmm) cc_final: 0.3773 (pp-130) REVERT: H 186 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6092 (pp) REVERT: J 61 MET cc_start: 0.3747 (pp-130) cc_final: 0.3498 (pp-130) REVERT: J 138 GLN cc_start: 0.5188 (OUTLIER) cc_final: 0.4274 (tt0) outliers start: 91 outliers final: 17 residues processed: 306 average time/residue: 1.1068 time to fit residues: 379.0612 Evaluate side-chains 231 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 138 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 99 optimal weight: 0.1980 chunk 146 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 91 optimal weight: 0.0370 chunk 182 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 160 optimal weight: 0.0870 chunk 209 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN I 116 GLN J 116 GLN J 138 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.262526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.261692 restraints weight = 19907.948| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 0.12 r_work: 0.4980 rms_B_bonded: 0.19 restraints_weight: 0.5000 r_work: 0.4968 rms_B_bonded: 0.43 restraints_weight: 0.2500 r_work: 0.4858 rms_B_bonded: 3.66 restraints_weight: 0.1250 r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4333 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16370 Z= 0.137 Angle : 0.826 15.125 22270 Z= 0.379 Chirality : 0.047 0.348 2730 Planarity : 0.005 0.054 2850 Dihedral : 4.831 25.953 2300 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.53 % Allowed : 30.30 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2180 helix: 0.77 (0.14), residues: 1400 sheet: -0.49 (0.26), residues: 360 loop : -1.67 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 211 HIS 0.007 0.001 HIS J 156 PHE 0.030 0.001 PHE A 207 TYR 0.025 0.002 TYR E 127 ARG 0.011 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 972) hydrogen bonds : angle 4.79703 ( 2892) covalent geometry : bond 0.00316 (16370) covalent geometry : angle 0.82556 (22270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3878 (pmm) cc_final: 0.2953 (pp-130) REVERT: B 138 GLN cc_start: 0.4990 (OUTLIER) cc_final: 0.4514 (tt0) REVERT: B 155 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.4016 (ppp) REVERT: C 138 GLN cc_start: 0.5020 (OUTLIER) cc_final: 0.4589 (tt0) REVERT: C 215 PHE cc_start: 0.3642 (OUTLIER) cc_final: 0.2248 (m-10) REVERT: D 61 MET cc_start: 0.3454 (pmm) cc_final: 0.2342 (pp-130) REVERT: E 197 TYR cc_start: 0.4677 (m-80) cc_final: 0.3809 (m-80) REVERT: F 47 HIS cc_start: 0.4121 (t-170) cc_final: 0.3689 (t-90) REVERT: G 61 MET cc_start: 0.4282 (pmm) cc_final: 0.3631 (pp-130) REVERT: G 138 GLN cc_start: 0.4974 (OUTLIER) cc_final: 0.4509 (tt0) REVERT: J 138 GLN cc_start: 0.4752 (OUTLIER) cc_final: 0.4522 (tm-30) outliers start: 59 outliers final: 13 residues processed: 271 average time/residue: 1.0675 time to fit residues: 325.2851 Evaluate side-chains 213 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 138 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 138 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.262909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.261900 restraints weight = 19602.980| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 0.15 r_work: 0.4977 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.4956 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4236 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16370 Z= 0.135 Angle : 0.817 15.292 22270 Z= 0.376 Chirality : 0.047 0.368 2730 Planarity : 0.005 0.052 2850 Dihedral : 4.739 25.894 2300 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.99 % Allowed : 31.14 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2180 helix: 0.85 (0.13), residues: 1400 sheet: -0.47 (0.26), residues: 360 loop : -1.64 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 211 HIS 0.007 0.001 HIS J 156 PHE 0.011 0.001 PHE D 207 TYR 0.029 0.002 TYR I 127 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 972) hydrogen bonds : angle 4.79488 ( 2892) covalent geometry : bond 0.00313 (16370) covalent geometry : angle 0.81730 (22270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3945 (pmm) cc_final: 0.3235 (pp-130) REVERT: C 91 GLU cc_start: 0.3248 (OUTLIER) cc_final: 0.2703 (tm-30) REVERT: C 138 GLN cc_start: 0.4881 (OUTLIER) cc_final: 0.4490 (tt0) REVERT: C 215 PHE cc_start: 0.3640 (OUTLIER) cc_final: 0.2204 (m-10) REVERT: D 61 MET cc_start: 0.3109 (pmm) cc_final: 0.2202 (pp-130) REVERT: D 131 TYR cc_start: 0.4632 (m-10) cc_final: 0.4280 (m-10) REVERT: E 6 ASP cc_start: 0.3095 (OUTLIER) cc_final: 0.2828 (p0) REVERT: E 197 TYR cc_start: 0.4695 (m-80) cc_final: 0.3781 (m-80) REVERT: F 47 HIS cc_start: 0.4085 (t-170) cc_final: 0.3748 (t-90) REVERT: G 61 MET cc_start: 0.4046 (pmm) cc_final: 0.3608 (pp-130) REVERT: G 138 GLN cc_start: 0.5044 (OUTLIER) cc_final: 0.4550 (tt0) REVERT: H 186 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5527 (pp) outliers start: 50 outliers final: 14 residues processed: 253 average time/residue: 1.1514 time to fit residues: 326.8949 Evaluate side-chains 215 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 135 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 123 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN C 47 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.259137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.258179 restraints weight = 19592.129| |-----------------------------------------------------------------------------| r_work (start): 0.4955 rms_B_bonded: 0.13 r_work: 0.4950 rms_B_bonded: 0.23 restraints_weight: 0.5000 r_work: 0.4928 rms_B_bonded: 0.69 restraints_weight: 0.2500 r_work (final): 0.4928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4436 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 16370 Z= 0.186 Angle : 0.896 15.330 22270 Z= 0.422 Chirality : 0.050 0.402 2730 Planarity : 0.006 0.051 2850 Dihedral : 5.301 26.857 2300 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.63 % Allowed : 32.57 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2180 helix: 0.38 (0.13), residues: 1400 sheet: -0.76 (0.26), residues: 360 loop : -1.69 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.007 0.002 HIS J 156 PHE 0.012 0.002 PHE A 20 TYR 0.028 0.002 TYR I 127 ARG 0.006 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 972) hydrogen bonds : angle 5.14699 ( 2892) covalent geometry : bond 0.00445 (16370) covalent geometry : angle 0.89613 (22270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.4059 (pmm) cc_final: 0.3190 (pp-130) REVERT: C 138 GLN cc_start: 0.5115 (OUTLIER) cc_final: 0.4896 (tt0) REVERT: C 215 PHE cc_start: 0.3673 (OUTLIER) cc_final: 0.2369 (m-10) REVERT: D 131 TYR cc_start: 0.4542 (m-10) cc_final: 0.4291 (m-10) REVERT: E 138 GLN cc_start: 0.5101 (OUTLIER) cc_final: 0.4673 (tt0) REVERT: E 197 TYR cc_start: 0.4713 (m-80) cc_final: 0.3857 (m-80) REVERT: F 47 HIS cc_start: 0.4341 (t-170) cc_final: 0.4072 (t-90) REVERT: G 1 MET cc_start: 0.5156 (tmt) cc_final: 0.4729 (tmm) REVERT: G 47 HIS cc_start: 0.4160 (t-170) cc_final: 0.3946 (t70) REVERT: G 61 MET cc_start: 0.4227 (pmm) cc_final: 0.3741 (pp-130) REVERT: G 138 GLN cc_start: 0.5039 (OUTLIER) cc_final: 0.4488 (tt0) REVERT: H 131 TYR cc_start: 0.5055 (m-80) cc_final: 0.4820 (m-10) outliers start: 44 outliers final: 12 residues processed: 238 average time/residue: 1.0418 time to fit residues: 280.1773 Evaluate side-chains 209 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.258544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.257688 restraints weight = 19818.201| |-----------------------------------------------------------------------------| r_work (start): 0.4956 rms_B_bonded: 0.12 r_work: 0.4952 rms_B_bonded: 0.19 restraints_weight: 0.5000 r_work: 0.4942 rms_B_bonded: 0.40 restraints_weight: 0.2500 r_work: 0.4830 rms_B_bonded: 3.54 restraints_weight: 0.1250 r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4556 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16370 Z= 0.175 Angle : 0.922 16.743 22270 Z= 0.429 Chirality : 0.050 0.356 2730 Planarity : 0.006 0.049 2850 Dihedral : 5.369 28.138 2300 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.10 % Allowed : 33.11 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2180 helix: 0.32 (0.13), residues: 1390 sheet: -0.86 (0.26), residues: 360 loop : -1.66 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 211 HIS 0.009 0.002 HIS J 156 PHE 0.023 0.002 PHE H 207 TYR 0.028 0.002 TYR I 127 ARG 0.007 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 972) hydrogen bonds : angle 5.21798 ( 2892) covalent geometry : bond 0.00427 (16370) covalent geometry : angle 0.92205 (22270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3947 (pmm) cc_final: 0.3107 (pp-130) REVERT: C 138 GLN cc_start: 0.5053 (OUTLIER) cc_final: 0.4778 (tt0) REVERT: C 215 PHE cc_start: 0.3869 (OUTLIER) cc_final: 0.2663 (m-10) REVERT: D 1 MET cc_start: 0.4855 (tmt) cc_final: 0.4566 (tmt) REVERT: D 61 MET cc_start: 0.3611 (pmm) cc_final: 0.2866 (pp-130) REVERT: D 131 TYR cc_start: 0.4623 (m-10) cc_final: 0.4382 (m-10) REVERT: E 138 GLN cc_start: 0.5066 (OUTLIER) cc_final: 0.4626 (tt0) REVERT: E 197 TYR cc_start: 0.4614 (m-80) cc_final: 0.3801 (m-80) REVERT: F 47 HIS cc_start: 0.4519 (t-170) cc_final: 0.4036 (t-90) REVERT: G 61 MET cc_start: 0.4437 (pmm) cc_final: 0.3774 (pp-130) REVERT: G 138 GLN cc_start: 0.5154 (OUTLIER) cc_final: 0.4568 (tt0) REVERT: H 131 TYR cc_start: 0.5125 (m-80) cc_final: 0.4878 (m-10) REVERT: H 207 PHE cc_start: 0.5378 (m-10) cc_final: 0.4678 (m-80) outliers start: 35 outliers final: 12 residues processed: 226 average time/residue: 1.0364 time to fit residues: 264.4498 Evaluate side-chains 198 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.260951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.260080 restraints weight = 19628.645| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 0.12 r_work: 0.4969 rms_B_bonded: 0.19 restraints_weight: 0.5000 r_work: 0.4954 rms_B_bonded: 0.47 restraints_weight: 0.2500 r_work: 0.4847 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.4847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4437 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16370 Z= 0.144 Angle : 0.913 16.600 22270 Z= 0.416 Chirality : 0.050 0.362 2730 Planarity : 0.005 0.050 2850 Dihedral : 4.915 22.479 2300 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 33.95 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2180 helix: 0.56 (0.13), residues: 1400 sheet: -0.70 (0.26), residues: 360 loop : -1.77 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 211 HIS 0.011 0.001 HIS J 156 PHE 0.013 0.001 PHE H 207 TYR 0.026 0.002 TYR I 127 ARG 0.011 0.001 ARG A 217 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 972) hydrogen bonds : angle 5.04239 ( 2892) covalent geometry : bond 0.00338 (16370) covalent geometry : angle 0.91263 (22270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10846.05 seconds wall clock time: 185 minutes 16.85 seconds (11116.85 seconds total)