Starting phenix.real_space_refine on Thu Sep 18 09:40:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7h_19772/09_2025/8s7h_19772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7h_19772/09_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_19772/09_2025/8s7h_19772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7h_19772/09_2025/8s7h_19772.map" model { file = "/net/cci-nas-00/data/ceres_data/8s7h_19772/09_2025/8s7h_19772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7h_19772/09_2025/8s7h_19772.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.93, per 1000 atoms: 0.24 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: 1.28 Conformation dependent library (CDL) restraints added in 740.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 3.09 Time building geometry restraints manager: 1.75 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: 0.01 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: 0.720 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.670 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 : 18.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (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 ARG 0.014 0.001 ARG H 217 TYR 0.008 0.001 TYR J 127 PHE 0.017 0.002 PHE A 207 TRP 0.035 0.002 TRP A 211 HIS 0.009 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00389 (16370) covalent geometry : angle 1.03405 (22270) hydrogen bonds : bond 0.09532 ( 972) hydrogen bonds : angle 5.96156 ( 2892) *********************** 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 : 0.482 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: 0.5160 time to fit residues: 276.7461 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 : 0.549 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.0570 chunk 212 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 138 GLN B 156 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 144 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 116 GLN I 138 GLN I 192 GLN J 156 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.265312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.263813 restraints weight = 19545.777| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 0.24 r_work: 0.4980 rms_B_bonded: 0.31 restraints_weight: 0.5000 r_work: 0.4962 rms_B_bonded: 0.64 restraints_weight: 0.2500 r_work: 0.4852 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3960 moved from start: 0.2424 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= 0.137 Angle : 0.802 15.792 22270 Z= 0.365 Chirality : 0.045 0.252 2730 Planarity : 0.005 0.056 2850 Dihedral : 5.055 55.661 2306 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.87 % Allowed : 22.87 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2180 helix: 1.24 (0.14), residues: 1380 sheet: 0.17 (0.25), residues: 410 loop : -1.04 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 55 TYR 0.011 0.001 TYR D 197 PHE 0.022 0.002 PHE A 207 TRP 0.007 0.001 TRP E 211 HIS 0.011 0.002 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00308 (16370) covalent geometry : angle 0.80198 (22270) hydrogen bonds : bond 0.03606 ( 972) hydrogen bonds : angle 4.87902 ( 2892) *********************** 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 390 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 292 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.2957 (pmm) cc_final: 0.2418 (pp-130) REVERT: A 207 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.5018 (m-80) REVERT: B 1 MET cc_start: 0.4403 (tmt) cc_final: 0.3993 (tmt) REVERT: B 61 MET cc_start: 0.3503 (pmm) cc_final: 0.3107 (pp-130) REVERT: B 131 TYR cc_start: 0.4027 (m-10) cc_final: 0.3807 (m-10) REVERT: E 197 TYR cc_start: 0.4765 (m-80) cc_final: 0.4098 (m-80) REVERT: F 1 MET cc_start: 0.4102 (tmt) cc_final: 0.3888 (tmt) REVERT: F 201 ASP cc_start: 0.4998 (m-30) cc_final: 0.4761 (m-30) REVERT: G 26 THR cc_start: 0.3802 (OUTLIER) cc_final: 0.3586 (t) REVERT: G 201 ASP cc_start: 0.5549 (m-30) cc_final: 0.4849 (m-30) REVERT: H 26 THR cc_start: 0.3629 (OUTLIER) cc_final: 0.3300 (t) REVERT: H 186 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4725 (pp) REVERT: I 61 MET cc_start: 0.1488 (pp-130) cc_final: 0.0948 (pmm) outliers start: 98 outliers final: 16 residues processed: 363 average time/residue: 0.4672 time to fit residues: 190.6771 Evaluate side-chains 249 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain E 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 186 LEU 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 J residue 27 THR Chi-restraints excluded: chain J residue 82 ILE 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 122 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN D 156 HIS F 138 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN I 138 GLN J 116 GLN J 209 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.264507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.263345 restraints weight = 19844.919| |-----------------------------------------------------------------------------| r_work (start): 0.4982 rms_B_bonded: 0.18 r_work: 0.4977 rms_B_bonded: 0.27 restraints_weight: 0.5000 r_work: 0.4957 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.4822 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3993 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16370 Z= 0.132 Angle : 0.743 13.618 22270 Z= 0.341 Chirality : 0.044 0.283 2730 Planarity : 0.005 0.049 2850 Dihedral : 4.509 23.211 2300 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.87 % Allowed : 24.01 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2180 helix: 1.11 (0.14), residues: 1400 sheet: 0.22 (0.27), residues: 360 loop : -1.30 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 55 TYR 0.016 0.001 TYR D 197 PHE 0.023 0.001 PHE A 207 TRP 0.011 0.001 TRP F 211 HIS 0.004 0.001 HIS F 156 Details of bonding type rmsd covalent geometry : bond 0.00295 (16370) covalent geometry : angle 0.74261 (22270) hydrogen bonds : bond 0.03410 ( 972) hydrogen bonds : angle 4.72120 ( 2892) *********************** 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 340 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 242 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3294 (pmm) cc_final: 0.2564 (pp-130) REVERT: A 127 TYR cc_start: 0.4730 (m-10) cc_final: 0.4211 (m-10) REVERT: A 207 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.4947 (m-80) REVERT: B 1 MET cc_start: 0.4365 (tmt) cc_final: 0.4059 (tmt) REVERT: B 61 MET cc_start: 0.4242 (pmm) cc_final: 0.3670 (ppp) REVERT: E 197 TYR cc_start: 0.4740 (m-80) cc_final: 0.4135 (m-80) REVERT: G 61 MET cc_start: 0.2815 (pmm) cc_final: 0.2181 (pp-130) REVERT: H 186 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4619 (pp) REVERT: I 61 MET cc_start: 0.1551 (pp-130) cc_final: 0.1122 (pmm) REVERT: I 201 ASP cc_start: 0.5144 (m-30) cc_final: 0.4323 (m-30) outliers start: 98 outliers final: 26 residues processed: 318 average time/residue: 0.4850 time to fit residues: 173.2216 Evaluate side-chains 233 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 118 LEU 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 204 VAL Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 27 THR 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 107 LEU 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 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 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 157 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 138 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 HIS ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 GLN J 138 GLN J 172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.263366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.262489 restraints weight = 19732.080| |-----------------------------------------------------------------------------| r_work (start): 0.4975 rms_B_bonded: 0.14 r_work: 0.4972 rms_B_bonded: 0.20 restraints_weight: 0.5000 r_work: 0.4956 rms_B_bonded: 0.51 restraints_weight: 0.2500 r_work: 0.4849 rms_B_bonded: 3.55 restraints_weight: 0.1250 r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4066 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16370 Z= 0.133 Angle : 0.727 9.310 22270 Z= 0.335 Chirality : 0.045 0.380 2730 Planarity : 0.005 0.049 2850 Dihedral : 4.539 24.783 2300 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.81 % Allowed : 24.37 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2180 helix: 1.08 (0.14), residues: 1400 sheet: 0.15 (0.28), residues: 360 loop : -1.38 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 55 TYR 0.016 0.001 TYR E 127 PHE 0.021 0.001 PHE A 207 TRP 0.007 0.001 TRP F 211 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00305 (16370) covalent geometry : angle 0.72734 (22270) hydrogen bonds : bond 0.03420 ( 972) hydrogen bonds : angle 4.66826 ( 2892) *********************** 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 330 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 233 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3642 (pmm) cc_final: 0.2948 (pp-130) REVERT: A 127 TYR cc_start: 0.4644 (m-10) cc_final: 0.4208 (m-10) REVERT: A 201 ASP cc_start: 0.5118 (m-30) cc_final: 0.4588 (m-30) REVERT: B 61 MET cc_start: 0.4261 (pmm) cc_final: 0.3598 (pp-130) REVERT: D 61 MET cc_start: 0.2665 (pmm) cc_final: 0.2299 (pmm) REVERT: E 197 TYR cc_start: 0.4944 (m-80) cc_final: 0.4285 (m-80) REVERT: E 201 ASP cc_start: 0.4900 (m-30) cc_final: 0.4372 (m-30) REVERT: G 61 MET cc_start: 0.3214 (pmm) cc_final: 0.2660 (pp-130) REVERT: H 26 THR cc_start: 0.3600 (OUTLIER) cc_final: 0.3327 (t) REVERT: H 186 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4714 (pp) outliers start: 97 outliers final: 30 residues processed: 308 average time/residue: 0.4841 time to fit residues: 167.5713 Evaluate side-chains 230 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 27 THR 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 26 THR 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 196 SER 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 27 THR Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 107 LEU 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 37 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 206 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 207 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 chunk 156 optimal weight: 0.9980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.264119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.263206 restraints weight = 19495.892| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 0.14 r_work: 0.4963 rms_B_bonded: 0.23 restraints_weight: 0.5000 r_work: 0.4941 rms_B_bonded: 0.64 restraints_weight: 0.2500 r_work: 0.4802 rms_B_bonded: 4.87 restraints_weight: 0.1250 r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4047 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16370 Z= 0.121 Angle : 0.708 10.281 22270 Z= 0.326 Chirality : 0.044 0.287 2730 Planarity : 0.005 0.048 2850 Dihedral : 4.430 23.362 2300 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.81 % Allowed : 24.37 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2180 helix: 1.17 (0.14), residues: 1400 sheet: 0.11 (0.28), residues: 360 loop : -1.44 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 55 TYR 0.012 0.001 TYR E 127 PHE 0.009 0.001 PHE E 167 TRP 0.009 0.001 TRP F 211 HIS 0.005 0.001 HIS F 156 Details of bonding type rmsd covalent geometry : bond 0.00269 (16370) covalent geometry : angle 0.70789 (22270) hydrogen bonds : bond 0.03103 ( 972) hydrogen bonds : angle 4.56787 ( 2892) *********************** 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 334 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 237 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3734 (pmm) cc_final: 0.3049 (pp-130) REVERT: A 127 TYR cc_start: 0.4511 (m-10) cc_final: 0.4180 (m-10) REVERT: A 201 ASP cc_start: 0.5070 (m-30) cc_final: 0.4623 (m-30) REVERT: B 1 MET cc_start: 0.4450 (tmt) cc_final: 0.4038 (tmt) REVERT: B 61 MET cc_start: 0.3966 (pmm) cc_final: 0.3581 (ppp) REVERT: C 208 GLU cc_start: 0.4711 (tp30) cc_final: 0.4414 (tp30) REVERT: D 61 MET cc_start: 0.2433 (pmm) cc_final: 0.1978 (pmm) REVERT: E 197 TYR cc_start: 0.5034 (m-80) cc_final: 0.4234 (m-80) REVERT: F 20 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4430 (m-80) REVERT: F 201 ASP cc_start: 0.5068 (m-30) cc_final: 0.4648 (m-30) REVERT: G 61 MET cc_start: 0.3374 (pmm) cc_final: 0.2915 (pp-130) REVERT: G 138 GLN cc_start: 0.5581 (OUTLIER) cc_final: 0.5035 (tt0) REVERT: H 26 THR cc_start: 0.3526 (OUTLIER) cc_final: 0.3242 (t) REVERT: H 186 LEU cc_start: 0.4892 (OUTLIER) cc_final: 0.4568 (pp) REVERT: I 50 MET cc_start: 0.2587 (mmt) cc_final: 0.2241 (mmm) outliers start: 97 outliers final: 25 residues processed: 319 average time/residue: 0.4528 time to fit residues: 162.9648 Evaluate side-chains 226 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 73 LEU 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 26 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 107 LEU 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 Chi-restraints excluded: chain J residue 196 SER Chi-restraints excluded: chain J residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 87 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 210 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 191 optimal weight: 0.0060 chunk 107 optimal weight: 9.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- 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** ** 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** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 GLN J 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.261162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.260692 restraints weight = 19639.552| |-----------------------------------------------------------------------------| r_work (start): 0.4972 rms_B_bonded: 0.07 r_work: 0.4970 rms_B_bonded: 0.10 restraints_weight: 0.5000 r_work: 0.4965 rms_B_bonded: 0.21 restraints_weight: 0.2500 r_work: 0.4913 rms_B_bonded: 1.37 restraints_weight: 0.1250 r_work (final): 0.4913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4168 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16370 Z= 0.151 Angle : 0.755 10.651 22270 Z= 0.351 Chirality : 0.046 0.416 2730 Planarity : 0.005 0.050 2850 Dihedral : 4.703 22.426 2300 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.91 % Allowed : 26.29 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2180 helix: 0.88 (0.14), residues: 1400 sheet: -0.18 (0.27), residues: 360 loop : -1.54 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.027 0.002 TYR C 127 PHE 0.027 0.002 PHE C 207 TRP 0.007 0.001 TRP F 211 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00356 (16370) covalent geometry : angle 0.75525 (22270) hydrogen bonds : bond 0.03574 ( 972) hydrogen bonds : angle 4.72273 ( 2892) *********************** 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 307 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 225 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3985 (pmm) cc_final: 0.3352 (pp-130) REVERT: A 127 TYR cc_start: 0.4613 (m-10) cc_final: 0.4264 (m-10) REVERT: B 1 MET cc_start: 0.4802 (tmt) cc_final: 0.4316 (tmt) REVERT: B 61 MET cc_start: 0.4267 (pmm) cc_final: 0.3631 (ppp) REVERT: C 118 LEU cc_start: 0.3508 (OUTLIER) cc_final: 0.2942 (tt) REVERT: D 61 MET cc_start: 0.3219 (pmm) cc_final: 0.2195 (pp-130) REVERT: E 138 GLN cc_start: 0.5108 (OUTLIER) cc_final: 0.4673 (tt0) REVERT: E 197 TYR cc_start: 0.4916 (m-80) cc_final: 0.4179 (m-80) REVERT: G 61 MET cc_start: 0.3940 (pmm) cc_final: 0.3700 (pp-130) REVERT: G 138 GLN cc_start: 0.5267 (OUTLIER) cc_final: 0.4737 (tt0) REVERT: H 186 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5089 (pp) REVERT: I 50 MET cc_start: 0.2735 (mmt) cc_final: 0.2391 (mmm) REVERT: J 138 GLN cc_start: 0.4963 (OUTLIER) cc_final: 0.4612 (tm-30) outliers start: 82 outliers final: 21 residues processed: 287 average time/residue: 0.4854 time to fit residues: 156.6954 Evaluate side-chains 223 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 107 LEU 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 27 THR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 HIS ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN I 116 GLN J 116 GLN J 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.263943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.262732 restraints weight = 19741.377| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 0.17 r_work: 0.4979 rms_B_bonded: 0.26 restraints_weight: 0.5000 r_work: 0.4961 rms_B_bonded: 0.63 restraints_weight: 0.2500 r_work: 0.4836 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.4836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4210 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16370 Z= 0.128 Angle : 0.781 13.705 22270 Z= 0.355 Chirality : 0.046 0.387 2730 Planarity : 0.005 0.051 2850 Dihedral : 4.541 23.291 2300 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.95 % Allowed : 28.26 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2180 helix: 1.00 (0.14), residues: 1400 sheet: -0.21 (0.27), residues: 360 loop : -1.56 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.023 0.001 TYR F 127 PHE 0.007 0.001 PHE B 167 TRP 0.008 0.001 TRP F 211 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00292 (16370) covalent geometry : angle 0.78101 (22270) hydrogen bonds : bond 0.03163 ( 972) hydrogen bonds : angle 4.64096 ( 2892) *********************** 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 288 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.3742 (pmm) cc_final: 0.3088 (pp-130) REVERT: A 127 TYR cc_start: 0.4394 (m-10) cc_final: 0.4056 (m-10) REVERT: B 61 MET cc_start: 0.4125 (pmm) cc_final: 0.3688 (ppp) REVERT: B 131 TYR cc_start: 0.4486 (m-10) cc_final: 0.4282 (m-10) REVERT: C 91 GLU cc_start: 0.2952 (OUTLIER) cc_final: 0.2368 (tm-30) REVERT: C 118 LEU cc_start: 0.3071 (OUTLIER) cc_final: 0.2586 (tt) REVERT: E 197 TYR cc_start: 0.5019 (m-80) cc_final: 0.4195 (m-80) REVERT: G 61 MET cc_start: 0.3881 (pmm) cc_final: 0.3199 (pp-130) REVERT: G 138 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.4874 (tt0) REVERT: H 186 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5409 (pp) REVERT: I 1 MET cc_start: 0.4595 (ppp) cc_final: 0.4236 (ppp) REVERT: I 50 MET cc_start: 0.2648 (mmt) cc_final: 0.2306 (mmm) REVERT: J 138 GLN cc_start: 0.5151 (OUTLIER) cc_final: 0.4810 (tm-30) outliers start: 66 outliers final: 18 residues processed: 270 average time/residue: 0.5085 time to fit residues: 153.8290 Evaluate side-chains 215 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 107 LEU 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 138 GLN Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 200 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 201 optimal weight: 0.0670 chunk 187 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 overall best weight: 1.5320 ------------------------------------------------------------------------------- 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 ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN I 116 GLN J 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.262864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.261713 restraints weight = 19899.904| |-----------------------------------------------------------------------------| r_work (start): 0.4977 rms_B_bonded: 0.17 r_work: 0.4972 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.4953 rms_B_bonded: 0.64 restraints_weight: 0.2500 r_work: 0.4825 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4291 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16370 Z= 0.138 Angle : 0.790 14.377 22270 Z= 0.364 Chirality : 0.047 0.368 2730 Planarity : 0.005 0.052 2850 Dihedral : 4.612 21.410 2300 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.07 % Allowed : 28.44 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2180 helix: 0.91 (0.14), residues: 1400 sheet: -0.27 (0.27), residues: 350 loop : -1.57 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.032 0.002 TYR H 127 PHE 0.011 0.001 PHE A 167 TRP 0.007 0.001 TRP F 211 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00320 (16370) covalent geometry : angle 0.78979 (22270) hydrogen bonds : bond 0.03383 ( 972) hydrogen bonds : angle 4.72458 ( 2892) *********************** 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 270 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.3648 (pmm) cc_final: 0.2930 (pp-130) REVERT: A 127 TYR cc_start: 0.4354 (m-10) cc_final: 0.3982 (m-10) REVERT: A 201 ASP cc_start: 0.5249 (m-30) cc_final: 0.4806 (m-30) REVERT: B 61 MET cc_start: 0.4540 (pmm) cc_final: 0.3872 (ppp) REVERT: B 131 TYR cc_start: 0.4494 (m-10) cc_final: 0.4291 (m-10) REVERT: C 118 LEU cc_start: 0.3429 (OUTLIER) cc_final: 0.3000 (tt) REVERT: E 6 ASP cc_start: 0.3130 (p0) cc_final: 0.2821 (p0) REVERT: E 171 ARG cc_start: 0.4010 (OUTLIER) cc_final: 0.3484 (tpp-160) REVERT: E 197 TYR cc_start: 0.5093 (m-80) cc_final: 0.4262 (m-80) REVERT: G 61 MET cc_start: 0.3776 (pmm) cc_final: 0.3125 (pp-130) REVERT: H 186 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5500 (pp) REVERT: J 127 TYR cc_start: 0.4862 (m-10) cc_final: 0.4650 (m-10) outliers start: 68 outliers final: 23 residues processed: 249 average time/residue: 0.4945 time to fit residues: 138.2761 Evaluate side-chains 221 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 118 LEU 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 107 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 196 SER 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 107 LEU 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 Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 128 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 68 optimal weight: 40.0000 chunk 162 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 HIS ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 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 = 0.261951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.261696 restraints weight = 19591.596| |-----------------------------------------------------------------------------| r_work (start): 0.4975 rms_B_bonded: 0.04 r_work: 0.4974 rms_B_bonded: 0.06 restraints_weight: 0.5000 r_work: 0.4972 rms_B_bonded: 0.12 restraints_weight: 0.2500 r_work: 0.4940 rms_B_bonded: 0.80 restraints_weight: 0.1250 r_work (final): 0.4940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4096 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16370 Z= 0.132 Angle : 0.803 14.444 22270 Z= 0.371 Chirality : 0.048 0.370 2730 Planarity : 0.005 0.052 2850 Dihedral : 4.511 22.764 2300 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.17 % Allowed : 29.82 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.17), residues: 2180 helix: 0.97 (0.14), residues: 1400 sheet: -0.23 (0.28), residues: 350 loop : -1.55 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.022 0.001 TYR C 127 PHE 0.011 0.001 PHE A 167 TRP 0.007 0.001 TRP F 211 HIS 0.006 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00301 (16370) covalent geometry : angle 0.80319 (22270) hydrogen bonds : bond 0.03276 ( 972) hydrogen bonds : angle 4.72905 ( 2892) *********************** 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 258 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.600 Fit side-chains REVERT: A 61 MET cc_start: 0.3880 (pmm) cc_final: 0.3341 (pp-130) REVERT: B 61 MET cc_start: 0.4231 (pmm) cc_final: 0.3950 (ppp) REVERT: B 131 TYR cc_start: 0.4526 (m-10) cc_final: 0.4311 (m-10) REVERT: C 91 GLU cc_start: 0.3291 (OUTLIER) cc_final: 0.2623 (tm-30) REVERT: D 1 MET cc_start: 0.4417 (tmt) cc_final: 0.3714 (tmt) REVERT: E 138 GLN cc_start: 0.4817 (OUTLIER) cc_final: 0.4385 (tt0) REVERT: E 197 TYR cc_start: 0.4764 (m-80) cc_final: 0.4066 (m-80) REVERT: F 47 HIS cc_start: 0.3824 (t-170) cc_final: 0.3479 (t-90) REVERT: G 61 MET cc_start: 0.3662 (pmm) cc_final: 0.3299 (pp-130) REVERT: H 186 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5121 (pp) outliers start: 53 outliers final: 20 residues processed: 243 average time/residue: 0.4581 time to fit residues: 125.1978 Evaluate side-chains 207 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 98 MET 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 107 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 204 VAL 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 204 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 211 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 87 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 GLN J 116 GLN J 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.262222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.261954 restraints weight = 19536.224| |-----------------------------------------------------------------------------| r_work (start): 0.4980 rms_B_bonded: 0.05 r_work: 0.4980 rms_B_bonded: 0.06 restraints_weight: 0.5000 r_work: 0.4977 rms_B_bonded: 0.13 restraints_weight: 0.2500 r_work: 0.4943 rms_B_bonded: 0.83 restraints_weight: 0.1250 r_work (final): 0.4943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4100 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16370 Z= 0.136 Angle : 0.852 16.492 22270 Z= 0.392 Chirality : 0.049 0.385 2730 Planarity : 0.005 0.051 2850 Dihedral : 4.512 20.789 2300 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.34 % Allowed : 31.08 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2180 helix: 0.97 (0.13), residues: 1400 sheet: -0.21 (0.27), residues: 360 loop : -1.58 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 55 TYR 0.019 0.001 TYR B 127 PHE 0.011 0.001 PHE H 207 TRP 0.007 0.001 TRP F 211 HIS 0.007 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00315 (16370) covalent geometry : angle 0.85227 (22270) hydrogen bonds : bond 0.03277 ( 972) hydrogen bonds : angle 4.74149 ( 2892) ********************** 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 242 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.3731 (pmm) cc_final: 0.3219 (pp-130) REVERT: B 61 MET cc_start: 0.4521 (pmm) cc_final: 0.4152 (ppp) REVERT: B 131 TYR cc_start: 0.4476 (m-10) cc_final: 0.4255 (m-10) REVERT: C 91 GLU cc_start: 0.3285 (OUTLIER) cc_final: 0.2642 (tm-30) REVERT: D 131 TYR cc_start: 0.4537 (m-10) cc_final: 0.4320 (m-10) REVERT: E 138 GLN cc_start: 0.4760 (OUTLIER) cc_final: 0.4298 (tt0) REVERT: E 197 TYR cc_start: 0.4792 (m-80) cc_final: 0.4064 (m-80) REVERT: F 47 HIS cc_start: 0.3889 (t-170) cc_final: 0.3529 (t-90) REVERT: G 61 MET cc_start: 0.3413 (pmm) cc_final: 0.3056 (pp-130) REVERT: G 138 GLN cc_start: 0.5013 (OUTLIER) cc_final: 0.4636 (tt0) REVERT: H 186 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.5132 (pp) outliers start: 39 outliers final: 17 residues processed: 229 average time/residue: 0.4327 time to fit residues: 111.2656 Evaluate side-chains 211 residues out of total 1670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain F residue 126 GLU 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 186 LEU Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain J residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 137 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 155 optimal weight: 0.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.261853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.261622 restraints weight = 19564.159| |-----------------------------------------------------------------------------| r_work (start): 0.4975 rms_B_bonded: 0.04 r_work: 0.4974 rms_B_bonded: 0.05 restraints_weight: 0.5000 r_work: 0.4971 rms_B_bonded: 0.11 restraints_weight: 0.2500 r_work: 0.4943 rms_B_bonded: 0.72 restraints_weight: 0.1250 r_work (final): 0.4943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4120 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16370 Z= 0.142 Angle : 0.866 16.317 22270 Z= 0.399 Chirality : 0.049 0.379 2730 Planarity : 0.005 0.050 2850 Dihedral : 4.560 23.523 2300 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.28 % Allowed : 31.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.17), residues: 2180 helix: 0.91 (0.13), residues: 1400 sheet: -0.22 (0.28), residues: 360 loop : -1.58 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 55 TYR 0.034 0.002 TYR E 127 PHE 0.014 0.001 PHE D 207 TRP 0.005 0.001 TRP F 211 HIS 0.011 0.001 HIS J 156 Details of bonding type rmsd covalent geometry : bond 0.00333 (16370) covalent geometry : angle 0.86576 (22270) hydrogen bonds : bond 0.03380 ( 972) hydrogen bonds : angle 4.82946 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.12 seconds wall clock time: 86 minutes 8.52 seconds (5168.52 seconds total)