Starting phenix.real_space_refine on Sat Feb 7 03:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c8e_45302/02_2026/9c8e_45302.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 9471 2.51 5 N 2497 2.21 5 O 2706 1.98 5 H 14714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29465 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2677 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2677 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "C" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "D" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "G" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "H" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "I" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "K" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2679 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.17 Number of scatterers: 29465 At special positions: 0 Unit cell: (156.867, 156.867, 60.0768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 O 2706 8.00 N 2497 7.00 C 9471 6.00 H 14714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 82 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 82 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 861.2 milliseconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 19.8% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.850A pdb=" N PHE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.806A pdb=" N TYR A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.777A pdb=" N TYR C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 221 through 229 removed outlier: 3.536A pdb=" N ARG E 224 " --> pdb=" O THR E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.838A pdb=" N TYR F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 122 Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 221 through 229 Processing helix chain 'H' and resid 117 through 122 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 164 through 170 removed outlier: 3.770A pdb=" N PHE H 170 " --> pdb=" O SER H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'I' and resid 117 through 122 Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 164 through 170 removed outlier: 4.052A pdb=" N PHE I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 229 Processing helix chain 'J' and resid 117 through 122 Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 164 through 169 Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 221 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66 removed outlier: 3.920A pdb=" N HIS A 62 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 216 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 214 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 212 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 211 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR A 106 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER A 185 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 108 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.561A pdb=" N PHE A 126 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 141 " --> pdb=" O CYS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66 removed outlier: 3.864A pdb=" N HIS B 62 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 216 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 212 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 211 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR B 106 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER B 185 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 108 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.974A pdb=" N SER B 141 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 66 removed outlier: 3.665A pdb=" N HIS C 62 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 216 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA C 212 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY C 211 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR C 106 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER C 185 " --> pdb=" O TYR C 106 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 108 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 90 removed outlier: 4.030A pdb=" N SER C 141 " --> pdb=" O CYS C 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 66 removed outlier: 3.543A pdb=" N HIS D 62 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 216 " --> pdb=" O HIS D 62 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 212 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY D 211 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR D 106 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER D 185 " --> pdb=" O TYR D 106 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 108 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 90 removed outlier: 4.021A pdb=" N SER D 141 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.622A pdb=" N HIS E 62 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA E 212 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY E 211 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR E 106 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER E 185 " --> pdb=" O TYR E 106 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 108 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL E 181 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 86 through 90 removed outlier: 3.828A pdb=" N SER E 141 " --> pdb=" O CYS E 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 66 removed outlier: 3.538A pdb=" N HIS F 62 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA F 212 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY F 211 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR F 106 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER F 185 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL F 108 " --> pdb=" O LEU F 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 90 removed outlier: 4.412A pdb=" N LEU F 127 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER F 141 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 61 through 66 removed outlier: 3.638A pdb=" N HIS G 62 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 212 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY G 211 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL G 108 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER G 185 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU G 110 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU G 183 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU G 112 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL G 181 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU G 114 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU G 179 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 86 through 90 removed outlier: 3.995A pdb=" N SER G 141 " --> pdb=" O CYS G 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 61 through 66 removed outlier: 3.909A pdb=" N HIS H 62 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE H 216 " --> pdb=" O HIS H 62 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA H 212 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY H 211 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 106 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER H 185 " --> pdb=" O TYR H 106 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL H 108 " --> pdb=" O LEU H 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 86 through 90 removed outlier: 4.345A pdb=" N LEU H 127 " --> pdb=" O HIS H 203 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER H 141 " --> pdb=" O CYS H 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 66 removed outlier: 3.632A pdb=" N HIS I 62 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE I 216 " --> pdb=" O HIS I 62 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU I 214 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA I 212 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR I 106 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SER I 185 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL I 108 " --> pdb=" O LEU I 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 86 through 90 removed outlier: 3.548A pdb=" N PHE I 126 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER I 141 " --> pdb=" O CYS I 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 61 through 66 removed outlier: 3.698A pdb=" N HIS J 62 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE J 216 " --> pdb=" O HIS J 62 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA J 212 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY J 211 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR J 106 " --> pdb=" O SER J 185 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER J 185 " --> pdb=" O TYR J 106 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL J 108 " --> pdb=" O LEU J 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.993A pdb=" N SER J 141 " --> pdb=" O CYS J 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 61 through 66 removed outlier: 3.635A pdb=" N HIS K 62 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA K 212 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY K 211 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR K 106 " --> pdb=" O SER K 185 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER K 185 " --> pdb=" O TYR K 106 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL K 108 " --> pdb=" O LEU K 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 86 through 90 removed outlier: 4.308A pdb=" N LEU K 127 " --> pdb=" O HIS K 203 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER K 141 " --> pdb=" O CYS K 132 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14685 1.03 - 1.23: 81 1.23 - 1.42: 6471 1.42 - 1.62: 8448 1.62 - 1.81: 121 Bond restraints: 29806 Sorted by residual: bond pdb=" CA HIS I 67 " pdb=" CB HIS I 67 " ideal model delta sigma weight residual 1.528 1.509 0.020 1.51e-02 4.39e+03 1.73e+00 bond pdb=" CA HIS K 67 " pdb=" CB HIS K 67 " ideal model delta sigma weight residual 1.527 1.506 0.021 1.75e-02 3.27e+03 1.42e+00 bond pdb=" CA ILE J 207 " pdb=" CB ILE J 207 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.11e-02 8.12e+03 1.20e+00 bond pdb=" N SER B 64 " pdb=" CA SER B 64 " ideal model delta sigma weight residual 1.462 1.451 0.011 1.07e-02 8.73e+03 1.11e+00 bond pdb=" CA HIS G 67 " pdb=" CB HIS G 67 " ideal model delta sigma weight residual 1.527 1.509 0.018 1.75e-02 3.27e+03 1.06e+00 ... (remaining 29801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 47761 0.80 - 1.60: 5312 1.60 - 2.40: 382 2.40 - 3.20: 68 3.20 - 4.00: 54 Bond angle restraints: 53577 Sorted by residual: angle pdb=" N THR E 72 " pdb=" CA THR E 72 " pdb=" C THR E 72 " ideal model delta sigma weight residual 110.61 114.02 -3.41 1.25e+00 6.40e-01 7.43e+00 angle pdb=" N GLU J 116 " pdb=" CA GLU J 116 " pdb=" C GLU J 116 " ideal model delta sigma weight residual 112.97 110.33 2.64 1.06e+00 8.90e-01 6.22e+00 angle pdb=" CA HIS D 203 " pdb=" C HIS D 203 " pdb=" N SER D 204 " ideal model delta sigma weight residual 114.90 118.24 -3.34 1.37e+00 5.33e-01 5.93e+00 angle pdb=" N THR J 221 " pdb=" CA THR J 221 " pdb=" C THR J 221 " ideal model delta sigma weight residual 112.93 109.70 3.23 1.33e+00 5.65e-01 5.89e+00 angle pdb=" N SER F 77 " pdb=" CA SER F 77 " pdb=" C SER F 77 " ideal model delta sigma weight residual 112.97 110.42 2.55 1.06e+00 8.90e-01 5.79e+00 ... (remaining 53572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13295 17.90 - 35.79: 685 35.79 - 53.69: 141 53.69 - 71.59: 64 71.59 - 89.48: 18 Dihedral angle restraints: 14203 sinusoidal: 7603 harmonic: 6600 Sorted by residual: dihedral pdb=" CB GLU H 111 " pdb=" CG GLU H 111 " pdb=" CD GLU H 111 " pdb=" OE1 GLU H 111 " ideal model delta sinusoidal sigma weight residual 0.00 89.48 -89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ALA A 87 " pdb=" C ALA A 87 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ALA E 87 " pdb=" C ALA E 87 " pdb=" N ASN E 88 " pdb=" CA ASN E 88 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 14200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1550 0.029 - 0.058: 569 0.058 - 0.086: 66 0.086 - 0.115: 137 0.115 - 0.144: 43 Chirality restraints: 2365 Sorted by residual: chirality pdb=" CA ILE C 199 " pdb=" N ILE C 199 " pdb=" C ILE C 199 " pdb=" CB ILE C 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE E 199 " pdb=" N ILE E 199 " pdb=" C ILE E 199 " pdb=" CB ILE E 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE J 199 " pdb=" N ILE J 199 " pdb=" C ILE J 199 " pdb=" CB ILE J 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2362 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 84 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO G 85 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 85 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 85 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 84 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 85 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 84 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO J 85 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 85 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 85 " 0.023 5.00e-02 4.00e+02 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 2350 2.24 - 2.83: 65595 2.83 - 3.42: 70559 3.42 - 4.01: 99713 4.01 - 4.60: 150151 Nonbonded interactions: 388368 Sorted by model distance: nonbonded pdb=" OE1 GLN E 121 " pdb="HE22 GLN E 157 " model vdw 1.644 2.450 nonbonded pdb=" OE1 GLN A 121 " pdb="HE22 GLN A 157 " model vdw 1.671 2.450 nonbonded pdb=" H TYR J 106 " pdb=" O TYR J 187 " model vdw 1.693 2.450 nonbonded pdb=" OE1 GLN J 121 " pdb="HE22 GLN J 157 " model vdw 1.694 2.450 nonbonded pdb="HH12 ARG C 152 " pdb=" OD2 ASP C 160 " model vdw 1.709 2.450 ... (remaining 388363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'D' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'E' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'F' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'G' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'H' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'I' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'J' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) selection = (chain 'K' and (resid 58 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 75 through 81 or (resid 82 and (name N or name CA or name C or name O \ or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 83 \ through 229)) } 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: 4.290 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: 0.140 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 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 : 0.003 0.037 15094 Z= 0.154 Angle : 0.522 3.996 20486 Z= 0.303 Chirality : 0.039 0.144 2365 Planarity : 0.004 0.045 2552 Dihedral : 11.518 89.483 5478 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1793 helix: 1.11 (0.33), residues: 264 sheet: 0.57 (0.20), residues: 638 loop : -0.40 (0.23), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.011 0.001 TYR H 213 PHE 0.008 0.001 PHE I 126 HIS 0.005 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00321 (15092) covalent geometry : angle 0.52231 (20482) SS BOND : bond 0.00007 ( 2) SS BOND : angle 0.42328 ( 4) hydrogen bonds : bond 0.25751 ( 544) hydrogen bonds : angle 9.76725 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.764 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6746 (mt-10) REVERT: A 117 SER cc_start: 0.7887 (p) cc_final: 0.7576 (m) REVERT: A 184 TYR cc_start: 0.8229 (m-80) cc_final: 0.7952 (m-80) REVERT: A 201 GLU cc_start: 0.7311 (tt0) cc_final: 0.6719 (tt0) REVERT: A 204 SER cc_start: 0.8118 (t) cc_final: 0.7895 (t) REVERT: C 64 SER cc_start: 0.8260 (m) cc_final: 0.7944 (p) REVERT: C 113 GLU cc_start: 0.6857 (tt0) cc_final: 0.6655 (mt-10) REVERT: C 204 SER cc_start: 0.8083 (t) cc_final: 0.7832 (t) REVERT: C 214 LEU cc_start: 0.7838 (tp) cc_final: 0.7607 (tp) REVERT: D 64 SER cc_start: 0.8185 (m) cc_final: 0.7738 (p) REVERT: D 176 LYS cc_start: 0.8130 (pttt) cc_final: 0.7624 (ptpt) REVERT: D 201 GLU cc_start: 0.7288 (tt0) cc_final: 0.7073 (tt0) REVERT: D 204 SER cc_start: 0.8211 (t) cc_final: 0.7989 (t) REVERT: D 216 ILE cc_start: 0.8238 (mt) cc_final: 0.7959 (mm) REVERT: E 176 LYS cc_start: 0.8111 (pttt) cc_final: 0.7592 (ptpt) REVERT: E 204 SER cc_start: 0.8002 (t) cc_final: 0.7761 (t) REVERT: F 64 SER cc_start: 0.7944 (m) cc_final: 0.7512 (p) REVERT: F 128 VAL cc_start: 0.7523 (t) cc_final: 0.7236 (m) REVERT: G 64 SER cc_start: 0.8185 (m) cc_final: 0.7852 (p) REVERT: H 64 SER cc_start: 0.8158 (m) cc_final: 0.7815 (p) REVERT: H 113 GLU cc_start: 0.7017 (tt0) cc_final: 0.6708 (mt-10) REVERT: H 185 SER cc_start: 0.7254 (p) cc_final: 0.7021 (t) REVERT: I 113 GLU cc_start: 0.7057 (tt0) cc_final: 0.6514 (mt-10) REVERT: I 117 SER cc_start: 0.7961 (p) cc_final: 0.7628 (m) REVERT: I 201 GLU cc_start: 0.7406 (tt0) cc_final: 0.7198 (tt0) REVERT: I 204 SER cc_start: 0.8321 (t) cc_final: 0.8103 (t) REVERT: J 113 GLU cc_start: 0.6994 (tt0) cc_final: 0.6520 (mt-10) REVERT: K 110 LEU cc_start: 0.6868 (tp) cc_final: 0.6634 (tp) REVERT: K 178 LEU cc_start: 0.7744 (mt) cc_final: 0.7503 (mt) REVERT: K 202 ILE cc_start: 0.8393 (mt) cc_final: 0.8186 (mm) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.2516 time to fit residues: 194.1988 Evaluate side-chains 452 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN E 157 GLN G 121 GLN G 157 GLN I 88 ASN K 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.161918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136533 restraints weight = 59411.570| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.86 r_work: 0.3664 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15094 Z= 0.214 Angle : 0.576 4.765 20486 Z= 0.299 Chirality : 0.042 0.160 2365 Planarity : 0.005 0.053 2552 Dihedral : 4.577 18.108 2068 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.56 % Allowed : 6.40 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1793 helix: 1.27 (0.33), residues: 264 sheet: 0.72 (0.20), residues: 638 loop : -0.58 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 107 TYR 0.018 0.002 TYR K 133 PHE 0.013 0.001 PHE I 126 HIS 0.009 0.002 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00477 (15092) covalent geometry : angle 0.57618 (20482) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.60934 ( 4) hydrogen bonds : bond 0.03887 ( 544) hydrogen bonds : angle 6.41005 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 474 time to evaluate : 0.586 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.8395 (m-80) cc_final: 0.8186 (m-80) REVERT: B 117 SER cc_start: 0.7874 (p) cc_final: 0.7670 (m) REVERT: B 162 LEU cc_start: 0.7812 (mt) cc_final: 0.7578 (mp) REVERT: B 176 LYS cc_start: 0.8321 (pttt) cc_final: 0.8035 (ptpt) REVERT: C 112 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7597 (mp) REVERT: C 214 LEU cc_start: 0.7995 (tp) cc_final: 0.7737 (tt) REVERT: D 117 SER cc_start: 0.8185 (OUTLIER) cc_final: 0.7817 (m) REVERT: D 176 LYS cc_start: 0.8384 (pttt) cc_final: 0.8064 (ptpt) REVERT: D 182 GLU cc_start: 0.7059 (tt0) cc_final: 0.6822 (tt0) REVERT: D 216 ILE cc_start: 0.8483 (mt) cc_final: 0.8202 (mm) REVERT: E 114 LEU cc_start: 0.8183 (mt) cc_final: 0.7926 (mm) REVERT: E 176 LYS cc_start: 0.8319 (pttt) cc_final: 0.7986 (ptpt) REVERT: F 113 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: F 117 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7608 (m) REVERT: G 117 SER cc_start: 0.8047 (p) cc_final: 0.7792 (m) REVERT: G 162 LEU cc_start: 0.7528 (tp) cc_final: 0.7248 (mt) REVERT: G 182 GLU cc_start: 0.7091 (tt0) cc_final: 0.6855 (tt0) REVERT: H 185 SER cc_start: 0.7689 (p) cc_final: 0.7482 (t) REVERT: I 101 MET cc_start: 0.5874 (ppp) cc_final: 0.5629 (ppp) REVERT: I 184 TYR cc_start: 0.8242 (m-80) cc_final: 0.7962 (m-80) REVERT: J 117 SER cc_start: 0.8054 (p) cc_final: 0.7824 (m) REVERT: K 110 LEU cc_start: 0.6902 (tp) cc_final: 0.6688 (tp) REVERT: K 180 GLU cc_start: 0.6807 (tt0) cc_final: 0.6597 (tt0) outliers start: 26 outliers final: 18 residues processed: 488 average time/residue: 0.2783 time to fit residues: 196.5173 Evaluate side-chains 475 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 453 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 ASN E 121 GLN E 157 GLN G 121 GLN G 157 GLN I 203 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136712 restraints weight = 58911.426| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.88 r_work: 0.3664 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15094 Z= 0.189 Angle : 0.537 5.160 20486 Z= 0.278 Chirality : 0.041 0.153 2365 Planarity : 0.005 0.047 2552 Dihedral : 4.452 18.263 2068 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.91 % Allowed : 8.91 % Favored : 89.17 % 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 are not related in a simple way. whole: 0.07 (0.20), residues: 1793 helix: 1.36 (0.33), residues: 264 sheet: 0.70 (0.20), residues: 660 loop : -0.89 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 206 TYR 0.013 0.001 TYR H 213 PHE 0.012 0.001 PHE E 126 HIS 0.006 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00421 (15092) covalent geometry : angle 0.53705 (20482) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.60063 ( 4) hydrogen bonds : bond 0.03579 ( 544) hydrogen bonds : angle 6.04558 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 452 time to evaluate : 0.666 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.8428 (m-80) cc_final: 0.8221 (m-80) REVERT: B 162 LEU cc_start: 0.7807 (mt) cc_final: 0.7558 (mp) REVERT: B 176 LYS cc_start: 0.8356 (pttt) cc_final: 0.8043 (ptpt) REVERT: C 69 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6735 (p-80) REVERT: C 214 LEU cc_start: 0.7987 (tp) cc_final: 0.7736 (tt) REVERT: D 101 MET cc_start: 0.5708 (ppp) cc_final: 0.5220 (ppp) REVERT: D 176 LYS cc_start: 0.8366 (pttt) cc_final: 0.8048 (ptpt) REVERT: D 216 ILE cc_start: 0.8494 (mt) cc_final: 0.8215 (mm) REVERT: E 114 LEU cc_start: 0.8168 (mt) cc_final: 0.7907 (mm) REVERT: E 176 LYS cc_start: 0.8331 (pttt) cc_final: 0.7991 (ptpt) REVERT: E 182 GLU cc_start: 0.6893 (tt0) cc_final: 0.6494 (tt0) REVERT: F 113 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: G 162 LEU cc_start: 0.7500 (tp) cc_final: 0.7195 (mt) REVERT: H 114 LEU cc_start: 0.8319 (mp) cc_final: 0.8038 (mm) REVERT: I 69 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6833 (p90) REVERT: I 184 TYR cc_start: 0.8269 (m-80) cc_final: 0.7937 (m-80) REVERT: K 180 GLU cc_start: 0.6903 (tt0) cc_final: 0.6666 (tt0) outliers start: 32 outliers final: 24 residues processed: 465 average time/residue: 0.2726 time to fit residues: 182.9978 Evaluate side-chains 470 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 443 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain J residue 217 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN J 88 ASN K 104 GLN K 203 HIS K 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.156957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132499 restraints weight = 58948.383| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.74 r_work: 0.3635 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15094 Z= 0.319 Angle : 0.636 5.477 20486 Z= 0.334 Chirality : 0.044 0.155 2365 Planarity : 0.006 0.056 2552 Dihedral : 4.982 24.322 2068 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.87 % Allowed : 11.06 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1793 helix: 0.96 (0.34), residues: 264 sheet: 0.39 (0.20), residues: 638 loop : -1.03 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 206 TYR 0.020 0.002 TYR I 213 PHE 0.014 0.001 PHE E 126 HIS 0.013 0.002 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00709 (15092) covalent geometry : angle 0.63559 (20482) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.21552 ( 4) hydrogen bonds : bond 0.04011 ( 544) hydrogen bonds : angle 6.30182 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 447 time to evaluate : 0.831 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: 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: symmetry clash REVERT: A 101 MET cc_start: 0.6310 (ppp) cc_final: 0.6013 (ppp) REVERT: A 184 TYR cc_start: 0.8519 (m-80) cc_final: 0.7787 (m-80) REVERT: B 101 MET cc_start: 0.6219 (ppp) cc_final: 0.5870 (ppp) REVERT: B 112 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7611 (tp) REVERT: B 117 SER cc_start: 0.8153 (p) cc_final: 0.7891 (m) REVERT: B 162 LEU cc_start: 0.7884 (mt) cc_final: 0.7626 (mp) REVERT: C 69 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6844 (p-80) REVERT: C 101 MET cc_start: 0.6173 (tmm) cc_final: 0.5943 (ppp) REVERT: C 214 LEU cc_start: 0.8138 (tp) cc_final: 0.7886 (tt) REVERT: D 176 LYS cc_start: 0.8515 (pttt) cc_final: 0.8219 (ptpt) REVERT: D 216 ILE cc_start: 0.8588 (mt) cc_final: 0.8343 (mm) REVERT: E 114 LEU cc_start: 0.8276 (mt) cc_final: 0.8053 (mm) REVERT: E 176 LYS cc_start: 0.8451 (pttt) cc_final: 0.8146 (ptpt) REVERT: E 182 GLU cc_start: 0.7119 (tt0) cc_final: 0.6741 (tt0) REVERT: F 101 MET cc_start: 0.6573 (ppp) cc_final: 0.6025 (ppp) REVERT: F 113 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: G 117 SER cc_start: 0.8145 (p) cc_final: 0.7908 (m) REVERT: H 114 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8054 (mm) REVERT: H 147 VAL cc_start: 0.8466 (p) cc_final: 0.8257 (m) REVERT: I 69 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6953 (p90) REVERT: I 184 TYR cc_start: 0.8402 (m-80) cc_final: 0.7752 (m-80) REVERT: J 105 PRO cc_start: 0.7310 (Cg_endo) cc_final: 0.7008 (Cg_exo) outliers start: 48 outliers final: 40 residues processed: 466 average time/residue: 0.2954 time to fit residues: 199.6469 Evaluate side-chains 489 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 444 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135646 restraints weight = 58806.834| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.85 r_work: 0.3660 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15094 Z= 0.173 Angle : 0.517 4.714 20486 Z= 0.267 Chirality : 0.042 0.159 2365 Planarity : 0.005 0.050 2552 Dihedral : 4.436 18.889 2068 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.39 % Allowed : 12.80 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1793 helix: 1.31 (0.34), residues: 264 sheet: 0.46 (0.20), residues: 638 loop : -0.86 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.012 0.001 TYR H 213 PHE 0.012 0.001 PHE E 126 HIS 0.005 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00385 (15092) covalent geometry : angle 0.51701 (20482) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.76489 ( 4) hydrogen bonds : bond 0.03098 ( 544) hydrogen bonds : angle 5.83358 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 435 time to evaluate : 0.860 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: 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 101 MET cc_start: 0.6326 (ppp) cc_final: 0.6103 (ppp) REVERT: A 184 TYR cc_start: 0.8470 (m-80) cc_final: 0.8104 (m-80) REVERT: B 101 MET cc_start: 0.6176 (ppp) cc_final: 0.5891 (ppp) REVERT: B 117 SER cc_start: 0.8077 (p) cc_final: 0.7804 (m) REVERT: B 162 LEU cc_start: 0.7883 (mt) cc_final: 0.7622 (mp) REVERT: B 176 LYS cc_start: 0.8484 (pttt) cc_final: 0.8199 (ptpt) REVERT: C 69 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6781 (p-80) REVERT: C 101 MET cc_start: 0.6301 (tmm) cc_final: 0.5919 (ppp) REVERT: C 180 GLU cc_start: 0.7449 (tt0) cc_final: 0.7218 (tt0) REVERT: C 214 LEU cc_start: 0.8113 (tp) cc_final: 0.7843 (tt) REVERT: D 106 TYR cc_start: 0.6752 (m-80) cc_final: 0.6198 (m-80) REVERT: D 176 LYS cc_start: 0.8463 (pttt) cc_final: 0.8168 (ptpt) REVERT: D 216 ILE cc_start: 0.8562 (mt) cc_final: 0.8292 (mm) REVERT: E 101 MET cc_start: 0.5865 (ppp) cc_final: 0.5197 (ppp) REVERT: E 114 LEU cc_start: 0.8259 (mt) cc_final: 0.8046 (mm) REVERT: E 176 LYS cc_start: 0.8437 (pttt) cc_final: 0.7985 (ptpp) REVERT: E 182 GLU cc_start: 0.7137 (tt0) cc_final: 0.6800 (tt0) REVERT: F 113 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: F 117 SER cc_start: 0.8262 (p) cc_final: 0.7795 (m) REVERT: G 117 SER cc_start: 0.8191 (p) cc_final: 0.7901 (m) REVERT: G 182 GLU cc_start: 0.7312 (tt0) cc_final: 0.6919 (tt0) REVERT: I 69 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6829 (p90) REVERT: J 105 PRO cc_start: 0.7266 (Cg_endo) cc_final: 0.7004 (Cg_exo) outliers start: 40 outliers final: 31 residues processed: 454 average time/residue: 0.3110 time to fit residues: 203.0281 Evaluate side-chains 465 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 431 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136372 restraints weight = 58650.059| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.82 r_work: 0.3656 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15094 Z= 0.172 Angle : 0.508 4.303 20486 Z= 0.261 Chirality : 0.041 0.154 2365 Planarity : 0.005 0.049 2552 Dihedral : 4.295 18.783 2068 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.21 % Allowed : 13.88 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1793 helix: 0.99 (0.33), residues: 286 sheet: 0.37 (0.20), residues: 649 loop : -0.93 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 71 TYR 0.016 0.001 TYR C 106 PHE 0.010 0.001 PHE G 126 HIS 0.005 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00385 (15092) covalent geometry : angle 0.50829 (20482) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.76590 ( 4) hydrogen bonds : bond 0.02977 ( 544) hydrogen bonds : angle 5.69382 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 438 time to evaluate : 0.795 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.8483 (m-80) cc_final: 0.8102 (m-80) REVERT: B 101 MET cc_start: 0.6194 (ppp) cc_final: 0.5928 (ppp) REVERT: B 117 SER cc_start: 0.8094 (p) cc_final: 0.7796 (m) REVERT: B 162 LEU cc_start: 0.7872 (mt) cc_final: 0.7643 (mp) REVERT: B 176 LYS cc_start: 0.8467 (pttt) cc_final: 0.8182 (ptpt) REVERT: C 69 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6756 (p-80) REVERT: C 101 MET cc_start: 0.6455 (tmm) cc_final: 0.5895 (ppp) REVERT: C 214 LEU cc_start: 0.8096 (tp) cc_final: 0.7801 (tt) REVERT: C 216 ILE cc_start: 0.8642 (mt) cc_final: 0.8342 (mm) REVERT: D 101 MET cc_start: 0.5627 (ppp) cc_final: 0.4994 (ppp) REVERT: D 106 TYR cc_start: 0.6806 (m-80) cc_final: 0.6226 (m-80) REVERT: D 176 LYS cc_start: 0.8469 (pttt) cc_final: 0.8189 (ptpt) REVERT: D 216 ILE cc_start: 0.8563 (mt) cc_final: 0.8283 (mm) REVERT: E 101 MET cc_start: 0.5932 (ppp) cc_final: 0.5383 (ppp) REVERT: E 114 LEU cc_start: 0.8271 (mt) cc_final: 0.8056 (mm) REVERT: E 176 LYS cc_start: 0.8440 (pttt) cc_final: 0.7975 (ptpp) REVERT: E 182 GLU cc_start: 0.7111 (tt0) cc_final: 0.6769 (tt0) REVERT: F 101 MET cc_start: 0.6535 (ppp) cc_final: 0.5947 (ppp) REVERT: F 113 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: F 117 SER cc_start: 0.8253 (p) cc_final: 0.7775 (m) REVERT: G 117 SER cc_start: 0.8190 (p) cc_final: 0.7899 (m) REVERT: I 69 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6790 (p90) REVERT: I 184 TYR cc_start: 0.8347 (m-80) cc_final: 0.7918 (m-80) REVERT: J 105 PRO cc_start: 0.7278 (Cg_endo) cc_final: 0.7011 (Cg_exo) REVERT: J 112 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7163 (mt) outliers start: 37 outliers final: 30 residues processed: 455 average time/residue: 0.2976 time to fit residues: 194.3311 Evaluate side-chains 467 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 433 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 28 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.159271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134082 restraints weight = 59163.706| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.84 r_work: 0.3636 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15094 Z= 0.230 Angle : 0.549 5.540 20486 Z= 0.284 Chirality : 0.042 0.168 2365 Planarity : 0.005 0.051 2552 Dihedral : 4.480 19.549 2068 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.87 % Allowed : 13.88 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1793 helix: 0.91 (0.33), residues: 286 sheet: 0.26 (0.20), residues: 649 loop : -1.06 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 71 TYR 0.015 0.001 TYR H 213 PHE 0.012 0.001 PHE E 126 HIS 0.007 0.002 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00512 (15092) covalent geometry : angle 0.54874 (20482) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.00389 ( 4) hydrogen bonds : bond 0.03291 ( 544) hydrogen bonds : angle 5.86989 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 0.883 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: 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: B 101 MET cc_start: 0.6248 (ppp) cc_final: 0.6018 (ppp) REVERT: B 117 SER cc_start: 0.8199 (p) cc_final: 0.7901 (m) REVERT: B 162 LEU cc_start: 0.7927 (mt) cc_final: 0.7649 (mp) REVERT: B 176 LYS cc_start: 0.8500 (pttt) cc_final: 0.8223 (ptpt) REVERT: C 69 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.6803 (p-80) REVERT: C 101 MET cc_start: 0.6479 (tmm) cc_final: 0.5958 (ppp) REVERT: C 214 LEU cc_start: 0.8110 (tp) cc_final: 0.7844 (tt) REVERT: D 101 MET cc_start: 0.5749 (ppp) cc_final: 0.5137 (ppp) REVERT: D 106 TYR cc_start: 0.6791 (m-80) cc_final: 0.6310 (m-80) REVERT: D 176 LYS cc_start: 0.8506 (pttt) cc_final: 0.8221 (ptpt) REVERT: D 216 ILE cc_start: 0.8573 (mt) cc_final: 0.8283 (mm) REVERT: E 101 MET cc_start: 0.6028 (ppp) cc_final: 0.5555 (ppp) REVERT: E 176 LYS cc_start: 0.8453 (pttt) cc_final: 0.8017 (ptpp) REVERT: E 182 GLU cc_start: 0.7166 (tt0) cc_final: 0.6725 (tt0) REVERT: F 113 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: G 69 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6864 (p90) REVERT: G 117 SER cc_start: 0.8215 (p) cc_final: 0.7961 (m) REVERT: H 112 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7180 (mp) REVERT: H 217 HIS cc_start: 0.6463 (OUTLIER) cc_final: 0.6225 (m-70) REVERT: I 69 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.6798 (p90) REVERT: I 112 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7467 (tp) REVERT: I 184 TYR cc_start: 0.8398 (m-80) cc_final: 0.7890 (m-80) REVERT: J 105 PRO cc_start: 0.7366 (Cg_endo) cc_final: 0.7125 (Cg_exo) REVERT: K 69 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6472 (p90) outliers start: 48 outliers final: 36 residues processed: 461 average time/residue: 0.2941 time to fit residues: 196.1973 Evaluate side-chains 478 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 434 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 204 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134723 restraints weight = 59248.454| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.83 r_work: 0.3642 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15094 Z= 0.178 Angle : 0.508 4.426 20486 Z= 0.261 Chirality : 0.041 0.164 2365 Planarity : 0.005 0.051 2552 Dihedral : 4.269 17.890 2068 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.63 % Allowed : 14.06 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1793 helix: 1.07 (0.33), residues: 286 sheet: 0.28 (0.20), residues: 671 loop : -1.23 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 206 TYR 0.015 0.001 TYR J 102 PHE 0.012 0.001 PHE E 126 HIS 0.005 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00397 (15092) covalent geometry : angle 0.50741 (20482) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.86491 ( 4) hydrogen bonds : bond 0.02951 ( 544) hydrogen bonds : angle 5.66673 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 433 time to evaluate : 0.915 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: 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: B 101 MET cc_start: 0.6242 (ppp) cc_final: 0.5988 (ppp) REVERT: B 117 SER cc_start: 0.8174 (p) cc_final: 0.7885 (m) REVERT: B 162 LEU cc_start: 0.7898 (mt) cc_final: 0.7619 (mp) REVERT: B 176 LYS cc_start: 0.8490 (pttt) cc_final: 0.8211 (ptpt) REVERT: C 69 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6722 (p-80) REVERT: C 101 MET cc_start: 0.6445 (tmm) cc_final: 0.5936 (ppp) REVERT: C 214 LEU cc_start: 0.8105 (tp) cc_final: 0.7828 (tt) REVERT: C 216 ILE cc_start: 0.8640 (mt) cc_final: 0.8346 (mm) REVERT: D 101 MET cc_start: 0.5805 (ppp) cc_final: 0.5184 (ppp) REVERT: D 106 TYR cc_start: 0.6726 (m-80) cc_final: 0.6250 (m-80) REVERT: D 176 LYS cc_start: 0.8461 (pttt) cc_final: 0.8179 (ptpt) REVERT: D 216 ILE cc_start: 0.8558 (mt) cc_final: 0.8268 (mm) REVERT: E 101 MET cc_start: 0.5999 (ppp) cc_final: 0.5574 (ppp) REVERT: E 176 LYS cc_start: 0.8446 (pttt) cc_final: 0.8017 (ptpp) REVERT: E 182 GLU cc_start: 0.7117 (tt0) cc_final: 0.6767 (tt0) REVERT: F 101 MET cc_start: 0.6634 (ppp) cc_final: 0.5975 (ppp) REVERT: F 113 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: F 184 TYR cc_start: 0.8470 (m-80) cc_final: 0.7872 (m-80) REVERT: G 69 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6866 (p90) REVERT: G 117 SER cc_start: 0.8176 (p) cc_final: 0.7942 (m) REVERT: H 112 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7178 (mp) REVERT: I 69 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6756 (p90) REVERT: J 105 PRO cc_start: 0.7371 (Cg_endo) cc_final: 0.7155 (Cg_exo) REVERT: J 182 GLU cc_start: 0.7350 (tt0) cc_final: 0.6903 (tt0) REVERT: K 69 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6437 (p90) outliers start: 44 outliers final: 36 residues processed: 454 average time/residue: 0.3098 time to fit residues: 203.3806 Evaluate side-chains 476 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 434 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 110 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 115 optimal weight: 0.0050 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.159736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134517 restraints weight = 58759.563| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.85 r_work: 0.3637 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15094 Z= 0.178 Angle : 0.508 4.709 20486 Z= 0.260 Chirality : 0.041 0.165 2365 Planarity : 0.005 0.050 2552 Dihedral : 4.234 17.648 2068 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.81 % Allowed : 14.06 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1793 helix: 1.15 (0.33), residues: 286 sheet: 0.33 (0.20), residues: 671 loop : -1.27 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 206 TYR 0.012 0.001 TYR H 213 PHE 0.011 0.001 PHE E 126 HIS 0.005 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00399 (15092) covalent geometry : angle 0.50787 (20482) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.86667 ( 4) hydrogen bonds : bond 0.02935 ( 544) hydrogen bonds : angle 5.63295 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 438 time to evaluate : 0.832 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: 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 101 MET cc_start: 0.6329 (ppp) cc_final: 0.5973 (ppp) REVERT: B 117 SER cc_start: 0.8182 (p) cc_final: 0.7860 (m) REVERT: B 162 LEU cc_start: 0.7895 (mt) cc_final: 0.7616 (mp) REVERT: B 176 LYS cc_start: 0.8476 (pttt) cc_final: 0.8197 (ptpt) REVERT: C 69 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6718 (p-80) REVERT: C 101 MET cc_start: 0.6448 (tmm) cc_final: 0.5954 (ppp) REVERT: C 214 LEU cc_start: 0.8112 (tp) cc_final: 0.7828 (tt) REVERT: C 216 ILE cc_start: 0.8640 (mt) cc_final: 0.8342 (mm) REVERT: D 106 TYR cc_start: 0.6721 (m-80) cc_final: 0.6252 (m-80) REVERT: D 176 LYS cc_start: 0.8446 (pttt) cc_final: 0.8164 (ptpt) REVERT: D 216 ILE cc_start: 0.8544 (mt) cc_final: 0.8246 (mm) REVERT: E 101 MET cc_start: 0.6031 (ppp) cc_final: 0.5625 (ppp) REVERT: E 176 LYS cc_start: 0.8442 (pttt) cc_final: 0.8006 (ptpp) REVERT: E 182 GLU cc_start: 0.7108 (tt0) cc_final: 0.6660 (tt0) REVERT: F 113 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7200 (mt-10) REVERT: F 114 LEU cc_start: 0.8355 (mt) cc_final: 0.8095 (mm) REVERT: F 180 GLU cc_start: 0.7368 (tt0) cc_final: 0.7158 (tp30) REVERT: F 184 TYR cc_start: 0.8484 (m-80) cc_final: 0.7859 (m-80) REVERT: G 69 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6890 (p90) REVERT: G 117 SER cc_start: 0.8191 (p) cc_final: 0.7947 (m) REVERT: H 112 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7177 (mp) REVERT: I 69 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6738 (p90) REVERT: J 105 PRO cc_start: 0.7335 (Cg_endo) cc_final: 0.7122 (Cg_exo) REVERT: J 182 GLU cc_start: 0.7400 (tt0) cc_final: 0.6943 (tt0) REVERT: K 69 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6395 (p90) outliers start: 47 outliers final: 38 residues processed: 461 average time/residue: 0.2981 time to fit residues: 199.3310 Evaluate side-chains 480 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 436 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 GLN G 121 GLN G 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134711 restraints weight = 58748.618| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.90 r_work: 0.3644 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15094 Z= 0.153 Angle : 0.491 4.604 20486 Z= 0.250 Chirality : 0.041 0.165 2365 Planarity : 0.005 0.050 2552 Dihedral : 4.129 16.744 2068 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.75 % Allowed : 14.47 % Favored : 82.78 % 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 are not related in a simple way. whole: -0.33 (0.20), residues: 1793 helix: 1.24 (0.33), residues: 286 sheet: 0.37 (0.20), residues: 671 loop : -1.24 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.011 0.001 TYR A 102 PHE 0.011 0.001 PHE E 126 HIS 0.005 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00347 (15092) covalent geometry : angle 0.49070 (20482) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.78619 ( 4) hydrogen bonds : bond 0.02747 ( 544) hydrogen bonds : angle 5.53624 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 434 time to evaluate : 0.491 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: 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 184 TYR cc_start: 0.8427 (m-80) cc_final: 0.7800 (m-80) REVERT: B 117 SER cc_start: 0.8000 (p) cc_final: 0.7688 (m) REVERT: B 162 LEU cc_start: 0.7871 (mt) cc_final: 0.7587 (mp) REVERT: B 176 LYS cc_start: 0.8367 (pttt) cc_final: 0.8080 (ptpt) REVERT: C 69 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6620 (p-80) REVERT: C 101 MET cc_start: 0.6383 (tmm) cc_final: 0.5928 (ppp) REVERT: C 214 LEU cc_start: 0.7974 (tp) cc_final: 0.7680 (tt) REVERT: C 216 ILE cc_start: 0.8586 (mt) cc_final: 0.8272 (mm) REVERT: D 106 TYR cc_start: 0.6553 (m-80) cc_final: 0.6162 (m-80) REVERT: D 176 LYS cc_start: 0.8332 (pttt) cc_final: 0.8040 (ptpt) REVERT: D 216 ILE cc_start: 0.8496 (mt) cc_final: 0.8188 (mm) REVERT: E 101 MET cc_start: 0.5952 (ppp) cc_final: 0.5560 (ppp) REVERT: E 176 LYS cc_start: 0.8335 (pttt) cc_final: 0.7887 (ptpp) REVERT: E 182 GLU cc_start: 0.6882 (tt0) cc_final: 0.6462 (tt0) REVERT: F 113 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: F 114 LEU cc_start: 0.8256 (mt) cc_final: 0.7976 (mm) REVERT: F 184 TYR cc_start: 0.8404 (m-80) cc_final: 0.7814 (m-80) REVERT: G 69 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6757 (p90) REVERT: G 117 SER cc_start: 0.8077 (p) cc_final: 0.7827 (m) REVERT: H 112 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7050 (mp) REVERT: I 69 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6596 (p90) REVERT: J 69 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6543 (p-80) REVERT: J 112 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7050 (mt) REVERT: J 182 GLU cc_start: 0.7191 (tt0) cc_final: 0.6740 (tt0) REVERT: K 69 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6310 (p90) outliers start: 46 outliers final: 37 residues processed: 457 average time/residue: 0.2786 time to fit residues: 183.7743 Evaluate side-chains 478 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 433 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 69 HIS Chi-restraints excluded: chain G residue 70 TYR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 217 HIS Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain J residue 69 HIS Chi-restraints excluded: chain J residue 70 TYR Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 217 HIS Chi-restraints excluded: chain K residue 69 HIS Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain K residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 GLN G 121 GLN G 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.159073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134185 restraints weight = 59087.595| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.82 r_work: 0.3648 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15094 Z= 0.219 Angle : 0.535 5.227 20486 Z= 0.275 Chirality : 0.042 0.172 2365 Planarity : 0.005 0.051 2552 Dihedral : 4.331 18.414 2068 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.99 % Allowed : 14.35 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1793 helix: 1.10 (0.33), residues: 286 sheet: 0.33 (0.20), residues: 649 loop : -1.08 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 206 TYR 0.015 0.001 TYR H 102 PHE 0.012 0.001 PHE E 126 HIS 0.007 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00489 (15092) covalent geometry : angle 0.53527 (20482) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.03658 ( 4) hydrogen bonds : bond 0.03144 ( 544) hydrogen bonds : angle 5.73835 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7760.37 seconds wall clock time: 132 minutes 30.29 seconds (7950.29 seconds total)