Starting phenix.real_space_refine on Fri Sep 27 21:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/09_2024/7tj2_25915.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/09_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_25915/09_2024/7tj2_25915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/09_2024/7tj2_25915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/09_2024/7tj2_25915.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/09_2024/7tj2_25915.cif" } 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. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.09, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 2.0 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: 6.13 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: 5.81 Time building geometry restraints manager: 4.70 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: 0.00 - 1.12: 23723 1.12 - 2.24: 271 2.24 - 3.35: 104 3.35 - 4.47: 9 4.47 - 5.59: 1 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 3.040 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.196 3.040 nonbonded pdb=" O GLY F 77 " pdb=" OG1 THR F 121 " model vdw 2.196 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 3.130 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.250 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- 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 : 1.841 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: 0.2945 time to fit residues: 177.9870 Evaluate side-chains 232 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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: 0.1980 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 D 30 ASN E 29 ASN E 30 ASN F 29 ASN F 30 ASN F 75 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17555 Z= 0.358 Angle : 0.563 10.259 24108 Z= 0.297 Chirality : 0.046 0.358 2824 Planarity : 0.004 0.057 2873 Dihedral : 12.756 91.567 3070 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.17 % Allowed : 8.65 % Favored : 88.19 % 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: -0.05 (0.19), residues: 1990 helix: 0.77 (0.24), residues: 504 sheet: 0.49 (0.30), residues: 348 loop : -0.54 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 87 HIS 0.004 0.001 HIS E 96 PHE 0.017 0.002 PHE E 269 TYR 0.015 0.001 TYR F 226 ARG 0.005 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 269 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 1.707 Fit side-chains REVERT: A 45 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: A 47 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7997 (mmtm) REVERT: A 110 LYS cc_start: 0.8739 (mttt) cc_final: 0.8321 (mmtm) REVERT: A 139 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7519 (mtp180) REVERT: A 265 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 297 ASP cc_start: 0.8694 (t0) cc_final: 0.8481 (t0) REVERT: B 105 MET cc_start: 0.8323 (mmm) cc_final: 0.7343 (mpp) REVERT: B 209 GLN cc_start: 0.7411 (tp40) cc_final: 0.7202 (pp30) REVERT: B 213 ASP cc_start: 0.7900 (m-30) cc_final: 0.7616 (m-30) REVERT: B 343 TYR cc_start: 0.8316 (p90) cc_final: 0.7893 (p90) REVERT: C 150 LYS cc_start: 0.8135 (mttt) cc_final: 0.7808 (mmtm) REVERT: C 166 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7889 (m) REVERT: E 245 GLN cc_start: 0.5810 (mt0) cc_final: 0.5087 (pp30) REVERT: F 273 ASP cc_start: 0.7642 (t70) cc_final: 0.7306 (t70) REVERT: F 305 GLU cc_start: 0.7621 (tt0) cc_final: 0.7371 (mt-10) REVERT: F 308 LYS cc_start: 0.7066 (mttt) cc_final: 0.6538 (ptmm) outliers start: 56 outliers final: 34 residues processed: 254 average time/residue: 0.3092 time to fit residues: 119.5398 Evaluate side-chains 218 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 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 97 ILE 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 296 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 329 SER 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 D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 102 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 184 optimal weight: 6.9990 chunk 199 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 189 GLN C 75 ASN C 176 GLN C 338 HIS D 83 ASN D 164 ASN E 176 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2563 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= 0.169 Angle : 0.458 8.531 24108 Z= 0.244 Chirality : 0.043 0.252 2824 Planarity : 0.004 0.039 2873 Dihedral : 12.549 96.380 3062 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.09 % Allowed : 11.19 % Favored : 86.72 % 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: 0.90 (0.24), residues: 509 sheet: 0.56 (0.29), residues: 348 loop : -0.54 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 333 HIS 0.002 0.000 HIS A 338 PHE 0.016 0.001 PHE F 303 TYR 0.015 0.001 TYR E 180 ARG 0.003 0.000 ARG C 139 *********************** 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 245 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.742 Fit side-chains REVERT: A 45 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: A 47 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8151 (mmtm) REVERT: A 110 LYS cc_start: 0.8788 (mttt) cc_final: 0.8370 (mmtm) REVERT: A 139 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7317 (mtp180) REVERT: A 297 ASP cc_start: 0.8611 (t0) cc_final: 0.8400 (t0) REVERT: B 47 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8056 (mmtp) REVERT: B 105 MET cc_start: 0.8257 (mmm) cc_final: 0.7355 (mpp) REVERT: B 213 ASP cc_start: 0.7912 (m-30) cc_final: 0.7608 (m-30) REVERT: B 343 TYR cc_start: 0.8206 (p90) cc_final: 0.7898 (p90) REVERT: C 150 LYS cc_start: 0.8175 (mttt) cc_final: 0.7870 (mmtm) REVERT: C 166 VAL cc_start: 0.8088 (p) cc_final: 0.7861 (m) REVERT: E 245 GLN cc_start: 0.5770 (mt0) cc_final: 0.5080 (pp30) REVERT: E 252 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7076 (tp) REVERT: F 214 PHE cc_start: 0.7194 (t80) cc_final: 0.6989 (t80) REVERT: F 308 LYS cc_start: 0.7089 (mttt) cc_final: 0.6533 (ptmm) outliers start: 37 outliers final: 20 residues processed: 237 average time/residue: 0.2884 time to fit residues: 102.2325 Evaluate side-chains 203 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 156 VAL 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 156 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 282 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 185 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 0.0670 chunk 52 optimal weight: 0.5980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17555 Z= 0.164 Angle : 0.453 8.504 24108 Z= 0.240 Chirality : 0.043 0.193 2824 Planarity : 0.003 0.041 2873 Dihedral : 12.492 96.214 3059 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.00 % Allowed : 11.59 % Favored : 85.42 % 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: 0.01 (0.19), residues: 1990 helix: 1.14 (0.24), residues: 499 sheet: 0.49 (0.28), residues: 348 loop : -0.65 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 333 HIS 0.004 0.000 HIS A 338 PHE 0.011 0.001 PHE E 280 TYR 0.015 0.001 TYR B 238 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 250 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 2.009 Fit side-chains REVERT: A 22 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: A 45 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: A 110 LYS cc_start: 0.8826 (mttt) cc_final: 0.8384 (mmtm) REVERT: A 139 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7261 (mtp180) REVERT: A 265 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: A 297 ASP cc_start: 0.8579 (t0) cc_final: 0.8310 (t0) REVERT: B 47 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8025 (mmtp) REVERT: B 105 MET cc_start: 0.8260 (mmm) cc_final: 0.7314 (mpp) REVERT: B 343 TYR cc_start: 0.8234 (p90) cc_final: 0.7961 (p90) REVERT: C 150 LYS cc_start: 0.8221 (mttt) cc_final: 0.7885 (mmtm) REVERT: C 166 VAL cc_start: 0.8090 (p) cc_final: 0.7856 (m) REVERT: E 245 GLN cc_start: 0.5814 (mt0) cc_final: 0.5101 (pp30) REVERT: F 255 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6201 (mm) REVERT: F 308 LYS cc_start: 0.7120 (mttt) cc_final: 0.6421 (ptmm) outliers start: 53 outliers final: 30 residues processed: 238 average time/residue: 0.2927 time to fit residues: 105.2173 Evaluate side-chains 212 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 166 VAL 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 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 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 276 VAL Chi-restraints excluded: chain E residue 296 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.0270 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3050 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= 0.193 Angle : 0.468 9.226 24108 Z= 0.245 Chirality : 0.043 0.172 2824 Planarity : 0.003 0.042 2873 Dihedral : 12.509 96.799 3059 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.50 % Allowed : 11.87 % Favored : 84.62 % 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: 1.09 (0.24), residues: 499 sheet: 0.48 (0.28), residues: 348 loop : -0.68 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.004 0.001 HIS A 338 PHE 0.016 0.001 PHE B 342 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 248 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 186 time to evaluate : 2.043 Fit side-chains REVERT: A 22 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8456 (mt-10) REVERT: A 110 LYS cc_start: 0.8817 (mttt) cc_final: 0.8403 (mmtm) REVERT: A 139 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7181 (mtp180) REVERT: A 265 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: A 297 ASP cc_start: 0.8597 (t0) cc_final: 0.8313 (t0) REVERT: B 105 MET cc_start: 0.8277 (mmm) cc_final: 0.7241 (mpp) REVERT: B 343 TYR cc_start: 0.8241 (p90) cc_final: 0.8016 (p90) REVERT: C 40 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: C 150 LYS cc_start: 0.8257 (mttt) cc_final: 0.7892 (mmtm) REVERT: C 166 VAL cc_start: 0.8091 (p) cc_final: 0.7856 (m) REVERT: D 135 PHE cc_start: 0.7624 (t80) cc_final: 0.7415 (t80) REVERT: E 194 TYR cc_start: 0.8347 (m-80) cc_final: 0.8139 (m-80) REVERT: E 245 GLN cc_start: 0.5814 (mt0) cc_final: 0.5093 (pp30) REVERT: F 255 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6310 (mm) REVERT: F 308 LYS cc_start: 0.7114 (mttt) cc_final: 0.6339 (ptmm) outliers start: 62 outliers final: 47 residues processed: 234 average time/residue: 0.2931 time to fit residues: 103.4743 Evaluate side-chains 230 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 179 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 322 THR 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 129 ASP 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 262 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 72 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 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 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 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 164 ASN F 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3160 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= 0.197 Angle : 0.463 8.955 24108 Z= 0.243 Chirality : 0.043 0.163 2824 Planarity : 0.003 0.043 2873 Dihedral : 12.517 97.065 3059 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.17 % Allowed : 12.72 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.19), residues: 1990 helix: 1.10 (0.24), residues: 499 sheet: 0.45 (0.28), residues: 348 loop : -0.71 (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 0.014 0.001 PHE B 342 TYR 0.018 0.001 TYR C 238 ARG 0.002 0.000 ARG C 139 *********************** 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 235 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 1.838 Fit side-chains REVERT: A 22 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: A 110 LYS cc_start: 0.8825 (mttt) cc_final: 0.8324 (mmtm) REVERT: A 114 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 139 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7180 (mtp180) REVERT: A 265 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: A 297 ASP cc_start: 0.8602 (t0) cc_final: 0.8331 (t0) REVERT: B 105 MET cc_start: 0.8278 (mmm) cc_final: 0.7231 (mpp) REVERT: C 40 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: C 150 LYS cc_start: 0.8261 (mttt) cc_final: 0.7866 (mmtm) REVERT: C 166 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7853 (m) REVERT: E 245 GLN cc_start: 0.5808 (mt0) cc_final: 0.5145 (pp30) REVERT: F 214 PHE cc_start: 0.7286 (t80) cc_final: 0.7048 (t80) REVERT: F 255 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6356 (mm) REVERT: F 308 LYS cc_start: 0.7226 (mttt) cc_final: 0.6348 (ptmm) outliers start: 56 outliers final: 41 residues processed: 220 average time/residue: 0.2822 time to fit residues: 94.2410 Evaluate side-chains 217 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 322 THR 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 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL 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 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE 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 72 ILE Chi-restraints excluded: chain E residue 97 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 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 F residue 67 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 282 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17555 Z= 0.287 Angle : 0.507 9.706 24108 Z= 0.265 Chirality : 0.044 0.169 2824 Planarity : 0.004 0.043 2873 Dihedral : 12.590 96.566 3059 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.17 % Allowed : 12.72 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.19), residues: 1990 helix: 0.97 (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 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS E 96 PHE 0.014 0.001 PHE B 342 TYR 0.021 0.001 TYR C 238 ARG 0.003 0.000 ARG C 127 *********************** 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 242 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 186 time to evaluate : 1.950 Fit side-chains REVERT: A 22 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: A 110 LYS cc_start: 0.8841 (mttt) cc_final: 0.8373 (mmtm) REVERT: A 139 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7355 (mtp180) REVERT: A 265 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7307 (tp30) REVERT: A 297 ASP cc_start: 0.8643 (t0) cc_final: 0.8338 (t0) REVERT: B 105 MET cc_start: 0.8307 (mmm) cc_final: 0.7212 (mpp) REVERT: C 150 LYS cc_start: 0.8281 (mttt) cc_final: 0.7847 (mmtm) REVERT: C 166 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7860 (m) REVERT: C 249 LEU cc_start: 0.7559 (tp) cc_final: 0.7324 (tt) REVERT: E 245 GLN cc_start: 0.5765 (mt0) cc_final: 0.5069 (pp30) REVERT: F 22 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: F 214 PHE cc_start: 0.7282 (t80) cc_final: 0.7080 (t80) REVERT: F 255 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6343 (mm) REVERT: F 273 ASP cc_start: 0.7545 (t70) cc_final: 0.7281 (t70) REVERT: F 308 LYS cc_start: 0.7241 (mttt) cc_final: 0.6363 (ptmm) outliers start: 56 outliers final: 45 residues processed: 227 average time/residue: 0.2915 time to fit residues: 100.8536 Evaluate side-chains 225 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR 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 129 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 VAL 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 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE 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 E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 122 VAL 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 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 255 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3398 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= 0.149 Angle : 0.464 8.916 24108 Z= 0.243 Chirality : 0.042 0.159 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.530 97.978 3059 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.83 % Allowed : 13.00 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.19), residues: 1990 helix: 1.07 (0.24), residues: 499 sheet: 0.46 (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 0.003 0.000 HIS A 338 PHE 0.014 0.001 PHE B 342 TYR 0.028 0.001 TYR B 343 ARG 0.004 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 243 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 193 time to evaluate : 1.835 Fit side-chains REVERT: A 22 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: A 45 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: A 110 LYS cc_start: 0.8698 (mttt) cc_final: 0.8281 (mmtm) REVERT: A 139 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7256 (mtp180) REVERT: A 265 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7344 (tp30) REVERT: A 297 ASP cc_start: 0.8575 (t0) cc_final: 0.8300 (t0) REVERT: B 105 MET cc_start: 0.8239 (mmm) cc_final: 0.7199 (mpp) REVERT: B 168 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8248 (pp) REVERT: B 255 LEU cc_start: 0.8029 (mt) cc_final: 0.7818 (mt) REVERT: C 150 LYS cc_start: 0.8257 (mttt) cc_final: 0.7830 (mmtm) REVERT: C 166 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (m) REVERT: D 135 PHE cc_start: 0.7596 (t80) cc_final: 0.7350 (t80) REVERT: E 245 GLN cc_start: 0.5792 (mt0) cc_final: 0.5135 (pp30) REVERT: F 22 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: F 214 PHE cc_start: 0.7327 (t80) cc_final: 0.7107 (t80) REVERT: F 255 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6209 (mm) REVERT: F 272 MET cc_start: 0.8051 (ttp) cc_final: 0.7834 (ttt) REVERT: F 297 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: F 308 LYS cc_start: 0.7138 (mttt) cc_final: 0.6200 (ptmm) outliers start: 50 outliers final: 38 residues processed: 231 average time/residue: 0.2751 time to fit residues: 97.1341 Evaluate side-chains 225 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR 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 168 LEU 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 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 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 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 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 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 297 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 30.0000 chunk 171 optimal weight: 0.0870 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3483 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= 0.203 Angle : 0.484 9.567 24108 Z= 0.254 Chirality : 0.043 0.161 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.561 97.377 3059 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % 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: -0.12 (0.19), residues: 1990 helix: 1.07 (0.24), residues: 499 sheet: 0.45 (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 0.003 0.001 HIS E 96 PHE 0.016 0.001 PHE E 280 TYR 0.028 0.001 TYR B 343 ARG 0.003 0.000 ARG C 139 *********************** 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 232 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 1.865 Fit side-chains REVERT: A 22 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: A 45 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 110 LYS cc_start: 0.8746 (mttt) cc_final: 0.8320 (mmtm) REVERT: A 139 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7296 (mtp180) REVERT: A 265 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7351 (tp30) REVERT: A 297 ASP cc_start: 0.8594 (t0) cc_final: 0.8289 (t0) REVERT: B 105 MET cc_start: 0.8249 (mmm) cc_final: 0.7163 (mpp) REVERT: B 168 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8284 (pp) REVERT: B 203 GLU cc_start: 0.7428 (mp0) cc_final: 0.6987 (pm20) REVERT: C 150 LYS cc_start: 0.8231 (mttt) cc_final: 0.7805 (mmtm) REVERT: C 166 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7844 (m) REVERT: C 219 MET cc_start: 0.7038 (mmm) cc_final: 0.6731 (mmm) REVERT: C 238 TYR cc_start: 0.6773 (m-80) cc_final: 0.6539 (m-10) REVERT: E 245 GLN cc_start: 0.5797 (mt0) cc_final: 0.5142 (pp30) REVERT: F 22 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: F 255 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6218 (mm) REVERT: F 273 ASP cc_start: 0.7473 (t70) cc_final: 0.7197 (t70) REVERT: F 297 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: F 308 LYS cc_start: 0.7128 (mttt) cc_final: 0.6171 (ptmm) outliers start: 49 outliers final: 40 residues processed: 220 average time/residue: 0.2990 time to fit residues: 100.5902 Evaluate side-chains 226 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR 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 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 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 276 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 296 ILE 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 255 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 297 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 202 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3571 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= 0.204 Angle : 0.486 10.305 24108 Z= 0.254 Chirality : 0.043 0.161 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.589 97.695 3059 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1990 helix: 1.07 (0.24), residues: 499 sheet: 0.46 (0.28), residues: 348 loop : -0.78 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 333 HIS 0.003 0.001 HIS E 96 PHE 0.021 0.001 PHE E 264 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 222 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 1.937 Fit side-chains REVERT: A 22 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8475 (mt-10) REVERT: A 45 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: A 110 LYS cc_start: 0.8748 (mttt) cc_final: 0.8323 (mmtm) REVERT: A 139 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7291 (mtp180) REVERT: A 265 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7332 (tp30) REVERT: A 297 ASP cc_start: 0.8601 (t0) cc_final: 0.8283 (t0) REVERT: B 105 MET cc_start: 0.8251 (mmm) cc_final: 0.7163 (mpp) REVERT: B 168 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8294 (pp) REVERT: C 150 LYS cc_start: 0.8228 (mttt) cc_final: 0.7765 (mmtm) REVERT: C 166 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7796 (m) REVERT: C 219 MET cc_start: 0.7105 (mmm) cc_final: 0.6814 (mmm) REVERT: C 238 TYR cc_start: 0.6787 (m-80) cc_final: 0.6528 (m-10) REVERT: E 245 GLN cc_start: 0.5803 (mt0) cc_final: 0.5156 (pp30) REVERT: E 265 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6672 (tt0) REVERT: F 22 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: F 214 PHE cc_start: 0.7231 (t80) cc_final: 0.6992 (t80) REVERT: F 255 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6208 (mm) REVERT: F 297 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: F 308 LYS cc_start: 0.7173 (mttt) cc_final: 0.6279 (ptmm) outliers start: 48 outliers final: 40 residues processed: 210 average time/residue: 0.3042 time to fit residues: 97.1961 Evaluate side-chains 211 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 164 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 322 THR 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 262 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 40 ASP 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 274 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 97 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 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 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 255 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 297 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 148 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155961 restraints weight = 19173.724| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.83 r_work: 0.3204 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3653 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= 0.153 Angle : 0.464 10.530 24108 Z= 0.243 Chirality : 0.042 0.158 2824 Planarity : 0.003 0.045 2873 Dihedral : 12.558 98.295 3059 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 13.79 % Favored : 83.44 % 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: 1.14 (0.24), residues: 499 sheet: 0.74 (0.28), residues: 338 loop : -0.74 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS E 96 PHE 0.021 0.001 PHE E 264 TYR 0.027 0.001 TYR B 343 ARG 0.003 0.000 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.75 seconds wall clock time: 63 minutes 0.56 seconds (3780.56 seconds total)