Starting phenix.real_space_refine on Thu Aug 6 13:16:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22rj_68620/08_2026/22rj_68620.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 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 K 4 8.98 5 S 80 5.16 5 C 9652 2.51 5 N 2480 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14952 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2621 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1116 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.53, per 1000 atoms: 0.17 Number of scatterers: 14952 At special positions: 0 Unit cell: (115.75, 115.75, 123.158, 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) K 4 19.00 S 80 16.00 O 2736 8.00 N 2480 7.00 C 9652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 517.5 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 79.6% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 150 through 179 Processing helix chain 'A' and resid 180 through 185 removed outlier: 6.216A pdb=" N ARG A 183 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 210 removed outlier: 3.658A pdb=" N VAL A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.710A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.543A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 365 removed outlier: 4.718A pdb=" N SER A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 517 through 537 Processing helix chain 'A' and resid 542 through 573 removed outlier: 3.895A pdb=" N VAL A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 124 through 143 Processing helix chain 'B' and resid 150 through 179 Processing helix chain 'B' and resid 180 through 185 removed outlier: 6.164A pdb=" N ARG B 183 " --> pdb=" O CYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 196 through 210 removed outlier: 3.656A pdb=" N VAL B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 227 through 239 removed outlier: 4.714A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.543A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 365 removed outlier: 4.722A pdb=" N SER B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 372 through 388 Processing helix chain 'B' and resid 517 through 539 removed outlier: 3.932A pdb=" N ARG B 539 " --> pdb=" O LYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 573 removed outlier: 3.912A pdb=" N VAL B 546 " --> pdb=" O ASP B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 124 through 143 Processing helix chain 'C' and resid 150 through 179 Processing helix chain 'C' and resid 180 through 185 removed outlier: 6.167A pdb=" N ARG C 183 " --> pdb=" O CYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 196 through 210 removed outlier: 3.658A pdb=" N VAL C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 227 through 239 removed outlier: 4.708A pdb=" N ILE C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 235 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 257 Processing helix chain 'C' and resid 257 through 284 Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.542A pdb=" N ALA C 306 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 365 removed outlier: 4.721A pdb=" N SER C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 372 through 388 Processing helix chain 'C' and resid 517 through 539 removed outlier: 3.942A pdb=" N ARG C 539 " --> pdb=" O LYS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 573 removed outlier: 3.890A pdb=" N VAL C 546 " --> pdb=" O ASP C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 124 through 143 Processing helix chain 'D' and resid 150 through 179 Processing helix chain 'D' and resid 180 through 185 removed outlier: 6.210A pdb=" N ARG D 183 " --> pdb=" O CYS D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 196 through 210 removed outlier: 3.657A pdb=" N VAL D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 227 through 239 removed outlier: 4.709A pdb=" N ILE D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 235 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 257 Processing helix chain 'D' and resid 257 through 284 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.542A pdb=" N ALA D 306 " --> pdb=" O THR D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 365 removed outlier: 4.718A pdb=" N SER D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 371 through 388 removed outlier: 4.716A pdb=" N ALA D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 537 Processing helix chain 'D' and resid 542 through 573 removed outlier: 3.902A pdb=" N VAL D 546 " --> pdb=" O ASP D 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.739A pdb=" N LEU E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.515A pdb=" N LEU E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.694A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 39 removed outlier: 3.867A pdb=" N LEU F 33 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG F 38 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.572A pdb=" N LEU F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.517A pdb=" N VAL F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.856A pdb=" N LEU G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 39 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 removed outlier: 3.582A pdb=" N LEU G 49 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 76 through 80 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.514A pdb=" N VAL G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 111 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.663A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.615A pdb=" N LEU H 49 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 76 through 81 removed outlier: 4.170A pdb=" N ASP H 81 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.682A pdb=" N VAL H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 145 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1066 hydrogen bonds defined for protein. 3138 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: 2.06 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2488 1.31 - 1.44: 4088 1.44 - 1.56: 8523 1.56 - 1.69: 1 1.69 - 1.81: 136 Bond restraints: 15236 Sorted by residual: bond pdb=" C TRP B 265 " pdb=" O TRP B 265 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.26e-02 6.30e+03 1.33e+01 bond pdb=" C TRP C 265 " pdb=" O TRP C 265 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.26e-02 6.30e+03 1.27e+01 bond pdb=" C TRP A 265 " pdb=" O TRP A 265 " ideal model delta sigma weight residual 1.236 1.192 0.045 1.26e-02 6.30e+03 1.25e+01 bond pdb=" C TRP D 265 " pdb=" O TRP D 265 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" CA TRP B 265 " pdb=" C TRP B 265 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.35e-02 5.49e+03 9.81e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19880 1.64 - 3.28: 564 3.28 - 4.91: 105 4.91 - 6.55: 25 6.55 - 8.19: 10 Bond angle restraints: 20584 Sorted by residual: angle pdb=" CA TYR D 541 " pdb=" CB TYR D 541 " pdb=" CG TYR D 541 " ideal model delta sigma weight residual 113.90 122.09 -8.19 1.80e+00 3.09e-01 2.07e+01 angle pdb=" CA TYR A 541 " pdb=" CB TYR A 541 " pdb=" CG TYR A 541 " ideal model delta sigma weight residual 113.90 122.02 -8.12 1.80e+00 3.09e-01 2.03e+01 angle pdb=" CA TYR B 541 " pdb=" CB TYR B 541 " pdb=" CG TYR B 541 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR C 541 " pdb=" CB TYR C 541 " pdb=" CG TYR C 541 " ideal model delta sigma weight residual 113.90 121.92 -8.02 1.80e+00 3.09e-01 1.99e+01 angle pdb=" N GLN D 526 " pdb=" CA GLN D 526 " pdb=" C GLN D 526 " ideal model delta sigma weight residual 111.28 106.57 4.71 1.09e+00 8.42e-01 1.86e+01 ... (remaining 20579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 7920 16.23 - 32.47: 833 32.47 - 48.70: 231 48.70 - 64.93: 22 64.93 - 81.16: 6 Dihedral angle restraints: 9012 sinusoidal: 3580 harmonic: 5432 Sorted by residual: dihedral pdb=" CA LEU A 226 " pdb=" C LEU A 226 " pdb=" N ARG A 227 " pdb=" CA ARG A 227 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU B 226 " pdb=" C LEU B 226 " pdb=" N ARG B 227 " pdb=" CA ARG B 227 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU D 226 " pdb=" C LEU D 226 " pdb=" N ARG D 227 " pdb=" CA ARG D 227 " ideal model delta harmonic sigma weight residual 180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 9009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1403 0.031 - 0.063: 653 0.063 - 0.094: 200 0.094 - 0.125: 66 0.125 - 0.157: 10 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA GLN F 144 " pdb=" N GLN F 144 " pdb=" C GLN F 144 " pdb=" CB GLN F 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA GLN G 144 " pdb=" N GLN G 144 " pdb=" C GLN G 144 " pdb=" CB GLN G 144 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CB ILE E 64 " pdb=" CA ILE E 64 " pdb=" CG1 ILE E 64 " pdb=" CG2 ILE E 64 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2329 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 541 " 0.023 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 541 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 541 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 541 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 541 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 541 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 541 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 541 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO E 67 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 541 " -0.019 2.00e-02 2.50e+03 1.36e-02 3.68e+00 pdb=" CG TYR D 541 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 541 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 541 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 541 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 541 " -0.004 2.00e-02 2.50e+03 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 3533 2.78 - 3.37: 17928 3.37 - 3.96: 28758 3.96 - 4.55: 40068 4.55 - 5.14: 57635 Nonbonded interactions: 147922 Sorted by model distance: nonbonded pdb=" O GLU H 46 " pdb=" NE2 GLN H 50 " model vdw 2.190 3.120 nonbonded pdb=" OD2 ASP F 134 " pdb=" NE2 GLN F 136 " model vdw 2.249 3.120 nonbonded pdb=" OD2 ASP G 134 " pdb=" NE2 GLN G 136 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP H 134 " pdb=" NE2 GLN H 136 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP E 134 " pdb=" NE2 GLN E 136 " model vdw 2.267 3.120 ... (remaining 147917 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' and resid 103 through 573) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.240 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 : 0.005 0.046 15236 Z= 0.265 Angle : 0.723 8.188 20584 Z= 0.426 Chirality : 0.041 0.157 2332 Planarity : 0.004 0.048 2588 Dihedral : 14.279 81.164 5508 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.17), residues: 1840 helix: -1.53 (0.12), residues: 1392 sheet: None (None), residues: 0 loop : -2.32 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 567 TYR 0.034 0.002 TYR B 541 PHE 0.011 0.002 PHE G 142 TRP 0.009 0.001 TRP A 308 HIS 0.007 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.27 (15236) covalent geometry : angle 0.72264 / 0.43 (20584) hydrogen bonds : bond 0.12378 / 8.13 ( 1066) hydrogen bonds : angle 5.80299 / 4.13 ( 3138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 0.395 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: A 117 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6639 (tmt-80) REVERT: A 192 LYS cc_start: 0.8863 (mptt) cc_final: 0.8561 (mmtt) REVERT: A 377 GLU cc_start: 0.7738 (tp30) cc_final: 0.7207 (tp30) REVERT: A 542 ASP cc_start: 0.8556 (t0) cc_final: 0.8271 (t70) REVERT: B 117 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6649 (tmt-80) REVERT: B 192 LYS cc_start: 0.8851 (mptt) cc_final: 0.8592 (mmtt) REVERT: B 377 GLU cc_start: 0.8014 (tp30) cc_final: 0.6919 (tp30) REVERT: B 530 TYR cc_start: 0.8975 (m-10) cc_final: 0.8733 (m-80) REVERT: B 542 ASP cc_start: 0.8584 (t0) cc_final: 0.8271 (t70) REVERT: C 117 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6648 (tmt-80) REVERT: C 192 LYS cc_start: 0.8865 (mptt) cc_final: 0.8562 (mmtt) REVERT: C 377 GLU cc_start: 0.7967 (tp30) cc_final: 0.7423 (tp30) REVERT: C 530 TYR cc_start: 0.8976 (m-10) cc_final: 0.8726 (m-80) REVERT: C 542 ASP cc_start: 0.8539 (t0) cc_final: 0.8290 (t70) REVERT: D 117 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6650 (tmt-80) REVERT: D 192 LYS cc_start: 0.8866 (mptt) cc_final: 0.8558 (mmtt) REVERT: D 542 ASP cc_start: 0.8536 (t0) cc_final: 0.8253 (t70) REVERT: E 37 MET cc_start: 0.8108 (mtt) cc_final: 0.7421 (mtt) REVERT: E 116 LYS cc_start: 0.8430 (mttt) cc_final: 0.8179 (mppt) REVERT: E 138 ASN cc_start: 0.3276 (t0) cc_final: 0.2220 (t0) REVERT: E 146 MET cc_start: 0.5916 (tpp) cc_final: 0.5274 (mmm) REVERT: F 13 PHE cc_start: 0.6779 (m-10) cc_final: 0.5973 (m-10) REVERT: F 146 MET cc_start: 0.5121 (tpt) cc_final: 0.4889 (ttt) REVERT: G 13 PHE cc_start: 0.6678 (m-10) cc_final: 0.5828 (m-10) REVERT: G 37 MET cc_start: 0.8322 (mtt) cc_final: 0.8058 (mtt) REVERT: G 146 MET cc_start: 0.5139 (tpt) cc_final: 0.4829 (ttt) REVERT: H 116 LYS cc_start: 0.8528 (mttt) cc_final: 0.8261 (mppt) REVERT: H 146 MET cc_start: 0.6276 (tpp) cc_final: 0.5716 (mmm) outliers start: 1 outliers final: 4 residues processed: 410 average time/residue: 0.4788 time to fit residues: 216.8444 Evaluate side-chains 340 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 336 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 563 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS B 257 HIS C 257 HIS D 257 HIS E 98 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN H 98 ASN H 112 ASN H 144 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.223148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137102 restraints weight = 21299.714| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.92 r_work: 0.3271 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15236 Z= 0.161 Angle : 0.648 9.207 20584 Z= 0.336 Chirality : 0.039 0.180 2332 Planarity : 0.004 0.042 2588 Dihedral : 5.296 90.563 2053 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.96 % Allowed : 14.48 % Favored : 81.56 % 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: -0.53 (0.19), residues: 1840 helix: 0.19 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -2.05 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 75 TYR 0.033 0.002 TYR A 530 PHE 0.026 0.002 PHE H 69 TRP 0.009 0.001 TRP B 308 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15236) covalent geometry : angle 0.64828 / 0.34 (20584) hydrogen bonds : bond 0.04372 / 2.94 ( 1066) hydrogen bonds : angle 4.50457 / 3.17 ( 3138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 0.421 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 117 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7174 (tmt-80) REVERT: A 365 GLN cc_start: 0.5966 (tm-30) cc_final: 0.5764 (tm-30) REVERT: A 380 GLN cc_start: 0.7815 (mt0) cc_final: 0.7591 (mt0) REVERT: A 542 ASP cc_start: 0.8606 (t0) cc_final: 0.8221 (t0) REVERT: B 117 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7139 (tmt-80) REVERT: B 365 GLN cc_start: 0.6054 (tt0) cc_final: 0.5788 (tm-30) REVERT: B 377 GLU cc_start: 0.8290 (tp30) cc_final: 0.7744 (tp30) REVERT: B 542 ASP cc_start: 0.8767 (t0) cc_final: 0.8389 (t70) REVERT: B 562 LYS cc_start: 0.8961 (tppt) cc_final: 0.8716 (tptp) REVERT: C 117 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7164 (tmt-80) REVERT: C 365 GLN cc_start: 0.6007 (tm-30) cc_final: 0.5805 (tm-30) REVERT: C 380 GLN cc_start: 0.7874 (mt0) cc_final: 0.7651 (mt0) REVERT: C 542 ASP cc_start: 0.8558 (t0) cc_final: 0.8250 (t0) REVERT: D 117 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7158 (tmt-80) REVERT: D 365 GLN cc_start: 0.6013 (tm-30) cc_final: 0.5807 (tm-30) REVERT: D 542 ASP cc_start: 0.8576 (t0) cc_final: 0.8176 (t0) REVERT: E 72 MET cc_start: 0.8591 (mmm) cc_final: 0.8323 (mpp) REVERT: E 77 MET cc_start: 0.8095 (mmp) cc_final: 0.7796 (mmp) REVERT: E 101 ILE cc_start: 0.8975 (mm) cc_final: 0.8744 (mp) REVERT: F 77 MET cc_start: 0.8203 (mmp) cc_final: 0.7825 (mmp) REVERT: G 139 TYR cc_start: 0.7885 (p90) cc_final: 0.7509 (p90) REVERT: H 146 MET cc_start: 0.6427 (tpp) cc_final: 0.5641 (mmm) outliers start: 61 outliers final: 22 residues processed: 378 average time/residue: 0.4429 time to fit residues: 185.7236 Evaluate side-chains 344 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 563 TYR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 380 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 112 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 112 ASN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 112 ASN H 144 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.223438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129173 restraints weight = 21506.871| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.52 r_work: 0.3249 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15236 Z= 0.158 Angle : 0.663 9.163 20584 Z= 0.338 Chirality : 0.039 0.198 2332 Planarity : 0.004 0.033 2588 Dihedral : 4.546 23.471 2050 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.22 % Allowed : 18.05 % Favored : 77.73 % 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: 0.61 (0.20), residues: 1840 helix: 0.97 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.37 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 75 TYR 0.030 0.001 TYR B 530 PHE 0.009 0.001 PHE H 69 TRP 0.009 0.001 TRP A 308 HIS 0.002 0.000 HIS G 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15236) covalent geometry : angle 0.66322 / 0.34 (20584) hydrogen bonds : bond 0.04333 / 2.91 ( 1066) hydrogen bonds : angle 4.28747 / 3.00 ( 3138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 0.555 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 362 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: A 542 ASP cc_start: 0.8558 (t0) cc_final: 0.8246 (t70) REVERT: B 117 ARG cc_start: 0.7370 (ttp80) cc_final: 0.7080 (tmt-80) REVERT: B 362 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: B 380 GLN cc_start: 0.7830 (mt0) cc_final: 0.7471 (mt0) REVERT: B 542 ASP cc_start: 0.8448 (t0) cc_final: 0.8235 (t70) REVERT: C 117 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7124 (tmt-80) REVERT: C 362 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: C 380 GLN cc_start: 0.7741 (mt0) cc_final: 0.7411 (mt0) REVERT: C 542 ASP cc_start: 0.8430 (t0) cc_final: 0.8134 (t0) REVERT: D 117 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7130 (tmt-80) REVERT: D 362 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: D 542 ASP cc_start: 0.8553 (t0) cc_final: 0.8254 (t0) REVERT: E 72 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7785 (mmm) REVERT: F 77 MET cc_start: 0.8165 (mmp) cc_final: 0.7704 (mmp) REVERT: F 79 ASP cc_start: 0.8326 (m-30) cc_final: 0.7760 (t70) REVERT: F 90 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: F 98 ASN cc_start: 0.6843 (p0) cc_final: 0.6223 (p0) REVERT: F 117 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (mt) REVERT: G 73 MET cc_start: 0.8280 (ttp) cc_final: 0.8068 (ttp) REVERT: G 75 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7264 (tmm160) REVERT: G 76 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8299 (tptt) REVERT: G 79 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7750 (t70) REVERT: G 90 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: G 98 ASN cc_start: 0.6815 (p0) cc_final: 0.6397 (p0) outliers start: 65 outliers final: 20 residues processed: 347 average time/residue: 0.4092 time to fit residues: 159.6379 Evaluate side-chains 322 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 144 GLN Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 145 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 112 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.222789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140137 restraints weight = 21434.207| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.50 r_work: 0.3296 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15236 Z= 0.140 Angle : 0.657 8.970 20584 Z= 0.331 Chirality : 0.037 0.153 2332 Planarity : 0.003 0.032 2588 Dihedral : 4.284 25.187 2046 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.55 % Allowed : 20.13 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1840 helix: 1.33 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -1.07 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 75 TYR 0.042 0.001 TYR B 530 PHE 0.016 0.001 PHE G 13 TRP 0.021 0.001 TRP B 176 HIS 0.002 0.000 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15236) covalent geometry : angle 0.65734 / 0.33 (20584) hydrogen bonds : bond 0.04074 / 2.72 ( 1066) hydrogen bonds : angle 4.18941 / 2.94 ( 3138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 320 time to evaluate : 0.404 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: A 240 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7915 (tpt) REVERT: A 362 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: A 542 ASP cc_start: 0.8450 (t0) cc_final: 0.8158 (t70) REVERT: B 240 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8010 (tpt) REVERT: B 362 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 542 ASP cc_start: 0.8441 (t0) cc_final: 0.8161 (t70) REVERT: C 117 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7109 (tmt-80) REVERT: C 240 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7929 (tpt) REVERT: C 362 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: C 542 ASP cc_start: 0.8229 (t0) cc_final: 0.8001 (t0) REVERT: D 240 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7931 (tpt) REVERT: D 362 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: D 526 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8493 (tp-100) REVERT: D 542 ASP cc_start: 0.8367 (t0) cc_final: 0.8049 (t0) REVERT: E 49 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8374 (mt) REVERT: E 52 MET cc_start: 0.7504 (ttp) cc_final: 0.6908 (ttm) REVERT: E 77 MET cc_start: 0.7833 (mmp) cc_final: 0.7504 (mmp) REVERT: E 98 ASN cc_start: 0.4459 (p0) cc_final: 0.3951 (p0) REVERT: E 109 VAL cc_start: 0.8533 (m) cc_final: 0.8235 (p) REVERT: F 73 MET cc_start: 0.8414 (ttp) cc_final: 0.7696 (ttp) REVERT: F 76 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8064 (tptt) REVERT: F 79 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7498 (t70) REVERT: F 98 ASN cc_start: 0.6505 (p0) cc_final: 0.5934 (p0) REVERT: G 79 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7518 (t70) REVERT: G 87 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8125 (mtm110) REVERT: G 90 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: G 98 ASN cc_start: 0.6596 (p0) cc_final: 0.5948 (p0) REVERT: G 139 TYR cc_start: 0.7952 (p90) cc_final: 0.7597 (p90) REVERT: G 146 MET cc_start: 0.6374 (ptm) cc_final: 0.6159 (ptt) REVERT: H 49 LEU cc_start: 0.8741 (mt) cc_final: 0.8452 (mt) REVERT: H 52 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7013 (ttm) REVERT: H 138 ASN cc_start: 0.6117 (m-40) cc_final: 0.5613 (m-40) REVERT: H 139 TYR cc_start: 0.7925 (p90) cc_final: 0.7665 (p90) outliers start: 70 outliers final: 23 residues processed: 349 average time/residue: 0.3917 time to fit residues: 153.5306 Evaluate side-chains 329 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 240 MET Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 GLN C 380 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.218119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132353 restraints weight = 21443.683| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.55 r_work: 0.3189 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 15236 Z= 0.313 Angle : 0.780 9.809 20584 Z= 0.398 Chirality : 0.045 0.193 2332 Planarity : 0.004 0.043 2588 Dihedral : 4.671 23.850 2046 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.94 % Allowed : 21.95 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1840 helix: 0.92 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 87 TYR 0.016 0.002 TYR C 550 PHE 0.017 0.002 PHE A 193 TRP 0.017 0.002 TRP B 176 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.31 (15236) covalent geometry : angle 0.77952 / 0.40 (20584) hydrogen bonds : bond 0.05321 / 3.59 ( 1066) hydrogen bonds : angle 4.57558 / 3.22 ( 3138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 288 time to evaluate : 0.485 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: A 361 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: A 362 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: A 542 ASP cc_start: 0.8706 (t0) cc_final: 0.8417 (t70) REVERT: B 361 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: B 362 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: B 380 GLN cc_start: 0.7935 (mt0) cc_final: 0.7625 (mt0) REVERT: B 542 ASP cc_start: 0.8601 (t0) cc_final: 0.8355 (t70) REVERT: C 362 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: C 542 ASP cc_start: 0.8542 (t0) cc_final: 0.8296 (t70) REVERT: D 361 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: D 362 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 526 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8502 (tp-100) REVERT: D 542 ASP cc_start: 0.8596 (t0) cc_final: 0.8301 (t70) REVERT: E 49 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8539 (mt) REVERT: E 52 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7217 (ttm) REVERT: E 141 GLU cc_start: 0.8456 (pm20) cc_final: 0.8159 (pm20) REVERT: F 13 PHE cc_start: 0.5878 (m-10) cc_final: 0.5639 (m-80) REVERT: F 75 ARG cc_start: 0.7838 (tmm160) cc_final: 0.7623 (tmm160) REVERT: F 90 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: F 98 ASN cc_start: 0.6585 (p0) cc_final: 0.6065 (p0) REVERT: F 139 TYR cc_start: 0.8015 (p90) cc_final: 0.7579 (p90) REVERT: G 13 PHE cc_start: 0.5891 (m-10) cc_final: 0.5671 (m-80) REVERT: G 69 PHE cc_start: 0.8383 (t80) cc_final: 0.8098 (t80) REVERT: G 73 MET cc_start: 0.8386 (ttp) cc_final: 0.7225 (ttm) REVERT: G 75 ARG cc_start: 0.7344 (tmm160) cc_final: 0.6940 (tmm160) REVERT: G 76 LYS cc_start: 0.8613 (mmmt) cc_final: 0.7848 (tptt) REVERT: G 87 ARG cc_start: 0.8378 (mtm110) cc_final: 0.8126 (mtm110) REVERT: G 98 ASN cc_start: 0.6669 (p0) cc_final: 0.6126 (p0) REVERT: H 52 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7175 (ttm) REVERT: H 72 MET cc_start: 0.7762 (ptp) cc_final: 0.7308 (tpt) REVERT: H 138 ASN cc_start: 0.6646 (m-40) cc_final: 0.5991 (m-40) REVERT: H 141 GLU cc_start: 0.8445 (pm20) cc_final: 0.8186 (pm20) REVERT: H 144 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8051 (mp10) outliers start: 76 outliers final: 31 residues processed: 323 average time/residue: 0.4161 time to fit residues: 150.8145 Evaluate side-chains 322 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain C residue 563 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 134 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 157 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 42 GLN E 98 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.221286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135450 restraints weight = 21310.752| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.77 r_work: 0.3300 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15236 Z= 0.152 Angle : 0.697 13.164 20584 Z= 0.346 Chirality : 0.039 0.233 2332 Planarity : 0.004 0.038 2588 Dihedral : 4.307 23.818 2046 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.16 % Allowed : 23.77 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1840 helix: 1.41 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 75 TYR 0.023 0.001 TYR B 563 PHE 0.013 0.001 PHE A 527 TRP 0.010 0.001 TRP B 308 HIS 0.001 0.000 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15236) covalent geometry : angle 0.69671 / 0.35 (20584) hydrogen bonds : bond 0.04158 / 2.78 ( 1066) hydrogen bonds : angle 4.25050 / 2.99 ( 3138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.490 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: A 361 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7592 (pp20) REVERT: A 362 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: A 542 ASP cc_start: 0.8301 (t0) cc_final: 0.8041 (t0) REVERT: B 143 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 361 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7580 (pp20) REVERT: B 362 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: B 380 GLN cc_start: 0.7954 (mt0) cc_final: 0.7728 (mt0) REVERT: B 542 ASP cc_start: 0.8380 (t0) cc_final: 0.8070 (t0) REVERT: C 143 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8526 (p) REVERT: C 362 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: C 380 GLN cc_start: 0.7839 (mt0) cc_final: 0.7626 (mt0) REVERT: C 530 TYR cc_start: 0.8651 (m-80) cc_final: 0.8379 (m-80) REVERT: C 542 ASP cc_start: 0.8268 (t0) cc_final: 0.8054 (t0) REVERT: D 143 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8514 (p) REVERT: D 361 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7540 (pp20) REVERT: D 362 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: D 377 GLU cc_start: 0.8571 (tp30) cc_final: 0.8307 (mm-30) REVERT: D 526 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8448 (tp-100) REVERT: E 42 GLN cc_start: 0.6211 (OUTLIER) cc_final: 0.5991 (pp30) REVERT: E 52 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7097 (ttm) REVERT: E 77 MET cc_start: 0.7662 (mmp) cc_final: 0.7378 (mmp) REVERT: F 13 PHE cc_start: 0.5836 (m-10) cc_final: 0.5626 (m-80) REVERT: F 79 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7338 (t70) REVERT: F 98 ASN cc_start: 0.6581 (p0) cc_final: 0.6143 (p0) REVERT: G 13 PHE cc_start: 0.5862 (m-10) cc_final: 0.5642 (m-80) REVERT: G 20 PHE cc_start: 0.7295 (m-80) cc_final: 0.7017 (t80) REVERT: G 37 MET cc_start: 0.8456 (mmt) cc_final: 0.8100 (mmt) REVERT: G 79 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7356 (t70) REVERT: G 90 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: G 98 ASN cc_start: 0.6457 (p0) cc_final: 0.6041 (p0) REVERT: G 111 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7518 (p) REVERT: G 145 MET cc_start: 0.6933 (pp-130) cc_final: 0.6579 (tmm) REVERT: H 52 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7049 (ttm) REVERT: H 73 MET cc_start: 0.8123 (ttp) cc_final: 0.7775 (ttp) REVERT: H 108 HIS cc_start: 0.8697 (t-90) cc_final: 0.8079 (t-90) REVERT: H 109 VAL cc_start: 0.8801 (p) cc_final: 0.8389 (p) REVERT: H 113 LEU cc_start: 0.8307 (tp) cc_final: 0.7999 (tp) REVERT: H 115 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7255 (tm-30) REVERT: H 138 ASN cc_start: 0.6489 (m-40) cc_final: 0.5905 (m-40) REVERT: H 139 TYR cc_start: 0.8115 (p90) cc_final: 0.7714 (p90) REVERT: H 146 MET cc_start: 0.6421 (ttm) cc_final: 0.5517 (mmm) outliers start: 64 outliers final: 21 residues processed: 321 average time/residue: 0.4117 time to fit residues: 148.6526 Evaluate side-chains 308 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.0040 chunk 164 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 144 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.222209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137889 restraints weight = 21225.321| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 4.01 r_work: 0.3279 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15236 Z= 0.139 Angle : 0.717 14.158 20584 Z= 0.352 Chirality : 0.039 0.192 2332 Planarity : 0.004 0.064 2588 Dihedral : 4.213 22.736 2046 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.16 % Allowed : 24.48 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1840 helix: 1.59 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 75 TYR 0.014 0.001 TYR C 563 PHE 0.016 0.001 PHE B 534 TRP 0.024 0.001 TRP A 176 HIS 0.002 0.000 HIS F 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15236) covalent geometry : angle 0.71737 / 0.35 (20584) hydrogen bonds : bond 0.03973 / 2.66 ( 1066) hydrogen bonds : angle 4.17121 / 2.94 ( 3138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 0.552 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: A 362 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: A 526 GLN cc_start: 0.8972 (tt0) cc_final: 0.8081 (tm-30) REVERT: A 562 LYS cc_start: 0.8978 (tppt) cc_final: 0.8651 (tptt) REVERT: B 362 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: B 542 ASP cc_start: 0.8225 (t0) cc_final: 0.7981 (t0) REVERT: B 562 LYS cc_start: 0.8947 (tppt) cc_final: 0.8692 (tptt) REVERT: C 362 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: C 530 TYR cc_start: 0.8636 (m-80) cc_final: 0.8335 (m-80) REVERT: D 362 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: D 526 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: E 52 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7066 (ttm) REVERT: E 64 ILE cc_start: 0.8908 (pt) cc_final: 0.8539 (mp) REVERT: E 111 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7354 (p) REVERT: F 66 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: F 73 MET cc_start: 0.8130 (ttp) cc_final: 0.7455 (ttp) REVERT: F 76 LYS cc_start: 0.8581 (mmmt) cc_final: 0.7952 (tptt) REVERT: F 79 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7443 (t70) REVERT: F 98 ASN cc_start: 0.6425 (p0) cc_final: 0.6054 (p0) REVERT: F 145 MET cc_start: 0.6768 (pp-130) cc_final: 0.6151 (tmm) REVERT: G 13 PHE cc_start: 0.5826 (m-10) cc_final: 0.5564 (m-80) REVERT: G 37 MET cc_start: 0.8633 (mmt) cc_final: 0.8399 (mmt) REVERT: G 66 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7678 (t80) REVERT: G 76 LYS cc_start: 0.8555 (mmmt) cc_final: 0.7945 (tptt) REVERT: G 79 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7420 (t70) REVERT: G 90 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: G 98 ASN cc_start: 0.6066 (p0) cc_final: 0.5715 (p0) REVERT: G 111 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7476 (p) REVERT: G 145 MET cc_start: 0.6998 (pp-130) cc_final: 0.6642 (tmm) REVERT: H 13 PHE cc_start: 0.5214 (m-10) cc_final: 0.5008 (m-80) REVERT: H 52 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6922 (ttm) REVERT: H 108 HIS cc_start: 0.8781 (t-90) cc_final: 0.8114 (t-90) REVERT: H 109 VAL cc_start: 0.8844 (p) cc_final: 0.8576 (p) REVERT: H 113 LEU cc_start: 0.8352 (tp) cc_final: 0.8099 (tp) REVERT: H 115 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7350 (tm-30) REVERT: H 138 ASN cc_start: 0.6137 (m-40) cc_final: 0.5679 (m-40) REVERT: H 139 TYR cc_start: 0.8193 (p90) cc_final: 0.7755 (p90) REVERT: H 146 MET cc_start: 0.6393 (ttm) cc_final: 0.5548 (mmm) outliers start: 64 outliers final: 14 residues processed: 307 average time/residue: 0.3958 time to fit residues: 136.9388 Evaluate side-chains 289 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 181 CYS Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 144 GLN Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.220759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.137274 restraints weight = 21377.782| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 4.12 r_work: 0.3274 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15236 Z= 0.173 Angle : 0.740 13.928 20584 Z= 0.366 Chirality : 0.039 0.163 2332 Planarity : 0.004 0.062 2588 Dihedral : 4.264 20.161 2044 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.12 % Allowed : 26.62 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1840 helix: 1.47 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 75 TYR 0.035 0.001 TYR B 530 PHE 0.032 0.002 PHE E 13 TRP 0.027 0.002 TRP C 176 HIS 0.001 0.000 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15236) covalent geometry : angle 0.74029 / 0.37 (20584) hydrogen bonds : bond 0.04302 / 2.89 ( 1066) hydrogen bonds : angle 4.24178 / 3.00 ( 3138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.096 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: A 192 LYS cc_start: 0.8764 (mptt) cc_final: 0.8555 (mmtm) REVERT: A 362 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: A 526 GLN cc_start: 0.9007 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 362 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: B 562 LYS cc_start: 0.8984 (tppt) cc_final: 0.8744 (tptt) REVERT: C 362 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: C 530 TYR cc_start: 0.8582 (m-80) cc_final: 0.8374 (m-80) REVERT: C 542 ASP cc_start: 0.8287 (t0) cc_final: 0.8056 (t0) REVERT: D 192 LYS cc_start: 0.8760 (mptt) cc_final: 0.8548 (mmtm) REVERT: D 362 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: D 526 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: E 52 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7087 (ttm) REVERT: E 111 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7367 (p) REVERT: F 13 PHE cc_start: 0.6249 (m-80) cc_final: 0.5968 (m-80) REVERT: F 66 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: F 79 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7273 (t70) REVERT: F 145 MET cc_start: 0.6545 (pp-130) cc_final: 0.5940 (tmm) REVERT: G 37 MET cc_start: 0.8663 (mmt) cc_final: 0.8431 (mmt) REVERT: G 73 MET cc_start: 0.8368 (ttm) cc_final: 0.7952 (ttt) REVERT: G 76 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7927 (tptt) REVERT: G 79 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7337 (t70) REVERT: G 98 ASN cc_start: 0.6020 (p0) cc_final: 0.5710 (p0) REVERT: G 111 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7565 (p) REVERT: G 145 MET cc_start: 0.6878 (pp-130) cc_final: 0.6497 (tmm) REVERT: H 13 PHE cc_start: 0.5394 (m-10) cc_final: 0.5186 (m-80) REVERT: H 52 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6908 (ttm) REVERT: H 108 HIS cc_start: 0.8793 (t-90) cc_final: 0.8031 (t-90) REVERT: H 109 VAL cc_start: 0.8923 (p) cc_final: 0.8582 (p) REVERT: H 113 LEU cc_start: 0.8437 (tp) cc_final: 0.8204 (tp) REVERT: H 115 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7348 (tm-30) REVERT: H 138 ASN cc_start: 0.6188 (m-40) cc_final: 0.5886 (m-40) REVERT: H 139 TYR cc_start: 0.8235 (p90) cc_final: 0.7840 (p90) REVERT: H 146 MET cc_start: 0.6393 (ttm) cc_final: 0.5556 (mmm) outliers start: 48 outliers final: 16 residues processed: 277 average time/residue: 0.4145 time to fit residues: 129.0485 Evaluate side-chains 283 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN H 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.218102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132743 restraints weight = 21443.578| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.83 r_work: 0.3224 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15236 Z= 0.267 Angle : 0.809 12.097 20584 Z= 0.405 Chirality : 0.044 0.185 2332 Planarity : 0.005 0.064 2588 Dihedral : 4.542 21.976 2044 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.31 % Allowed : 26.95 % Favored : 69.74 % 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: 0.93 (0.20), residues: 1840 helix: 1.15 (0.14), residues: 1404 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 87 TYR 0.029 0.002 TYR B 530 PHE 0.026 0.002 PHE E 13 TRP 0.026 0.002 TRP C 176 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (15236) covalent geometry : angle 0.80851 / 0.40 (20584) hydrogen bonds : bond 0.04997 / 3.37 ( 1066) hydrogen bonds : angle 4.53311 / 3.22 ( 3138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 0.400 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: A 149 GLU cc_start: 0.8272 (tt0) cc_final: 0.7938 (tt0) REVERT: A 192 LYS cc_start: 0.8731 (mptt) cc_final: 0.8516 (mmtm) REVERT: A 362 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: B 149 GLU cc_start: 0.8260 (tt0) cc_final: 0.7915 (tt0) REVERT: B 192 LYS cc_start: 0.8722 (mptt) cc_final: 0.8514 (mmtm) REVERT: B 362 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: C 149 GLU cc_start: 0.8257 (tt0) cc_final: 0.7925 (tt0) REVERT: C 192 LYS cc_start: 0.8699 (mptt) cc_final: 0.8492 (mmtm) REVERT: C 362 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: C 530 TYR cc_start: 0.8850 (m-80) cc_final: 0.8635 (m-80) REVERT: C 542 ASP cc_start: 0.8495 (t0) cc_final: 0.8263 (t0) REVERT: D 149 GLU cc_start: 0.8267 (tt0) cc_final: 0.7929 (tt0) REVERT: D 192 LYS cc_start: 0.8781 (mptt) cc_final: 0.8552 (mmtm) REVERT: D 362 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: D 526 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: E 49 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8439 (mt) REVERT: E 52 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7202 (ttm) REVERT: E 111 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7500 (p) REVERT: E 125 MET cc_start: 0.7283 (mmt) cc_final: 0.7079 (mmp) REVERT: F 66 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: F 145 MET cc_start: 0.6522 (pp-130) cc_final: 0.6072 (tmm) REVERT: G 13 PHE cc_start: 0.5893 (m-80) cc_final: 0.5460 (m-80) REVERT: G 66 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: G 98 ASN cc_start: 0.6290 (OUTLIER) cc_final: 0.6045 (p0) REVERT: G 111 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7637 (p) REVERT: G 145 MET cc_start: 0.7033 (pp-130) cc_final: 0.6712 (tmm) REVERT: H 37 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8232 (pmm) REVERT: H 49 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8323 (mt) REVERT: H 52 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.7012 (ttm) REVERT: H 108 HIS cc_start: 0.8768 (t-90) cc_final: 0.8033 (t-90) REVERT: H 109 VAL cc_start: 0.8899 (p) cc_final: 0.8557 (p) REVERT: H 113 LEU cc_start: 0.8456 (tp) cc_final: 0.8236 (tp) REVERT: H 115 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 138 ASN cc_start: 0.6712 (m-40) cc_final: 0.5915 (m-40) REVERT: H 139 TYR cc_start: 0.8365 (p90) cc_final: 0.7972 (p90) REVERT: H 146 MET cc_start: 0.6572 (ttm) cc_final: 0.5812 (mmm) outliers start: 51 outliers final: 18 residues processed: 282 average time/residue: 0.4231 time to fit residues: 133.8729 Evaluate side-chains 284 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 181 CYS Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 142 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 380 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.221937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137799 restraints weight = 21482.416| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.94 r_work: 0.3285 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15236 Z= 0.149 Angle : 0.778 12.780 20584 Z= 0.381 Chirality : 0.039 0.165 2332 Planarity : 0.004 0.055 2588 Dihedral : 4.321 21.885 2044 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.40 % Allowed : 27.86 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1840 helix: 1.51 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 75 TYR 0.024 0.001 TYR B 563 PHE 0.026 0.001 PHE D 193 TRP 0.022 0.001 TRP C 176 HIS 0.001 0.000 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15236) covalent geometry : angle 0.77847 / 0.38 (20584) hydrogen bonds : bond 0.04033 / 2.67 ( 1066) hydrogen bonds : angle 4.28155 / 3.02 ( 3138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 0.453 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: A 192 LYS cc_start: 0.8672 (mptt) cc_final: 0.8462 (mmtm) REVERT: A 362 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 562 LYS cc_start: 0.9050 (tppt) cc_final: 0.8581 (tptt) REVERT: B 192 LYS cc_start: 0.8697 (mptt) cc_final: 0.8492 (mmtm) REVERT: B 362 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: B 562 LYS cc_start: 0.9064 (tppt) cc_final: 0.8675 (tptt) REVERT: C 362 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: C 530 TYR cc_start: 0.8683 (m-80) cc_final: 0.8400 (m-80) REVERT: C 542 ASP cc_start: 0.8185 (t0) cc_final: 0.7972 (t0) REVERT: D 192 LYS cc_start: 0.8687 (mptt) cc_final: 0.8484 (mmtm) REVERT: D 362 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: D 526 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: E 49 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8344 (mt) REVERT: E 77 MET cc_start: 0.7556 (mmp) cc_final: 0.7277 (mmt) REVERT: E 111 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7386 (p) REVERT: F 73 MET cc_start: 0.7731 (ttt) cc_final: 0.7473 (ttt) REVERT: F 76 LYS cc_start: 0.8604 (mmmt) cc_final: 0.7910 (tptp) REVERT: F 79 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7352 (t70) REVERT: F 90 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: F 145 MET cc_start: 0.6282 (pp-130) cc_final: 0.5869 (tmm) REVERT: G 37 MET cc_start: 0.8201 (mmt) cc_final: 0.7983 (mmt) REVERT: G 73 MET cc_start: 0.8112 (ttt) cc_final: 0.7869 (ttt) REVERT: G 76 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7830 (tptp) REVERT: G 79 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7306 (t70) REVERT: G 90 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: G 145 MET cc_start: 0.6749 (pp-130) cc_final: 0.6404 (tmm) REVERT: G 146 MET cc_start: 0.6513 (ptm) cc_final: 0.6212 (ptt) REVERT: H 37 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (pmm) REVERT: H 52 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7028 (ttm) REVERT: H 108 HIS cc_start: 0.8782 (t-90) cc_final: 0.8012 (t-90) REVERT: H 109 VAL cc_start: 0.8821 (p) cc_final: 0.8339 (p) REVERT: H 113 LEU cc_start: 0.8513 (tp) cc_final: 0.8280 (tp) REVERT: H 115 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7364 (tm-30) REVERT: H 116 LYS cc_start: 0.8468 (mppt) cc_final: 0.8069 (mmtp) REVERT: H 138 ASN cc_start: 0.6443 (m-40) cc_final: 0.6106 (m-40) REVERT: H 139 TYR cc_start: 0.8247 (p90) cc_final: 0.7710 (p90) outliers start: 37 outliers final: 11 residues processed: 259 average time/residue: 0.3910 time to fit residues: 113.8311 Evaluate side-chains 268 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 362 GLN Chi-restraints excluded: chain D residue 526 GLN Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 90 PHE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 0.0670 chunk 25 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.221697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136881 restraints weight = 21241.009| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.92 r_work: 0.3279 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15236 Z= 0.155 Angle : 0.787 12.836 20584 Z= 0.384 Chirality : 0.040 0.436 2332 Planarity : 0.004 0.058 2588 Dihedral : 4.223 21.614 2044 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.01 % Allowed : 28.51 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1840 helix: 1.48 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 75 TYR 0.024 0.001 TYR B 563 PHE 0.025 0.001 PHE B 193 TRP 0.023 0.001 TRP D 176 HIS 0.001 0.000 HIS D 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15236) covalent geometry : angle 0.78682 / 0.38 (20584) hydrogen bonds : bond 0.04119 / 2.73 ( 1066) hydrogen bonds : angle 4.29004 / 3.03 ( 3138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6673.74 seconds wall clock time: 113 minutes 46.36 seconds (6826.36 seconds total)