Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 16:41:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/10_2023/7tj2_25915.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/10_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_25915/10_2023/7tj2_25915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/10_2023/7tj2_25915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/10_2023/7tj2_25915.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj2_25915/10_2023/7tj2_25915.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 57 5.16 5 C 10718 2.51 5 N 2788 2.21 5 O 3458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 17083 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2733 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2108 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 257} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 29} Chain: "H" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 651 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 18} Link IDs: {'rna3p': 30} Time building chain proxies: 9.53, per 1000 atoms: 0.56 Number of scatterers: 17083 At special positions: 0 Unit cell: (119.087, 121.835, 134.659, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 62 15.00 O 3458 8.00 N 2788 7.00 C 10718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.07 Conformation dependent library (CDL) restraints added in 2.1 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: 6.00 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: 5.78 Time building geometry restraints manager: 7.55 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 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 50.640 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.350 ------------------------------------------------------------------------------- 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 : 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 % 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 *********************** 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 : 1.810 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 409 average time/residue: 0.2949 time to fit residues: 178.5713 Evaluate side-chains 223 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1523 time to fit residues: 5.4413 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.2514 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= 0.487 Angle : 0.622 9.820 24108 Z= 0.328 Chirality : 0.049 0.359 2824 Planarity : 0.004 0.041 2873 Dihedral : 7.048 86.330 2851 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.22 % Allowed : 9.84 % Favored : 86.94 % 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: -0.23 (0.19), residues: 1990 helix: 0.53 (0.24), residues: 509 sheet: 0.40 (0.30), residues: 348 loop : -0.61 (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 267 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 210 time to evaluate : 1.933 Fit side-chains outliers start: 57 outliers final: 36 residues processed: 255 average time/residue: 0.2901 time to fit residues: 111.2423 Evaluate side-chains 210 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1523 time to fit residues: 13.0148 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 199 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 83 ASN D 164 ASN E 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2687 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 : 0.463 8.687 24108 Z= 0.246 Chirality : 0.043 0.237 2824 Planarity : 0.004 0.042 2873 Dihedral : 6.658 92.395 2851 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.02 % Allowed : 12.10 % Favored : 86.89 % 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: 0.96 (0.24), residues: 504 sheet: 0.52 (0.29), residues: 348 loop : -0.59 (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 213 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.894 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 208 average time/residue: 0.2964 time to fit residues: 93.2594 Evaluate side-chains 181 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1598 time to fit residues: 6.2435 ------------------------------------------------------------------------------- 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: 0.7980 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7477 moved from start: 0.2904 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= 0.189 Angle : 0.462 8.365 24108 Z= 0.244 Chirality : 0.043 0.201 2824 Planarity : 0.003 0.045 2873 Dihedral : 6.589 93.353 2851 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.64 % Allowed : 12.66 % Favored : 85.70 % 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: -0.03 (0.19), residues: 1990 helix: 1.08 (0.24), residues: 499 sheet: 0.48 (0.29), residues: 348 loop : -0.67 (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 206 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.853 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 198 average time/residue: 0.2971 time to fit residues: 88.6575 Evaluate side-chains 183 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1802 time to fit residues: 6.6347 ------------------------------------------------------------------------------- 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: 5.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 0.0170 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 167 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 0 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3100 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= 0.118 Angle : 0.439 9.166 24108 Z= 0.230 Chirality : 0.042 0.178 2824 Planarity : 0.003 0.046 2873 Dihedral : 6.482 96.507 2851 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.90 % Allowed : 13.85 % Favored : 85.25 % 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: 0.07 (0.19), residues: 1990 helix: 1.25 (0.24), residues: 499 sheet: 0.59 (0.28), residues: 348 loop : -0.68 (0.17), 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 223 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 1.860 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 217 average time/residue: 0.2960 time to fit residues: 97.9196 Evaluate side-chains 176 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1596 time to fit residues: 3.8830 ------------------------------------------------------------------------------- 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: 1.9990 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17555 Z= 0.334 Angle : 0.526 10.263 24108 Z= 0.274 Chirality : 0.046 0.171 2824 Planarity : 0.004 0.046 2873 Dihedral : 6.745 93.729 2851 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 14.98 % Favored : 83.55 % 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: -0.11 (0.19), residues: 1990 helix: 1.04 (0.24), residues: 499 sheet: 0.47 (0.28), residues: 348 loop : -0.75 (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 194 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.862 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.3127 time to fit residues: 87.0040 Evaluate side-chains 176 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1551 time to fit residues: 7.8472 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 29 ASN ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN F 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17555 Z= 0.404 Angle : 0.564 10.578 24108 Z= 0.295 Chirality : 0.047 0.178 2824 Planarity : 0.004 0.046 2873 Dihedral : 6.989 93.869 2851 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.07 % Allowed : 14.47 % Favored : 84.45 % 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: -0.42 (0.18), residues: 1990 helix: 0.69 (0.24), residues: 499 sheet: 0.34 (0.28), residues: 348 loop : -0.92 (0.17), 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 187 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.943 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 183 average time/residue: 0.3125 time to fit residues: 85.9923 Evaluate side-chains 169 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1890 time to fit residues: 6.9968 ------------------------------------------------------------------------------- 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: 0.7980 chunk 116 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17555 Z= 0.164 Angle : 0.470 10.758 24108 Z= 0.246 Chirality : 0.043 0.166 2824 Planarity : 0.003 0.048 2873 Dihedral : 6.799 95.509 2851 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.28 % Allowed : 15.83 % Favored : 83.89 % 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: 1.02 (0.24), residues: 499 sheet: 0.60 (0.28), residues: 338 loop : -0.82 (0.17), residues: 1153 *********************** 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 172 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.942 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 171 average time/residue: 0.3100 time to fit residues: 79.3413 Evaluate side-chains 162 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.857 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1404 time to fit residues: 2.8376 ------------------------------------------------------------------------------- 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: 9.9990 chunk 171 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 164 optimal weight: 0.4980 chunk 172 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3566 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= 0.160 Angle : 0.464 8.695 24108 Z= 0.243 Chirality : 0.043 0.161 2824 Planarity : 0.003 0.048 2873 Dihedral : 6.797 96.091 2851 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.51 % Allowed : 15.94 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1990 helix: 1.12 (0.24), residues: 499 sheet: 0.48 (0.28), residues: 348 loop : -0.78 (0.18), residues: 1143 *********************** 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 171 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.091 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 169 average time/residue: 0.3181 time to fit residues: 80.3313 Evaluate side-chains 162 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1577 time to fit residues: 3.1937 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 202 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 127 optimal weight: 0.0170 overall best weight: 0.6622 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.3652 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= 0.130 Angle : 0.458 11.224 24108 Z= 0.237 Chirality : 0.042 0.156 2824 Planarity : 0.003 0.049 2873 Dihedral : 6.794 96.746 2851 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.11 % Allowed : 16.11 % Favored : 83.78 % 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: 1.21 (0.24), residues: 499 sheet: 0.83 (0.29), residues: 321 loop : -0.72 (0.17), residues: 1170 ********************** 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 175 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.846 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 175 average time/residue: 0.3097 time to fit residues: 80.5771 Evaluate side-chains 163 residues out of total 1781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1510 time to fit residues: 2.9252 ------------------------------------------------------------------------------- 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: 7.9990 chunk 148 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- 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** C 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.202377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151338 restraints weight = 18959.579| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 4.13 r_work: 0.3104 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3708 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= 0.284 Angle : 0.509 8.991 24108 Z= 0.264 Chirality : 0.045 0.166 2824 Planarity : 0.004 0.047 2873 Dihedral : 7.002 95.357 2851 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.17 % Allowed : 16.79 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1990 helix: 1.06 (0.24), residues: 499 sheet: 0.53 (0.28), residues: 348 loop : -0.78 (0.18), residues: 1143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.22 seconds wall clock time: 61 minutes 18.71 seconds (3678.71 seconds total)