Starting phenix.real_space_refine (version: dev) on Wed Apr 6 03:18:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/04_2022/7tqv_26073.pdb" } resolution = 3.43 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= 0.029 sd= 0.106 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 17792 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: 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: "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: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 710 Classifications: {'RNA': 33} Modifications used: {'rna3p_pyr': 12, 'rna3p_pur': 20, 'rna2p_pyr': 1} Link IDs: {'rna3p': 31, 'rna2p': 1} Chain: "H" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 691 Classifications: {'RNA': 33} Modifications used: {'rna3p_pyr': 20, 'rna3p_pur': 13} Link IDs: {'rna3p': 32} Time building chain proxies: 10.67, per 1000 atoms: 0.60 Number of scatterers: 17792 At special positions: 0 Unit cell: (111.187, 133.786, 140.114, 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 61 16.00 P 66 15.00 O 3606 8.00 N 2899 7.00 C 11160 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: 6.73 Conformation dependent library (CDL) restraints added in 2.6 seconds 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 42 sheets defined 26.1% alpha, 21.9% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 6.15 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 227 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) 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 removed outlier: 3.618A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) 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: 3.619A 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 208 through 217 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.619A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 299 through 309 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: 3.618A 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 removed outlier: 3.513A pdb=" N GLU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) 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: 3.618A 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: 6.785A 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: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.683A pdb=" N GLU A 265 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.349A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 343 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.011A 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: 6.784A 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: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.682A pdb=" N GLU B 265 " --> pdb=" O THR B 282 " (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: 6.784A 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: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.682A pdb=" N GLU C 265 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323 Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.784A 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: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.681A pdb=" N GLU D 265 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 316 through 323 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.784A 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: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.123A 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: 3.682A pdb=" N GLU E 265 " --> pdb=" O THR E 282 " (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: 6.784A 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: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 4.122A 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: 3.683A pdb=" N GLU F 265 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323 662 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 7.38 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: 5452 1.34 - 1.45: 2792 1.45 - 1.57: 9825 1.57 - 1.69: 130 1.69 - 1.81: 92 Bond restraints: 18291 Sorted by residual: bond pdb=" C GLN A 189 " pdb=" N LEU A 190 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.83e-02 1.25e+03 2.54e+00 bond pdb=" C ALA F 118 " pdb=" N PRO F 119 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.38e-01 bond pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 1.524 1.515 0.010 1.05e-02 9.07e+03 8.28e-01 bond pdb=" C ALA E 118 " pdb=" N PRO E 119 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.17e-01 bond pdb=" C ALA C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 1.339 1.370 -0.030 3.40e-02 8.65e+02 8.03e-01 ... (remaining 18286 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.32: 862 107.32 - 113.98: 10605 113.98 - 120.64: 7035 120.64 - 127.30: 6354 127.30 - 133.96: 267 Bond angle restraints: 25123 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 121.48 129.04 -7.56 2.04e+00 2.40e-01 1.37e+01 angle pdb=" C ASP E 336 " pdb=" N GLY E 337 " pdb=" CA GLY E 337 " ideal model delta sigma weight residual 123.30 121.34 1.96 1.06e+00 8.90e-01 3.40e+00 angle pdb=" C ASP D 336 " pdb=" N GLY D 337 " pdb=" CA GLY D 337 " ideal model delta sigma weight residual 123.30 121.35 1.95 1.06e+00 8.90e-01 3.38e+00 angle pdb=" C ASP F 336 " pdb=" N GLY F 337 " pdb=" CA GLY F 337 " ideal model delta sigma weight residual 123.30 121.36 1.94 1.06e+00 8.90e-01 3.35e+00 angle pdb=" C ASP C 336 " pdb=" N GLY C 337 " pdb=" CA GLY C 337 " ideal model delta sigma weight residual 123.30 121.36 1.94 1.06e+00 8.90e-01 3.34e+00 ... (remaining 25118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.94: 10536 18.94 - 37.87: 219 37.87 - 56.81: 32 56.81 - 75.75: 4 75.75 - 94.68: 1 Dihedral angle restraints: 10792 sinusoidal: 4761 harmonic: 6031 Sorted by residual: dihedral pdb=" O5' A G 19 " pdb=" C5' A G 19 " pdb=" C4' A G 19 " pdb=" C3' A G 19 " ideal model delta sinusoidal sigma weight residual -65.00 -122.89 57.89 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" O5' U H 43 " pdb=" C5' U H 43 " pdb=" C4' U H 43 " pdb=" C3' U H 43 " ideal model delta sinusoidal sigma weight residual 55.00 112.78 -57.78 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN E 310 " pdb=" CA GLN E 310 " pdb=" CB GLN E 310 " pdb=" CG GLN E 310 " ideal model delta sinusoidal sigma weight residual -180.00 -131.87 -48.13 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 10789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1742 0.025 - 0.051: 674 0.051 - 0.076: 257 0.076 - 0.101: 135 0.101 - 0.126: 126 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE F 28 " pdb=" N ILE F 28 " pdb=" C ILE F 28 " pdb=" CB ILE F 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 2931 not shown) Planarity restraints: 2989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 51 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO B 51 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 50 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO E 51 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " 0.016 5.00e-02 4.00e+02 ... (remaining 2986 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 541 2.71 - 3.26: 16653 3.26 - 3.80: 28201 3.80 - 4.35: 36417 4.35 - 4.90: 60871 Nonbonded interactions: 142683 Sorted by model distance: nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.162 2.440 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.163 2.440 nonbonded pdb=" O GLY D 77 " pdb=" OG1 THR D 121 " model vdw 2.164 2.440 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.164 2.440 nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.164 2.440 ... (remaining 142678 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 'D' 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 66 5.49 5 S 61 5.16 5 C 11160 2.51 5 N 2899 2.21 5 O 3606 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.240 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.150 Process input model: 52.430 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 0.045 18291 Z= 0.156 Angle : 0.383 7.561 25123 Z= 0.208 Chirality : 0.040 0.126 2934 Planarity : 0.003 0.028 2989 Dihedral : 7.789 94.682 6904 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.82 % 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: -0.34 (0.19), residues: 2070 helix: 0.18 (0.22), residues: 534 sheet: 0.20 (0.30), residues: 378 loop : -0.50 (0.19), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 350 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 365 average time/residue: 0.3102 time to fit residues: 166.4352 Evaluate side-chains 144 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1568 time to fit residues: 3.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 190 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: A 5 ASN A 12 ASN A 75 ASN A 176 GLN A 209 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS B 5 ASN B 176 GLN B 209 GLN B 338 HIS C 5 ASN C 164 ASN C 176 GLN D 5 ASN D 176 GLN E 5 ASN E 176 GLN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 164 ASN F 176 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 18291 Z= 0.177 Angle : 0.507 9.439 25123 Z= 0.268 Chirality : 0.043 0.181 2934 Planarity : 0.004 0.080 2989 Dihedral : 6.471 92.272 2983 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.96 % 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: -0.26 (0.19), residues: 2070 helix: 0.37 (0.22), residues: 552 sheet: 0.33 (0.31), residues: 360 loop : -0.56 (0.18), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 189 average time/residue: 0.2845 time to fit residues: 84.0443 Evaluate side-chains 133 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1561 time to fit residues: 7.0742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 0.0270 chunk 65 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 209 GLN D 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 164 ASN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 18291 Z= 0.353 Angle : 0.603 10.496 25123 Z= 0.318 Chirality : 0.046 0.155 2934 Planarity : 0.004 0.060 2989 Dihedral : 6.915 90.718 2983 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 2.18 % 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: -0.76 (0.18), residues: 2070 helix: 0.02 (0.22), residues: 552 sheet: -0.16 (0.29), residues: 360 loop : -0.84 (0.18), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 167 average time/residue: 0.2592 time to fit residues: 69.8263 Evaluate side-chains 130 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1578 time to fit residues: 8.4897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN D 75 ASN D 189 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 18291 Z= 0.245 Angle : 0.523 9.531 25123 Z= 0.273 Chirality : 0.044 0.138 2934 Planarity : 0.004 0.052 2989 Dihedral : 6.786 91.933 2983 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2070 helix: 0.22 (0.22), residues: 552 sheet: -0.23 (0.28), residues: 360 loop : -0.89 (0.17), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 144 average time/residue: 0.2768 time to fit residues: 64.6645 Evaluate side-chains 120 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1600 time to fit residues: 6.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN E 176 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 18291 Z= 0.161 Angle : 0.484 9.069 25123 Z= 0.251 Chirality : 0.043 0.169 2934 Planarity : 0.004 0.043 2989 Dihedral : 6.636 92.919 2983 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.03 % 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: -0.61 (0.18), residues: 2070 helix: 0.52 (0.22), residues: 552 sheet: -0.29 (0.28), residues: 360 loop : -0.87 (0.17), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 0.2709 time to fit residues: 62.6057 Evaluate side-chains 123 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1618 time to fit residues: 6.0183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18291 Z= 0.197 Angle : 0.502 10.247 25123 Z= 0.259 Chirality : 0.043 0.163 2934 Planarity : 0.004 0.038 2989 Dihedral : 6.648 92.263 2983 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.82 % 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: -0.61 (0.18), residues: 2070 helix: 0.53 (0.22), residues: 552 sheet: -0.29 (0.28), residues: 360 loop : -0.88 (0.17), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 2.039 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 0.2566 time to fit residues: 53.5320 Evaluate side-chains 113 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1510 time to fit residues: 4.5773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN D 189 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18291 Z= 0.172 Angle : 0.493 11.225 25123 Z= 0.254 Chirality : 0.043 0.157 2934 Planarity : 0.003 0.039 2989 Dihedral : 6.608 92.531 2983 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.60 % 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: -0.53 (0.18), residues: 2070 helix: 0.59 (0.23), residues: 552 sheet: -0.17 (0.27), residues: 378 loop : -0.87 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 2.098 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 133 average time/residue: 0.2598 time to fit residues: 56.9861 Evaluate side-chains 116 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1707 time to fit residues: 4.3411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 18291 Z= 0.350 Angle : 0.595 11.500 25123 Z= 0.310 Chirality : 0.046 0.200 2934 Planarity : 0.004 0.043 2989 Dihedral : 7.028 89.800 2983 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.98 % 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: -0.87 (0.18), residues: 2070 helix: 0.20 (0.22), residues: 552 sheet: -0.43 (0.28), residues: 366 loop : -0.99 (0.17), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.2710 time to fit residues: 56.5059 Evaluate side-chains 117 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1610 time to fit residues: 5.3956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 8.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 0.0020 chunk 187 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS D 189 GLN D 310 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.177 18291 Z= 0.246 Angle : 0.553 13.317 25123 Z= 0.289 Chirality : 0.044 0.153 2934 Planarity : 0.004 0.098 2989 Dihedral : 6.838 91.174 2983 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.33 % 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: -0.74 (0.18), residues: 2070 helix: 0.46 (0.23), residues: 546 sheet: -0.45 (0.28), residues: 366 loop : -0.94 (0.18), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 2.053 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 118 average time/residue: 0.2640 time to fit residues: 51.5046 Evaluate side-chains 109 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1983 time to fit residues: 3.2966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 0.0970 chunk 209 optimal weight: 40.0000 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN D 338 HIS E 96 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.129 18291 Z= 0.154 Angle : 0.511 13.996 25123 Z= 0.262 Chirality : 0.042 0.145 2934 Planarity : 0.004 0.065 2989 Dihedral : 6.610 93.056 2983 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.22 % 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: -0.59 (0.18), residues: 2070 helix: 0.68 (0.23), residues: 546 sheet: -0.46 (0.28), residues: 342 loop : -0.86 (0.18), residues: 1182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 2.591 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 123 average time/residue: 0.2527 time to fit residues: 51.6999 Evaluate side-chains 112 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1635 time to fit residues: 3.4404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.127346 restraints weight = 28181.947| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.35 r_work: 0.3885 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.3845 rms_B_bonded: 2.24 restraints_weight: 0.1250 r_work: 0.3820 rms_B_bonded: 2.48 restraints_weight: 0.0625 r_work: 0.3788 rms_B_bonded: 2.87 restraints_weight: 0.0312 r_work: 0.3747 rms_B_bonded: 3.48 restraints_weight: 0.0156 r_work: 0.3690 rms_B_bonded: 4.44 restraints_weight: 0.0078 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.119 18291 Z= 0.152 Angle : 0.510 14.573 25123 Z= 0.259 Chirality : 0.043 0.183 2934 Planarity : 0.004 0.047 2989 Dihedral : 6.563 92.360 2983 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.22 % 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: -0.53 (0.18), residues: 2070 helix: 0.75 (0.23), residues: 546 sheet: -0.48 (0.28), residues: 342 loop : -0.82 (0.18), residues: 1182 =============================================================================== Job complete usr+sys time: 2596.39 seconds wall clock time: 49 minutes 3.30 seconds (2943.30 seconds total)