Starting phenix.real_space_refine (version: dev) on Wed Feb 22 09:47:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/02_2023/7tj2_25915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/02_2023/7tj2_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_25915/02_2023/7tj2_25915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/02_2023/7tj2_25915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/02_2023/7tj2_25915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/02_2023/7tj2_25915.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17083 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2733 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 257} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 29} Chain: "H" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 651 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna3p': 30} Time building chain proxies: 9.63, per 1000 atoms: 0.56 Number of scatterers: 17083 At special positions: 0 Unit cell: (119.087, 121.835, 134.659, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 62 15.00 O 3458 8.00 N 2788 7.00 C 10718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 2.4 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: 4.92 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: 5.70 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5248 1.34 - 1.45: 2661 1.45 - 1.57: 9439 1.57 - 1.69: 122 1.69 - 1.81: 85 Bond restraints: 17555 Sorted by residual: bond pdb=" C ALA E 118 " pdb=" N PRO E 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.12e+00 bond pdb=" C ALA B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.339 1.375 -0.036 3.40e-02 8.65e+02 1.10e+00 bond pdb=" C ALA D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.339 1.375 -0.035 3.40e-02 8.65e+02 1.08e+00 bond pdb=" C ALA A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 bond pdb=" C ALA C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 1.339 1.374 -0.035 3.40e-02 8.65e+02 1.07e+00 ... (remaining 17550 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 769 107.13 - 113.84: 10097 113.84 - 120.56: 6499 120.56 - 127.28: 6483 127.28 - 133.99: 260 Bond angle restraints: 24108 Sorted by residual: angle pdb=" C THR F 49 " pdb=" N LEU F 50 " pdb=" CA LEU F 50 " ideal model delta sigma weight residual 121.48 124.92 -3.44 2.04e+00 2.40e-01 2.84e+00 angle pdb=" C GLN F 310 " pdb=" N ASP F 311 " pdb=" CA ASP F 311 " ideal model delta sigma weight residual 121.54 124.60 -3.06 1.91e+00 2.74e-01 2.56e+00 angle pdb=" C GLN C 310 " pdb=" N ASP C 311 " pdb=" CA ASP C 311 " ideal model delta sigma weight residual 121.54 124.39 -2.85 1.91e+00 2.74e-01 2.22e+00 angle pdb=" C2' G G 8 " pdb=" C1' G G 8 " pdb=" N9 G G 8 " ideal model delta sigma weight residual 112.00 114.13 -2.13 1.50e+00 4.44e-01 2.02e+00 angle pdb=" C GLN E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 124.20 -2.66 1.91e+00 2.74e-01 1.94e+00 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10075 18.04 - 36.09: 243 36.09 - 54.13: 32 54.13 - 72.18: 14 72.18 - 90.22: 3 Dihedral angle restraints: 10367 sinusoidal: 4560 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 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1703 0.026 - 0.052: 629 0.052 - 0.078: 254 0.078 - 0.103: 124 0.103 - 0.129: 114 Chirality restraints: 2824 Sorted by residual: chirality pdb=" CA ILE C 80 " pdb=" N ILE C 80 " pdb=" C ILE C 80 " pdb=" CB ILE C 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE F 80 " pdb=" N ILE F 80 " pdb=" C ILE F 80 " pdb=" CB ILE F 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE E 80 " pdb=" N ILE E 80 " pdb=" C ILE E 80 " pdb=" CB ILE E 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 2821 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 334 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C CYS B 334 " 0.020 2.00e-02 2.50e+03 pdb=" O CYS B 334 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 335 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO D 51 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO B 51 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.015 5.00e-02 4.00e+02 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1067 2.74 - 3.28: 15965 3.28 - 3.82: 28253 3.82 - 4.36: 34467 4.36 - 4.90: 58658 Nonbonded interactions: 138410 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.196 2.440 nonbonded pdb=" O GLY F 77 " pdb=" OG1 THR F 121 " model vdw 2.196 2.440 ... (remaining 138405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = (chain 'C' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C \ or name O or name CB )) or resid 2 through 345)) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.090 Check model and map are aligned: 0.270 Process input model: 48.000 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 8.616 90.221 6621 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 % 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 *********************** 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 : 1.942 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 409 average time/residue: 0.2973 time to fit residues: 180.7155 Evaluate side-chains 223 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1541 time to fit residues: 5.5360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 310 GLN B 29 ASN B 30 ASN B 83 ASN B 140 ASN B 176 GLN C 278 ASN D 30 ASN E 29 ASN E 30 ASN E 278 ASN F 29 ASN F 30 ASN F 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.064 17555 Z= 0.491 Angle : 0.628 9.998 24108 Z= 0.331 Chirality : 0.049 0.367 2824 Planarity : 0.004 0.041 2873 Dihedral : 7.064 86.229 2851 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1990 helix: 0.51 (0.24), residues: 509 sheet: 0.39 (0.30), residues: 348 loop : -0.62 (0.18), residues: 1133 *********************** 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: 58 poor density : 211 time to evaluate : 1.898 Fit side-chains outliers start: 58 outliers final: 35 residues processed: 257 average time/residue: 0.2914 time to fit residues: 113.1957 Evaluate side-chains 210 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1490 time to fit residues: 12.5716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 0.0060 chunk 153 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 chunk 164 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 0.0370 overall best weight: 0.7076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 176 GLN C 338 HIS D 83 ASN D 164 ASN E 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2705 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= 0.137 Angle : 0.461 8.659 24108 Z= 0.245 Chirality : 0.043 0.235 2824 Planarity : 0.004 0.042 2873 Dihedral : 6.669 92.292 2851 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.02 % 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: 0.97 (0.24), residues: 504 sheet: 0.53 (0.30), residues: 348 loop : -0.58 (0.18), residues: 1138 *********************** 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 214 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 1.963 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 210 average time/residue: 0.3002 time to fit residues: 95.6763 Evaluate side-chains 183 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1576 time to fit residues: 5.8937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 124 optimal weight: 0.0870 chunk 185 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17555 Z= 0.205 Angle : 0.470 8.357 24108 Z= 0.248 Chirality : 0.044 0.199 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.613 93.308 2851 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.70 % 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: -0.02 (0.19), residues: 1990 helix: 1.08 (0.24), residues: 499 sheet: 0.50 (0.29), residues: 348 loop : -0.66 (0.18), residues: 1143 *********************** 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 207 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 2.126 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 197 average time/residue: 0.2927 time to fit residues: 87.5626 Evaluate side-chains 179 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1584 time to fit residues: 6.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 167 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3125 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= 0.188 Angle : 0.461 8.996 24108 Z= 0.242 Chirality : 0.043 0.178 2824 Planarity : 0.003 0.046 2873 Dihedral : 6.586 95.688 2851 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.30 % 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: -0.02 (0.19), residues: 1990 helix: 1.12 (0.24), residues: 499 sheet: 0.51 (0.29), residues: 348 loop : -0.69 (0.18), residues: 1143 *********************** 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 209 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.911 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 203 average time/residue: 0.3024 time to fit residues: 92.5251 Evaluate side-chains 173 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1351 time to fit residues: 4.6363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.0870 chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 163 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN F 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3248 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= 0.171 Angle : 0.461 10.394 24108 Z= 0.240 Chirality : 0.043 0.165 2824 Planarity : 0.003 0.046 2873 Dihedral : 6.622 95.298 2851 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 1.02 % 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: 0.02 (0.19), residues: 1990 helix: 1.21 (0.24), residues: 499 sheet: 0.53 (0.28), residues: 348 loop : -0.69 (0.18), residues: 1143 *********************** 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 183 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 1.782 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 176 average time/residue: 0.3026 time to fit residues: 81.2440 Evaluate side-chains 166 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1601 time to fit residues: 5.7669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 17555 Z= 0.374 Angle : 0.543 10.821 24108 Z= 0.284 Chirality : 0.046 0.174 2824 Planarity : 0.004 0.047 2873 Dihedral : 6.920 94.452 2851 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.07 % 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: -0.24 (0.19), residues: 1990 helix: 0.85 (0.24), residues: 499 sheet: 0.46 (0.29), residues: 348 loop : -0.82 (0.18), residues: 1143 *********************** 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 190 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.908 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 185 average time/residue: 0.3061 time to fit residues: 85.7186 Evaluate side-chains 174 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1489 time to fit residues: 6.0872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3453 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= 0.196 Angle : 0.479 10.912 24108 Z= 0.249 Chirality : 0.043 0.165 2824 Planarity : 0.003 0.048 2873 Dihedral : 6.817 95.509 2851 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 1990 helix: 1.04 (0.24), residues: 499 sheet: 0.48 (0.28), residues: 348 loop : -0.79 (0.18), residues: 1143 *********************** 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 175 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.793 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 172 average time/residue: 0.2979 time to fit residues: 77.3241 Evaluate side-chains 165 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1465 time to fit residues: 3.2441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 164 optimal weight: 0.0970 chunk 172 optimal weight: 0.0970 chunk 181 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN F 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3554 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= 0.117 Angle : 0.442 9.100 24108 Z= 0.232 Chirality : 0.042 0.153 2824 Planarity : 0.003 0.049 2873 Dihedral : 6.731 97.094 2851 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1990 helix: 1.25 (0.24), residues: 499 sheet: 0.83 (0.29), residues: 321 loop : -0.70 (0.17), residues: 1170 *********************** 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 193 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 2.026 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 190 average time/residue: 0.3112 time to fit residues: 89.2366 Evaluate side-chains 172 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1602 time to fit residues: 3.3729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 202 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 197 GLN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN D 164 ASN F 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3641 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 : 0.546 11.403 24108 Z= 0.283 Chirality : 0.046 0.170 2824 Planarity : 0.004 0.046 2873 Dihedral : 7.036 94.779 2851 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1990 helix: 0.98 (0.24), residues: 499 sheet: 0.49 (0.28), residues: 348 loop : -0.82 (0.18), residues: 1143 ********************** 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 171 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.931 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 168 average time/residue: 0.3133 time to fit residues: 79.3157 Evaluate side-chains 161 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1519 time to fit residues: 3.4110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133007 restraints weight = 18989.828| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.26 r_work: 0.3274 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 17555 Z= 0.257 Angle : 0.508 9.987 24108 Z= 0.263 Chirality : 0.044 0.167 2824 Planarity : 0.003 0.047 2873 Dihedral : 7.027 95.729 2851 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1990 helix: 1.01 (0.24), residues: 499 sheet: 0.47 (0.28), residues: 348 loop : -0.81 (0.18), residues: 1143 =============================================================================== Job complete usr+sys time: 3459.99 seconds wall clock time: 63 minutes 23.17 seconds (3803.17 seconds total)