Starting phenix.real_space_refine on Tue Jul 29 02:25:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0n_18798/07_2025/8r0n_18798.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 7219 2.51 5 N 1717 2.21 5 O 1945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10921 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2115 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2106 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2123 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2112 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2106 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'LMT': 2, 'RET': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'LMT': 2, 'RET': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'LFA': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 12.58, per 1000 atoms: 1.15 Number of scatterers: 10921 At special positions: 0 Unit cell: (93.632, 92.378, 83.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1945 8.00 N 1717 7.00 C 7219 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 81.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.902A pdb=" N ALA A 11 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 43 through 46 removed outlier: 3.903A pdb=" N VAL A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 77 removed outlier: 4.128A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.855A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.947A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.579A pdb=" N THR A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.714A pdb=" N ALA A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 263 removed outlier: 4.594A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.886A pdb=" N ALA B 11 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.907A pdb=" N VAL B 46 " --> pdb=" O ARG B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.131A pdb=" N VAL B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 97 through 117 removed outlier: 3.859A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.950A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 149 removed outlier: 3.584A pdb=" N THR B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 207 Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.712A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 263 removed outlier: 4.582A pdb=" N CYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.911A pdb=" N ALA C 11 " --> pdb=" O PRO C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 43 through 46 removed outlier: 3.910A pdb=" N VAL C 46 " --> pdb=" O ARG C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 77 removed outlier: 4.128A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.867A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.947A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 149 removed outlier: 3.579A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 207 Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.710A pdb=" N ALA C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 263 removed outlier: 4.587A pdb=" N CYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.898A pdb=" N ALA D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.907A pdb=" N VAL D 46 " --> pdb=" O ARG D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 50 through 77 removed outlier: 4.124A pdb=" N VAL D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 97 through 117 removed outlier: 3.870A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.950A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 149 removed outlier: 3.600A pdb=" N THR D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 207 Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.712A pdb=" N ALA D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 263 removed outlier: 4.291A pdb=" N CYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.901A pdb=" N ALA E 11 " --> pdb=" O PRO E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.916A pdb=" N VAL E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 50 through 77 removed outlier: 4.131A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 97 through 117 removed outlier: 3.852A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.950A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 149 removed outlier: 3.596A pdb=" N THR E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 207 Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.716A pdb=" N ALA E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 263 removed outlier: 4.531A pdb=" N CYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.463A pdb=" N ILE A 271 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.462A pdb=" N ILE B 271 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.453A pdb=" N ILE C 271 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.461A pdb=" N ILE D 271 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 272 removed outlier: 6.460A pdb=" N ILE E 271 " --> pdb=" O GLN E 278 " (cutoff:3.500A) 862 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2862 1.34 - 1.47: 3312 1.47 - 1.60: 4853 1.60 - 1.73: 0 1.73 - 1.86: 70 Bond restraints: 11097 Sorted by residual: bond pdb=" C10 RET C 403 " pdb=" C11 RET C 403 " ideal model delta sigma weight residual 1.433 1.353 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C10 RET B 401 " pdb=" C11 RET B 401 " ideal model delta sigma weight residual 1.433 1.353 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C10 RET D 402 " pdb=" C11 RET D 402 " ideal model delta sigma weight residual 1.433 1.354 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C10 RET E 402 " pdb=" C11 RET E 402 " ideal model delta sigma weight residual 1.433 1.354 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C10 RET A 403 " pdb=" C11 RET A 403 " ideal model delta sigma weight residual 1.433 1.354 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 11092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12979 1.89 - 3.79: 1986 3.79 - 5.68: 177 5.68 - 7.57: 20 7.57 - 9.47: 7 Bond angle restraints: 15169 Sorted by residual: angle pdb=" N GLU D 269 " pdb=" CA GLU D 269 " pdb=" CB GLU D 269 " ideal model delta sigma weight residual 111.20 103.37 7.83 1.62e+00 3.81e-01 2.33e+01 angle pdb=" N GLN D 278 " pdb=" CA GLN D 278 " pdb=" C GLN D 278 " ideal model delta sigma weight residual 113.41 107.87 5.54 1.22e+00 6.72e-01 2.06e+01 angle pdb=" N LEU B 66 " pdb=" CA LEU B 66 " pdb=" CB LEU B 66 " ideal model delta sigma weight residual 110.16 116.77 -6.61 1.48e+00 4.57e-01 2.00e+01 angle pdb=" N GLN E 278 " pdb=" CA GLN E 278 " pdb=" C GLN E 278 " ideal model delta sigma weight residual 113.41 107.98 5.43 1.22e+00 6.72e-01 1.98e+01 angle pdb=" N ILE C 165 " pdb=" CA ILE C 165 " pdb=" C ILE C 165 " ideal model delta sigma weight residual 110.53 106.34 4.19 9.40e-01 1.13e+00 1.98e+01 ... (remaining 15164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.15: 6315 24.15 - 48.29: 199 48.29 - 72.44: 19 72.44 - 96.58: 10 96.58 - 120.73: 4 Dihedral angle restraints: 6547 sinusoidal: 2492 harmonic: 4055 Sorted by residual: dihedral pdb=" C LEU B 66 " pdb=" N LEU B 66 " pdb=" CA LEU B 66 " pdb=" CB LEU B 66 " ideal model delta harmonic sigma weight residual -122.60 -136.95 14.35 0 2.50e+00 1.60e-01 3.29e+01 dihedral pdb=" N LEU B 66 " pdb=" C LEU B 66 " pdb=" CA LEU B 66 " pdb=" CB LEU B 66 " ideal model delta harmonic sigma weight residual 122.80 136.16 -13.36 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" CD ARG A 261 " pdb=" NE ARG A 261 " pdb=" CZ ARG A 261 " pdb=" NH1 ARG A 261 " ideal model delta sinusoidal sigma weight residual 0.00 -42.39 42.39 1 1.00e+01 1.00e-02 2.51e+01 ... (remaining 6544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1656 0.108 - 0.215: 242 0.215 - 0.323: 6 0.323 - 0.430: 0 0.430 - 0.538: 1 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA LEU B 66 " pdb=" N LEU B 66 " pdb=" C LEU B 66 " pdb=" CB LEU B 66 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CA THR D 226 " pdb=" N THR D 226 " pdb=" C THR D 226 " pdb=" CB THR D 226 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA PHE C 24 " pdb=" N PHE C 24 " pdb=" C PHE C 24 " pdb=" CB PHE C 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1902 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET D 402 " -0.062 2.00e-02 2.50e+03 6.71e-02 5.63e+01 pdb=" C13 RET D 402 " 0.022 2.00e-02 2.50e+03 pdb=" C14 RET D 402 " 0.108 2.00e-02 2.50e+03 pdb=" C15 RET D 402 " -0.080 2.00e-02 2.50e+03 pdb=" C20 RET D 402 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 261 " 0.618 9.50e-02 1.11e+02 2.78e-01 5.28e+01 pdb=" NE ARG A 261 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 261 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 261 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 261 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 38 " -0.597 9.50e-02 1.11e+02 2.68e-01 4.85e+01 pdb=" NE ARG D 38 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG D 38 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG D 38 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 38 " -0.006 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 21 2.38 - 3.01: 6758 3.01 - 3.64: 17232 3.64 - 4.27: 29004 4.27 - 4.90: 46569 Nonbonded interactions: 99584 Sorted by model distance: nonbonded pdb=" OG SER C 77 " pdb=" OE2 GLU C 91 " model vdw 1.754 3.040 nonbonded pdb=" O SER C 121 " pdb=" OG SER C 124 " model vdw 2.125 3.040 nonbonded pdb=" O SER E 121 " pdb=" OG SER E 124 " model vdw 2.145 3.040 nonbonded pdb=" O SER B 121 " pdb=" OG SER B 124 " model vdw 2.146 3.040 nonbonded pdb=" O SER A 121 " pdb=" OG SER A 124 " model vdw 2.149 3.040 ... (remaining 99579 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 3 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 126 or (resid 127 and (name N or na \ me CA or name C or name O or name CB )) or resid 128 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 190 \ or (resid 191 through 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 285)) selection = (chain 'B' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB )) or resid 183 through 285)) selection = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 79 or (resid 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 90 or (resid 91 through 92 and (name N or name \ CA or name C or name O or name CB )) or resid 93 through 126 or (resid 127 and \ (name N or name CA or name C or name O or name CB )) or resid 128 through 153 or \ (resid 154 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or resid 155 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB )) or resid 183 through 285)) selection = (chain 'D' and (resid 3 through 178 or (resid 179 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 180 through 190 or (re \ sid 191 through 194 and (name N or name CA or name C or name O or name CB )) or \ resid 195 through 285)) selection = (chain 'E' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB )) or resid 183 through 285)) } 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: 19.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.012 0.080 11102 Z= 0.766 Angle : 1.367 9.468 15169 Z= 0.929 Chirality : 0.069 0.538 1905 Planarity : 0.018 0.278 1773 Dihedral : 12.924 120.727 3937 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.87 % Allowed : 2.15 % Favored : 95.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.18), residues: 1405 helix: -1.61 (0.13), residues: 1020 sheet: None (None), residues: 0 loop : -2.32 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.012 TRP B 272 HIS 0.014 0.004 HIS E 18 PHE 0.047 0.011 PHE C 220 TYR 0.046 0.010 TYR A 50 ARG 0.042 0.006 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.16832 ( 862) hydrogen bonds : angle 7.36271 ( 2526) covalent geometry : bond 0.01184 (11097) covalent geometry : angle 1.36741 (15169) Misc. bond : bond 0.01956 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.049 Fit side-chains REVERT: A 4 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.7027 (tpt) REVERT: B 4 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6618 (tpp) REVERT: B 120 LEU cc_start: 0.7297 (mp) cc_final: 0.7094 (mt) REVERT: B 250 ARG cc_start: 0.8697 (ttm170) cc_final: 0.8471 (ttp80) REVERT: C 4 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: D 40 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.7576 (m-90) REVERT: D 179 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7337 (mtp85) REVERT: D 186 PRO cc_start: 0.8950 (Cg_exo) cc_final: 0.8732 (Cg_endo) REVERT: D 226 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8612 (m) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.9790 time to fit residues: 159.3861 Evaluate side-chains 113 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 40 TRP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 237 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098812 restraints weight = 11642.332| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.45 r_work: 0.3009 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11102 Z= 0.129 Angle : 0.504 7.118 15169 Z= 0.260 Chirality : 0.039 0.126 1905 Planarity : 0.004 0.030 1773 Dihedral : 10.582 97.028 1881 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.81 % Allowed : 5.62 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1405 helix: 2.01 (0.15), residues: 1000 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.006 0.001 HIS D 18 PHE 0.009 0.001 PHE C 24 TYR 0.016 0.002 TYR E 68 ARG 0.005 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 862) hydrogen bonds : angle 3.76969 ( 2526) covalent geometry : bond 0.00283 (11097) covalent geometry : angle 0.50397 (15169) Misc. bond : bond 0.00030 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.089 Fit side-chains REVERT: A 4 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6505 (tpt) REVERT: A 183 HIS cc_start: 0.7292 (t70) cc_final: 0.7076 (t70) REVERT: B 4 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6325 (tpt) REVERT: B 250 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7834 (ttp80) REVERT: C 4 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6457 (tpt) REVERT: C 22 PHE cc_start: 0.6533 (t80) cc_final: 0.6042 (t80) REVERT: C 66 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7239 (mp) REVERT: C 183 HIS cc_start: 0.7323 (t70) cc_final: 0.7117 (t70) REVERT: D 179 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6752 (mtp85) REVERT: D 226 THR cc_start: 0.8363 (t) cc_final: 0.7949 (p) outliers start: 30 outliers final: 13 residues processed: 152 average time/residue: 1.3714 time to fit residues: 225.9532 Evaluate side-chains 142 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 217 GLN B 81 HIS B 217 GLN C 217 GLN D 81 HIS D 217 GLN E 217 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101283 restraints weight = 12229.134| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.24 r_work: 0.3099 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11102 Z= 0.182 Angle : 0.511 5.866 15169 Z= 0.268 Chirality : 0.041 0.133 1905 Planarity : 0.005 0.038 1773 Dihedral : 8.159 59.943 1877 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.37 % Allowed : 8.05 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.22), residues: 1405 helix: 2.54 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.73 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.005 0.001 HIS B 18 PHE 0.011 0.002 PHE B 137 TYR 0.016 0.002 TYR E 68 ARG 0.004 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 862) hydrogen bonds : angle 3.65803 ( 2526) covalent geometry : bond 0.00442 (11097) covalent geometry : angle 0.51058 (15169) Misc. bond : bond 0.00058 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.177 Fit side-chains REVERT: A 4 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6555 (tpt) REVERT: A 66 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7503 (mp) REVERT: B 4 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6429 (tpt) REVERT: B 250 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7868 (ttp80) REVERT: C 4 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6499 (tpt) REVERT: C 66 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7461 (mp) REVERT: D 4 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6448 (tpt) REVERT: D 226 THR cc_start: 0.8578 (t) cc_final: 0.8154 (p) outliers start: 36 outliers final: 19 residues processed: 157 average time/residue: 1.0360 time to fit residues: 178.1567 Evaluate side-chains 152 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 217 GLN C 217 GLN D 217 GLN E 81 HIS E 217 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102120 restraints weight = 12049.105| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.24 r_work: 0.3112 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11102 Z= 0.161 Angle : 0.480 5.671 15169 Z= 0.253 Chirality : 0.040 0.128 1905 Planarity : 0.004 0.039 1773 Dihedral : 7.738 59.900 1875 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.28 % Allowed : 9.27 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.22), residues: 1405 helix: 2.78 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.004 0.001 HIS C 18 PHE 0.010 0.001 PHE C 137 TYR 0.014 0.002 TYR C 68 ARG 0.003 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 862) hydrogen bonds : angle 3.57112 ( 2526) covalent geometry : bond 0.00390 (11097) covalent geometry : angle 0.48016 (15169) Misc. bond : bond 0.00050 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.108 Fit side-chains REVERT: A 4 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6493 (tpt) REVERT: A 66 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7506 (mp) REVERT: B 4 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6528 (tpt) REVERT: B 6 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8088 (t) REVERT: B 250 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7922 (ttp80) REVERT: C 4 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6429 (tpt) REVERT: C 6 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (t) REVERT: C 66 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7480 (mp) REVERT: D 226 THR cc_start: 0.8601 (t) cc_final: 0.8190 (p) outliers start: 35 outliers final: 17 residues processed: 151 average time/residue: 1.0614 time to fit residues: 175.1806 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103078 restraints weight = 11937.115| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.23 r_work: 0.3124 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11102 Z= 0.140 Angle : 0.461 5.617 15169 Z= 0.242 Chirality : 0.040 0.136 1905 Planarity : 0.004 0.040 1773 Dihedral : 7.518 59.987 1873 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.00 % Allowed : 10.49 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.22), residues: 1405 helix: 2.93 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.004 0.001 HIS C 18 PHE 0.010 0.001 PHE C 137 TYR 0.013 0.002 TYR C 68 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 862) hydrogen bonds : angle 3.50441 ( 2526) covalent geometry : bond 0.00331 (11097) covalent geometry : angle 0.46073 (15169) Misc. bond : bond 0.00037 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.025 Fit side-chains REVERT: B 4 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6540 (tpt) REVERT: B 6 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8108 (t) REVERT: B 250 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7917 (ttp80) REVERT: C 4 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6389 (tpt) REVERT: C 6 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8011 (t) REVERT: C 66 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7478 (mp) REVERT: D 4 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6358 (tpt) REVERT: D 226 THR cc_start: 0.8587 (t) cc_final: 0.8192 (p) outliers start: 32 outliers final: 13 residues processed: 156 average time/residue: 1.0438 time to fit residues: 178.2108 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 116 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 111 optimal weight: 0.0270 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105221 restraints weight = 11949.304| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.25 r_work: 0.3150 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11102 Z= 0.110 Angle : 0.431 5.610 15169 Z= 0.226 Chirality : 0.038 0.139 1905 Planarity : 0.004 0.039 1773 Dihedral : 7.013 56.838 1864 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.87 % Allowed : 11.89 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1405 helix: 3.14 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.004 0.001 HIS D 18 PHE 0.008 0.001 PHE C 137 TYR 0.011 0.001 TYR D 68 ARG 0.001 0.000 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 862) hydrogen bonds : angle 3.41110 ( 2526) covalent geometry : bond 0.00244 (11097) covalent geometry : angle 0.43093 (15169) Misc. bond : bond 0.00018 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.066 Fit side-chains REVERT: B 4 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6435 (tpt) REVERT: B 6 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8109 (t) REVERT: B 250 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7916 (ttp80) REVERT: D 4 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6208 (tpt) REVERT: D 226 THR cc_start: 0.8540 (t) cc_final: 0.8188 (p) outliers start: 20 outliers final: 8 residues processed: 154 average time/residue: 1.1050 time to fit residues: 185.7110 Evaluate side-chains 144 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103232 restraints weight = 12188.285| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.26 r_work: 0.3121 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11102 Z= 0.145 Angle : 0.470 7.640 15169 Z= 0.244 Chirality : 0.040 0.149 1905 Planarity : 0.004 0.039 1773 Dihedral : 7.057 59.850 1859 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.43 % Allowed : 11.89 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1405 helix: 3.05 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.004 0.001 HIS D 18 PHE 0.010 0.001 PHE C 137 TYR 0.013 0.002 TYR C 68 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 862) hydrogen bonds : angle 3.46623 ( 2526) covalent geometry : bond 0.00344 (11097) covalent geometry : angle 0.46977 (15169) Misc. bond : bond 0.00040 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 1.066 Fit side-chains REVERT: B 6 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8119 (t) REVERT: B 250 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7922 (ttp80) REVERT: C 5 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.6590 (tt) REVERT: C 6 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7919 (t) REVERT: D 4 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6275 (tpt) REVERT: D 226 THR cc_start: 0.8575 (t) cc_final: 0.8199 (p) REVERT: E 66 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7551 (mp) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 1.0759 time to fit residues: 176.4192 Evaluate side-chains 152 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103475 restraints weight = 12006.372| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.25 r_work: 0.3127 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11102 Z= 0.141 Angle : 0.464 7.372 15169 Z= 0.242 Chirality : 0.040 0.147 1905 Planarity : 0.004 0.039 1773 Dihedral : 6.960 59.216 1856 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.62 % Allowed : 11.61 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1405 helix: 3.04 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.40 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 225 HIS 0.004 0.001 HIS C 18 PHE 0.010 0.001 PHE C 137 TYR 0.013 0.002 TYR D 68 ARG 0.002 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 862) hydrogen bonds : angle 3.46607 ( 2526) covalent geometry : bond 0.00333 (11097) covalent geometry : angle 0.46448 (15169) Misc. bond : bond 0.00039 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.155 Fit side-chains REVERT: B 4 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6445 (tpt) REVERT: B 6 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8115 (t) REVERT: B 250 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7919 (ttp80) REVERT: C 5 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.6542 (tt) REVERT: C 6 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7947 (t) REVERT: D 226 THR cc_start: 0.8574 (t) cc_final: 0.8196 (p) REVERT: E 66 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7566 (mp) outliers start: 28 outliers final: 19 residues processed: 153 average time/residue: 1.0002 time to fit residues: 168.0124 Evaluate side-chains 153 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 0.0070 chunk 135 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104823 restraints weight = 11936.023| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.25 r_work: 0.3144 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11102 Z= 0.119 Angle : 0.443 6.700 15169 Z= 0.231 Chirality : 0.039 0.139 1905 Planarity : 0.004 0.039 1773 Dihedral : 6.778 56.738 1856 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.25 % Allowed : 12.27 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.22), residues: 1405 helix: 3.14 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.004 0.001 HIS D 18 PHE 0.009 0.001 PHE C 137 TYR 0.012 0.001 TYR D 68 ARG 0.001 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 862) hydrogen bonds : angle 3.41697 ( 2526) covalent geometry : bond 0.00270 (11097) covalent geometry : angle 0.44292 (15169) Misc. bond : bond 0.00025 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.052 Fit side-chains REVERT: A 4 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6424 (tpt) REVERT: B 4 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6412 (tpt) REVERT: B 6 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 250 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7911 (ttp80) REVERT: C 5 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.6552 (tt) REVERT: C 66 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7573 (mp) REVERT: D 226 THR cc_start: 0.8549 (t) cc_final: 0.8192 (p) REVERT: E 66 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7568 (mp) outliers start: 24 outliers final: 13 residues processed: 151 average time/residue: 0.9995 time to fit residues: 165.7851 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104743 restraints weight = 11970.741| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.25 r_work: 0.3144 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11102 Z= 0.120 Angle : 0.444 6.836 15169 Z= 0.232 Chirality : 0.039 0.140 1905 Planarity : 0.004 0.039 1773 Dihedral : 6.749 57.319 1856 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.97 % Allowed : 12.64 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.22), residues: 1405 helix: 3.12 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.31 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 162 HIS 0.004 0.001 HIS D 18 PHE 0.009 0.001 PHE C 137 TYR 0.011 0.001 TYR A 68 ARG 0.001 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 862) hydrogen bonds : angle 3.40291 ( 2526) covalent geometry : bond 0.00274 (11097) covalent geometry : angle 0.44428 (15169) Misc. bond : bond 0.00025 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.161 Fit side-chains REVERT: A 4 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6436 (tpt) REVERT: B 4 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6418 (tpt) REVERT: B 6 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8108 (t) REVERT: B 250 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7904 (ttp80) REVERT: C 5 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.6567 (tt) REVERT: D 226 THR cc_start: 0.8553 (t) cc_final: 0.8198 (p) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 1.0286 time to fit residues: 163.7221 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 275 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 111 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 217 GLN D 217 GLN E 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104674 restraints weight = 11937.370| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.25 r_work: 0.3143 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11102 Z= 0.123 Angle : 0.447 6.779 15169 Z= 0.234 Chirality : 0.039 0.137 1905 Planarity : 0.004 0.039 1773 Dihedral : 6.754 57.533 1856 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.87 % Allowed : 12.92 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.22), residues: 1405 helix: 3.11 (0.15), residues: 1020 sheet: None (None), residues: 0 loop : -1.30 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.004 0.001 HIS D 18 PHE 0.009 0.001 PHE C 137 TYR 0.011 0.002 TYR A 68 ARG 0.001 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 862) hydrogen bonds : angle 3.40718 ( 2526) covalent geometry : bond 0.00282 (11097) covalent geometry : angle 0.44748 (15169) Misc. bond : bond 0.00026 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7634.59 seconds wall clock time: 132 minutes 48.36 seconds (7968.36 seconds total)