Starting phenix.real_space_refine on Sun Mar 17 08:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/03_2024/7tj2_25915.pdb" } resolution = 3.2 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= 0.005 sd= 0.107 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 P 62 5.49 5 S 57 5.16 5 C 10718 2.51 5 N 2788 2.21 5 O 3458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17083 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2733 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 257} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 29} Chain: "H" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 651 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna3p': 30} Time building chain proxies: 9.53, per 1000 atoms: 0.56 Number of scatterers: 17083 At special positions: 0 Unit cell: (119.087, 121.835, 134.659, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 62 15.00 O 3458 8.00 N 2788 7.00 C 10718 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 - 3.50 Amino acid : False - 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: 6.31 Conformation dependent library (CDL) restraints added in 2.6 seconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3746 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 42 sheets defined 25.2% alpha, 23.6% beta 30 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.750A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 77 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 227 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.752A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 299 through 309 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 77 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.776A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 155 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.825A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 343 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.237A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 155 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.237A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 316 through 323 Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 155 " --> pdb=" O TYR C 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323 removed outlier: 5.239A pdb=" N LYS C 335 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.659A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 155 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 320 through 323 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.659A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 155 " --> pdb=" O TYR E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'E' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 316 through 323 Processing sheet with id=AD9, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.658A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 155 " --> pdb=" O TYR F 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.238A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AE5, first strand: chain 'F' and resid 264 through 267 removed outlier: 5.080A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323 636 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5248 1.34 - 1.45: 2661 1.45 - 1.57: 9439 1.57 - 1.69: 122 1.69 - 1.81: 85 Bond restraints: 17555 Sorted by residual: bond pdb=" C ALA E 118 " pdb=" N PRO E 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" C ALA B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.10e+00 bond pdb=" C ALA D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.339 1.375 -0.035 3.40e-02 8.65e+02 1.08e+00 bond pdb=" C ALA A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 bond pdb=" C ALA C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 ... (remaining 17550 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 769 107.13 - 113.84: 10097 113.84 - 120.56: 6499 120.56 - 127.28: 6483 127.28 - 133.99: 260 Bond angle restraints: 24108 Sorted by residual: angle pdb=" C THR F 49 " pdb=" N LEU F 50 " pdb=" CA LEU F 50 " ideal model delta sigma weight residual 121.48 124.92 -3.44 2.04e+00 2.40e-01 2.84e+00 angle pdb=" C GLN F 310 " pdb=" N ASP F 311 " pdb=" CA ASP F 311 " ideal model delta sigma weight residual 121.54 124.60 -3.06 1.91e+00 2.74e-01 2.56e+00 angle pdb=" C GLN C 310 " pdb=" N ASP C 311 " pdb=" CA ASP C 311 " ideal model delta sigma weight residual 121.54 124.39 -2.85 1.91e+00 2.74e-01 2.22e+00 angle pdb=" C2' G G 8 " pdb=" C1' G G 8 " pdb=" N9 G G 8 " ideal model delta sigma weight residual 112.00 114.13 -2.13 1.50e+00 4.44e-01 2.02e+00 angle pdb=" C GLN E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 124.20 -2.66 1.91e+00 2.74e-01 1.94e+00 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10137 18.04 - 36.09: 276 36.09 - 54.13: 69 54.13 - 72.18: 71 72.18 - 90.22: 16 Dihedral angle restraints: 10569 sinusoidal: 4762 harmonic: 5807 Sorted by residual: dihedral pdb=" CA CYS F 334 " pdb=" C CYS F 334 " pdb=" N LYS F 335 " pdb=" CA LYS F 335 " ideal model delta harmonic sigma weight residual 180.00 164.35 15.65 0 5.00e+00 4.00e-02 9.79e+00 dihedral pdb=" O5' U H 31 " pdb=" C5' U H 31 " pdb=" C4' U H 31 " pdb=" C3' U H 31 " ideal model delta sinusoidal sigma weight residual 55.00 113.85 -58.85 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN B 310 " pdb=" CA GLN B 310 " pdb=" CB GLN B 310 " pdb=" CG GLN B 310 " ideal model delta sinusoidal sigma weight residual 180.00 -121.71 -58.29 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 10566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1703 0.026 - 0.052: 629 0.052 - 0.078: 254 0.078 - 0.103: 124 0.103 - 0.129: 114 Chirality restraints: 2824 Sorted by residual: chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE F 80 " pdb=" N ILE F 80 " pdb=" C ILE F 80 " pdb=" CB ILE F 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE E 80 " pdb=" N ILE E 80 " pdb=" C ILE E 80 " pdb=" CB ILE E 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 2821 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 334 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C CYS B 334 " 0.020 2.00e-02 2.50e+03 pdb=" O CYS B 334 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 335 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO D 51 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO B 51 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.015 5.00e-02 4.00e+02 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1067 2.74 - 3.28: 15965 3.28 - 3.82: 28253 3.82 - 4.36: 34467 4.36 - 4.90: 58658 Nonbonded interactions: 138410 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY F 77 " pdb=" OG1 THR F 121 " model vdw 2.196 2.440 ... (remaining 138405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = (chain 'C' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C \ or name O or name CB )) or resid 2 through 345)) selection = chain 'E' selection = chain 'F' } 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: 1.740 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: 4.700 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 50.410 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.002 0.036 17555 Z= 0.110 Angle : 0.370 5.591 24108 Z= 0.191 Chirality : 0.041 0.129 2824 Planarity : 0.003 0.027 2873 Dihedral : 11.301 90.221 6823 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.64 % Allowed : 2.37 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1990 helix: 1.26 (0.24), residues: 492 sheet: 0.55 (0.33), residues: 316 loop : -0.48 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 87 HIS 0.001 0.000 HIS F 338 PHE 0.006 0.001 PHE A 342 TYR 0.006 0.001 TYR A 226 ARG 0.002 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 389 time to evaluate : 1.940 Fit side-chains revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8597 (mttt) cc_final: 0.8350 (mmtm) REVERT: A 267 GLU cc_start: 0.7933 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 47 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8212 (mmtp) REVERT: B 105 MET cc_start: 0.8115 (mmm) cc_final: 0.7367 (mpp) REVERT: B 107 ASP cc_start: 0.7999 (m-30) cc_final: 0.7724 (m-30) REVERT: B 343 TYR cc_start: 0.8254 (p90) cc_final: 0.7953 (p90) REVERT: C 40 ASP cc_start: 0.8115 (m-30) cc_final: 0.7514 (m-30) REVERT: C 150 LYS cc_start: 0.8070 (mttt) cc_final: 0.7650 (mmtm) REVERT: C 153 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7777 (mm-40) REVERT: C 166 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (m) REVERT: D 19 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6789 (mm-40) REVERT: D 105 MET cc_start: 0.7242 (mmm) cc_final: 0.6932 (mpp) REVERT: D 107 ASP cc_start: 0.7880 (m-30) cc_final: 0.6839 (p0) REVERT: E 245 GLN cc_start: 0.5823 (mt0) cc_final: 0.5057 (pp30) REVERT: E 252 LEU cc_start: 0.7821 (tp) cc_final: 0.7546 (tp) REVERT: F 107 ASP cc_start: 0.8291 (m-30) cc_final: 0.8024 (m-30) REVERT: F 168 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (pp) REVERT: F 305 GLU cc_start: 0.7592 (tt0) cc_final: 0.7359 (mt-10) REVERT: F 308 LYS cc_start: 0.7097 (mttt) cc_final: 0.6497 (ptmm) outliers start: 29 outliers final: 10 residues processed: 409 average time/residue: 0.2888 time to fit residues: 174.4156 Evaluate side-chains 232 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 310 GLN B 29 ASN B 30 ASN B 83 ASN B 140 ASN B 176 GLN C 278 ASN D 30 ASN D 83 ASN E 29 ASN E 30 ASN F 29 ASN F 30 ASN F 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17555 Z= 0.418 Angle : 0.587 9.828 24108 Z= 0.309 Chirality : 0.048 0.356 2824 Planarity : 0.004 0.040 2873 Dihedral : 12.796 86.978 3070 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.56 % Allowed : 9.10 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1990 helix: 0.65 (0.24), residues: 509 sheet: 0.44 (0.30), residues: 348 loop : -0.56 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 59 HIS 0.005 0.001 HIS E 96 PHE 0.019 0.002 PHE E 269 TYR 0.014 0.002 TYR E 343 ARG 0.006 0.001 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 212 time to evaluate : 1.886 Fit side-chains REVERT: A 47 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7690 (mmtm) REVERT: A 105 MET cc_start: 0.8518 (mmm) cc_final: 0.8227 (tpt) REVERT: A 110 LYS cc_start: 0.8790 (mttt) cc_final: 0.8333 (mmtm) REVERT: A 139 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7476 (mtp180) REVERT: A 265 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 297 ASP cc_start: 0.8737 (t0) cc_final: 0.8494 (t0) REVERT: B 105 MET cc_start: 0.8359 (mmm) cc_final: 0.7389 (mpp) REVERT: B 166 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8293 (m) REVERT: B 343 TYR cc_start: 0.8367 (p90) cc_final: 0.7924 (p90) REVERT: C 40 ASP cc_start: 0.8076 (m-30) cc_final: 0.7806 (m-30) REVERT: C 150 LYS cc_start: 0.8113 (mttt) cc_final: 0.7733 (mmtm) REVERT: C 166 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7841 (m) REVERT: C 246 LEU cc_start: 0.8201 (mp) cc_final: 0.8000 (mt) REVERT: D 105 MET cc_start: 0.7223 (mmm) cc_final: 0.7012 (mpp) REVERT: E 245 GLN cc_start: 0.5721 (mt0) cc_final: 0.5045 (pp30) REVERT: F 305 GLU cc_start: 0.7662 (tt0) cc_final: 0.7338 (mt-10) REVERT: F 308 LYS cc_start: 0.7150 (mttt) cc_final: 0.6513 (ptmm) outliers start: 63 outliers final: 37 residues processed: 262 average time/residue: 0.2955 time to fit residues: 115.1944 Evaluate side-chains 222 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17555 Z= 0.249 Angle : 0.491 8.760 24108 Z= 0.260 Chirality : 0.044 0.245 2824 Planarity : 0.004 0.041 2873 Dihedral : 12.611 90.520 3067 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.94 % Allowed : 11.42 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1990 helix: 0.84 (0.24), residues: 504 sheet: 0.48 (0.29), residues: 348 loop : -0.62 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.003 0.001 HIS E 96 PHE 0.015 0.001 PHE F 303 TYR 0.012 0.001 TYR E 180 ARG 0.003 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 1.722 Fit side-chains REVERT: A 47 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7982 (mmtp) REVERT: A 105 MET cc_start: 0.8464 (mmm) cc_final: 0.8176 (tpt) REVERT: A 110 LYS cc_start: 0.8839 (mttt) cc_final: 0.8383 (mmtm) REVERT: A 139 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7191 (mtp180) REVERT: A 297 ASP cc_start: 0.8651 (t0) cc_final: 0.8392 (t0) REVERT: B 47 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8099 (mmtp) REVERT: B 105 MET cc_start: 0.8279 (mmm) cc_final: 0.7468 (mpp) REVERT: B 343 TYR cc_start: 0.8273 (p90) cc_final: 0.7900 (p90) REVERT: C 40 ASP cc_start: 0.8082 (m-30) cc_final: 0.7805 (m-30) REVERT: C 150 LYS cc_start: 0.8143 (mttt) cc_final: 0.7711 (mmtm) REVERT: C 166 VAL cc_start: 0.8121 (p) cc_final: 0.7880 (m) REVERT: D 107 ASP cc_start: 0.8222 (m-30) cc_final: 0.7900 (m-30) REVERT: D 272 MET cc_start: 0.7342 (ttp) cc_final: 0.7135 (ttt) REVERT: E 245 GLN cc_start: 0.5695 (mt0) cc_final: 0.5048 (pp30) REVERT: F 194 TYR cc_start: 0.7904 (m-80) cc_final: 0.7646 (m-80) REVERT: F 219 MET cc_start: 0.5755 (mtm) cc_final: 0.5513 (mtm) REVERT: F 272 MET cc_start: 0.8091 (ttp) cc_final: 0.7851 (ttt) REVERT: F 308 LYS cc_start: 0.7198 (mttt) cc_final: 0.6580 (ptmm) outliers start: 52 outliers final: 38 residues processed: 238 average time/residue: 0.2911 time to fit residues: 104.0571 Evaluate side-chains 213 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0470 chunk 138 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN D 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17555 Z= 0.214 Angle : 0.466 8.472 24108 Z= 0.247 Chirality : 0.044 0.205 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.560 93.131 3064 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.90 % Allowed : 11.81 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1990 helix: 1.01 (0.24), residues: 499 sheet: 0.43 (0.29), residues: 348 loop : -0.70 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.003 0.001 HIS A 338 PHE 0.019 0.001 PHE F 214 TYR 0.016 0.001 TYR E 180 ARG 0.003 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 192 time to evaluate : 1.717 Fit side-chains REVERT: A 22 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: A 45 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: A 47 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8029 (mmtp) REVERT: A 110 LYS cc_start: 0.8834 (mttt) cc_final: 0.8310 (mmtm) REVERT: A 114 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 139 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7260 (mtp180) REVERT: A 265 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: A 297 ASP cc_start: 0.8552 (t0) cc_final: 0.8247 (t0) REVERT: B 105 MET cc_start: 0.8267 (mmm) cc_final: 0.7482 (mpp) REVERT: B 343 TYR cc_start: 0.8272 (p90) cc_final: 0.8008 (p90) REVERT: C 40 ASP cc_start: 0.8064 (m-30) cc_final: 0.7784 (m-30) REVERT: C 150 LYS cc_start: 0.8175 (mttt) cc_final: 0.7782 (mmtm) REVERT: C 166 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7874 (m) REVERT: C 246 LEU cc_start: 0.8182 (mp) cc_final: 0.7917 (mt) REVERT: D 153 GLN cc_start: 0.4654 (tt0) cc_final: 0.4448 (pt0) REVERT: D 272 MET cc_start: 0.7421 (ttp) cc_final: 0.7206 (ttt) REVERT: E 245 GLN cc_start: 0.5804 (mt0) cc_final: 0.5105 (pp30) REVERT: F 255 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6247 (mm) REVERT: F 308 LYS cc_start: 0.7161 (mttt) cc_final: 0.6489 (ptmm) outliers start: 69 outliers final: 45 residues processed: 245 average time/residue: 0.2789 time to fit residues: 103.7832 Evaluate side-chains 227 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17555 Z= 0.209 Angle : 0.470 9.110 24108 Z= 0.247 Chirality : 0.043 0.176 2824 Planarity : 0.003 0.046 2873 Dihedral : 12.544 94.517 3064 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.34 % Allowed : 13.17 % Favored : 83.49 % 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: -0.14 (0.19), residues: 1990 helix: 1.04 (0.24), residues: 499 sheet: 0.40 (0.28), residues: 348 loop : -0.76 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.003 0.001 HIS A 338 PHE 0.015 0.001 PHE D 280 TYR 0.014 0.001 TYR E 180 ARG 0.003 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 193 time to evaluate : 1.876 Fit side-chains REVERT: A 47 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7987 (mmtp) REVERT: A 110 LYS cc_start: 0.8866 (mttt) cc_final: 0.8379 (mmtm) REVERT: A 114 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 139 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7248 (mtp180) REVERT: A 265 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: A 297 ASP cc_start: 0.8522 (t0) cc_final: 0.8166 (t0) REVERT: B 105 MET cc_start: 0.8266 (mmm) cc_final: 0.7506 (mpp) REVERT: B 343 TYR cc_start: 0.8289 (p90) cc_final: 0.8046 (p90) REVERT: C 40 ASP cc_start: 0.8063 (m-30) cc_final: 0.7774 (m-30) REVERT: C 150 LYS cc_start: 0.8178 (mttt) cc_final: 0.7740 (mmtm) REVERT: C 166 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (m) REVERT: D 135 PHE cc_start: 0.7696 (t80) cc_final: 0.7467 (t80) REVERT: E 245 GLN cc_start: 0.5804 (mt0) cc_final: 0.5092 (pp30) REVERT: F 174 LYS cc_start: 0.6691 (ttmt) cc_final: 0.5735 (mtpt) REVERT: F 308 LYS cc_start: 0.7126 (mttt) cc_final: 0.6416 (ptmm) outliers start: 59 outliers final: 47 residues processed: 235 average time/residue: 0.2869 time to fit residues: 101.2467 Evaluate side-chains 221 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 110 LYS Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17555 Z= 0.191 Angle : 0.459 8.780 24108 Z= 0.241 Chirality : 0.043 0.167 2824 Planarity : 0.003 0.046 2873 Dihedral : 12.534 95.288 3064 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.67 % Allowed : 13.45 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 1990 helix: 1.06 (0.24), residues: 499 sheet: 0.42 (0.28), residues: 348 loop : -0.76 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.003 0.001 HIS E 96 PHE 0.018 0.001 PHE B 342 TYR 0.016 0.001 TYR E 180 ARG 0.003 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 182 time to evaluate : 1.696 Fit side-chains REVERT: A 22 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: A 45 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: A 47 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8048 (mmtp) REVERT: A 110 LYS cc_start: 0.8859 (mttt) cc_final: 0.8389 (mmtm) REVERT: A 139 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7263 (mtp180) REVERT: A 200 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7607 (p0) REVERT: A 265 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: A 297 ASP cc_start: 0.8481 (t0) cc_final: 0.8153 (t0) REVERT: B 105 MET cc_start: 0.8298 (mmm) cc_final: 0.7525 (mpp) REVERT: B 168 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (pp) REVERT: B 343 TYR cc_start: 0.8286 (p90) cc_final: 0.8073 (p90) REVERT: C 40 ASP cc_start: 0.8056 (m-30) cc_final: 0.7771 (m-30) REVERT: C 150 LYS cc_start: 0.8186 (mttt) cc_final: 0.7739 (mmtm) REVERT: C 166 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7846 (m) REVERT: C 249 LEU cc_start: 0.7569 (tp) cc_final: 0.7309 (tt) REVERT: C 299 LEU cc_start: 0.8331 (tp) cc_final: 0.8117 (tp) REVERT: D 197 GLN cc_start: 0.7975 (mm110) cc_final: 0.7045 (tt0) REVERT: E 245 GLN cc_start: 0.5764 (mt0) cc_final: 0.5073 (pp30) REVERT: F 174 LYS cc_start: 0.6655 (ttmt) cc_final: 0.5712 (mtpt) REVERT: F 255 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6196 (mm) REVERT: F 308 LYS cc_start: 0.7064 (mttt) cc_final: 0.6281 (ptmm) outliers start: 65 outliers final: 45 residues processed: 231 average time/residue: 0.2864 time to fit residues: 98.9724 Evaluate side-chains 222 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17555 Z= 0.181 Angle : 0.455 9.761 24108 Z= 0.239 Chirality : 0.043 0.161 2824 Planarity : 0.003 0.047 2873 Dihedral : 12.531 95.586 3064 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.45 % Allowed : 14.02 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1990 helix: 1.14 (0.24), residues: 499 sheet: 0.47 (0.28), residues: 348 loop : -0.76 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.003 0.000 HIS E 96 PHE 0.016 0.001 PHE B 342 TYR 0.015 0.001 TYR E 180 ARG 0.004 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 1.928 Fit side-chains REVERT: A 22 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: A 45 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: A 47 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8027 (mmtp) REVERT: A 110 LYS cc_start: 0.8761 (mttt) cc_final: 0.8341 (mmtm) REVERT: A 139 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7265 (mtp180) REVERT: A 200 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7602 (p0) REVERT: A 265 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: B 105 MET cc_start: 0.8309 (mmm) cc_final: 0.7559 (mpp) REVERT: B 168 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8303 (pp) REVERT: C 40 ASP cc_start: 0.8063 (m-30) cc_final: 0.7779 (m-30) REVERT: C 150 LYS cc_start: 0.8148 (mttt) cc_final: 0.7698 (mmtm) REVERT: C 166 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7830 (m) REVERT: C 249 LEU cc_start: 0.7587 (tp) cc_final: 0.7318 (tt) REVERT: D 135 PHE cc_start: 0.7641 (t80) cc_final: 0.7384 (t80) REVERT: D 197 GLN cc_start: 0.7992 (mm110) cc_final: 0.7068 (tt0) REVERT: E 245 GLN cc_start: 0.5796 (mt0) cc_final: 0.5107 (pp30) REVERT: F 174 LYS cc_start: 0.6673 (ttmt) cc_final: 0.5759 (mtpt) REVERT: F 255 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6229 (mm) REVERT: F 272 MET cc_start: 0.8056 (ttp) cc_final: 0.7774 (ttt) REVERT: F 308 LYS cc_start: 0.7165 (mttt) cc_final: 0.6281 (ptmm) outliers start: 61 outliers final: 48 residues processed: 219 average time/residue: 0.2949 time to fit residues: 97.3558 Evaluate side-chains 221 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.0030 chunk 116 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 177 optimal weight: 8.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN E 176 GLN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17555 Z= 0.144 Angle : 0.445 9.287 24108 Z= 0.233 Chirality : 0.042 0.158 2824 Planarity : 0.003 0.047 2873 Dihedral : 12.511 96.395 3064 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 14.36 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1990 helix: 1.19 (0.24), residues: 499 sheet: 0.56 (0.28), residues: 348 loop : -0.72 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 333 HIS 0.002 0.000 HIS A 338 PHE 0.017 0.001 PHE F 259 TYR 0.020 0.001 TYR B 343 ARG 0.003 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 1.801 Fit side-chains REVERT: A 45 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: A 47 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8040 (mmtp) REVERT: A 110 LYS cc_start: 0.8777 (mttt) cc_final: 0.8367 (mmtm) REVERT: A 139 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7206 (mtp180) REVERT: A 265 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: B 105 MET cc_start: 0.8317 (mmm) cc_final: 0.7607 (mpp) REVERT: B 168 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8267 (pp) REVERT: C 40 ASP cc_start: 0.8061 (m-30) cc_final: 0.7761 (m-30) REVERT: C 150 LYS cc_start: 0.8179 (mttt) cc_final: 0.7705 (mmtm) REVERT: C 166 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (m) REVERT: C 249 LEU cc_start: 0.7562 (tp) cc_final: 0.7338 (tt) REVERT: D 135 PHE cc_start: 0.7593 (t80) cc_final: 0.7370 (t80) REVERT: D 197 GLN cc_start: 0.7984 (mm110) cc_final: 0.7069 (tt0) REVERT: E 245 GLN cc_start: 0.5752 (mt0) cc_final: 0.5098 (pp30) REVERT: F 22 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: F 174 LYS cc_start: 0.6605 (ttmt) cc_final: 0.5689 (mtpt) REVERT: F 255 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6240 (mm) REVERT: F 272 MET cc_start: 0.7985 (ttp) cc_final: 0.7720 (ttt) REVERT: F 308 LYS cc_start: 0.7131 (mttt) cc_final: 0.6259 (ptmm) outliers start: 57 outliers final: 45 residues processed: 224 average time/residue: 0.2706 time to fit residues: 91.5993 Evaluate side-chains 217 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17555 Z= 0.263 Angle : 0.498 8.934 24108 Z= 0.260 Chirality : 0.044 0.181 2824 Planarity : 0.003 0.046 2873 Dihedral : 12.623 95.305 3064 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.67 % Allowed : 14.58 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1990 helix: 1.05 (0.24), residues: 499 sheet: 0.55 (0.28), residues: 348 loop : -0.77 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS E 96 PHE 0.015 0.001 PHE B 342 TYR 0.028 0.001 TYR B 343 ARG 0.003 0.000 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 174 time to evaluate : 1.857 Fit side-chains REVERT: A 45 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 47 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8013 (mmtp) REVERT: A 110 LYS cc_start: 0.8786 (mttt) cc_final: 0.8326 (mmtm) REVERT: A 139 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7395 (mtp180) REVERT: A 200 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 265 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: B 105 MET cc_start: 0.8375 (mmm) cc_final: 0.7661 (mpp) REVERT: B 168 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (pp) REVERT: C 150 LYS cc_start: 0.8192 (mttt) cc_final: 0.7706 (mmtm) REVERT: C 166 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7831 (m) REVERT: D 197 GLN cc_start: 0.7999 (mm110) cc_final: 0.7060 (tt0) REVERT: E 245 GLN cc_start: 0.5778 (mt0) cc_final: 0.5094 (pp30) REVERT: F 22 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: F 174 LYS cc_start: 0.6654 (ttmt) cc_final: 0.5742 (mtpt) REVERT: F 255 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6235 (mm) REVERT: F 272 MET cc_start: 0.8082 (ttp) cc_final: 0.7826 (ttt) REVERT: F 308 LYS cc_start: 0.7142 (mttt) cc_final: 0.6272 (ptmm) outliers start: 65 outliers final: 49 residues processed: 222 average time/residue: 0.2784 time to fit residues: 93.1914 Evaluate side-chains 225 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 202 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN E 164 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17555 Z= 0.154 Angle : 0.462 11.383 24108 Z= 0.240 Chirality : 0.042 0.162 2824 Planarity : 0.003 0.046 2873 Dihedral : 12.583 96.660 3064 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.00 % Allowed : 15.38 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1990 helix: 1.13 (0.24), residues: 499 sheet: 0.59 (0.28), residues: 348 loop : -0.74 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 333 HIS 0.002 0.000 HIS E 96 PHE 0.016 0.001 PHE B 342 TYR 0.028 0.001 TYR B 343 ARG 0.003 0.000 ARG C 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.886 Fit side-chains REVERT: A 45 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: A 47 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8029 (mmtp) REVERT: A 110 LYS cc_start: 0.8765 (mttt) cc_final: 0.8337 (mmtm) REVERT: A 139 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7256 (mtp180) REVERT: A 221 GLU cc_start: 0.7620 (tp30) cc_final: 0.6662 (tp30) REVERT: A 265 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: B 105 MET cc_start: 0.8334 (mmm) cc_final: 0.7629 (mpp) REVERT: B 168 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (pp) REVERT: C 40 ASP cc_start: 0.8050 (m-30) cc_final: 0.7757 (m-30) REVERT: C 150 LYS cc_start: 0.8175 (mttt) cc_final: 0.7701 (mmtm) REVERT: C 166 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (m) REVERT: E 245 GLN cc_start: 0.5764 (mt0) cc_final: 0.5107 (pp30) REVERT: F 22 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: F 174 LYS cc_start: 0.6637 (ttmt) cc_final: 0.5711 (mtpt) REVERT: F 255 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6235 (mm) REVERT: F 272 MET cc_start: 0.7981 (ttp) cc_final: 0.7740 (ttt) REVERT: F 308 LYS cc_start: 0.7125 (mttt) cc_final: 0.6248 (ptmm) outliers start: 53 outliers final: 46 residues processed: 214 average time/residue: 0.2916 time to fit residues: 94.2659 Evaluate side-chains 214 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 162 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN D 164 ASN E 164 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.202891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152146 restraints weight = 19053.356| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 4.15 r_work: 0.3090 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17555 Z= 0.271 Angle : 0.503 9.588 24108 Z= 0.262 Chirality : 0.044 0.164 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.680 95.491 3064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.34 % Allowed : 15.26 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 1990 helix: 0.92 (0.24), residues: 504 sheet: 0.53 (0.28), residues: 348 loop : -0.79 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 333 HIS 0.004 0.001 HIS E 96 PHE 0.021 0.002 PHE F 259 TYR 0.028 0.001 TYR B 343 ARG 0.005 0.000 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.38 seconds wall clock time: 62 minutes 25.89 seconds (3745.89 seconds total)