Starting phenix.real_space_refine on Sun Mar 17 13:15:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/03_2024/7tqv_26073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/03_2024/7tqv_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_26073/03_2024/7tqv_26073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/03_2024/7tqv_26073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/03_2024/7tqv_26073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/03_2024/7tqv_26073.pdb" } resolution = 3.43 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= 0.029 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 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. 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-5265/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: {'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 31} Chain: "H" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 691 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 20} Link IDs: {'rna3p': 32} Time building chain proxies: 8.89, per 1000 atoms: 0.50 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: 7.07 Conformation dependent library (CDL) restraints added in 2.8 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: 6.24 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: 5.99 Time building geometry restraints manager: 7.59 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: 10607 18.94 - 37.87: 254 37.87 - 56.81: 76 56.81 - 75.75: 76 75.75 - 94.68: 1 Dihedral angle restraints: 11014 sinusoidal: 4983 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 11011 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 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.590 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 51.320 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 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 : 10.867 94.682 7126 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 % Allowed : 4.14 % Favored : 95.05 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 87 HIS 0.002 0.001 HIS D 15 PHE 0.006 0.001 PHE D 44 TYR 0.008 0.001 TYR A 325 ARG 0.001 0.000 ARG F 199 *********************** 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 : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8754 (m) cc_final: 0.8522 (m) REVERT: A 166 VAL cc_start: 0.8174 (t) cc_final: 0.7939 (p) REVERT: A 186 VAL cc_start: 0.7468 (t) cc_final: 0.7182 (p) REVERT: A 205 LYS cc_start: 0.8242 (mttm) cc_final: 0.7808 (pttt) REVERT: C 105 MET cc_start: 0.7703 (tmm) cc_final: 0.7399 (tmm) REVERT: C 162 SER cc_start: 0.8454 (t) cc_final: 0.7931 (p) REVERT: C 225 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8075 (ttm110) REVERT: D 12 ASN cc_start: 0.8078 (m-40) cc_final: 0.7728 (t0) REVERT: D 110 LYS cc_start: 0.7443 (mttt) cc_final: 0.6709 (tptp) REVERT: D 205 LYS cc_start: 0.7621 (mttm) cc_final: 0.7210 (ptpp) REVERT: D 331 MET cc_start: 0.4884 (tpp) cc_final: 0.4249 (tpp) REVERT: D 343 TYR cc_start: 0.6999 (p90) cc_final: 0.6460 (p90) REVERT: E 34 THR cc_start: 0.8498 (t) cc_final: 0.8127 (m) REVERT: E 92 ASP cc_start: 0.7803 (m-30) cc_final: 0.7138 (t0) REVERT: E 106 THR cc_start: 0.8365 (p) cc_final: 0.8109 (t) REVERT: E 116 ILE cc_start: 0.7163 (tt) cc_final: 0.6903 (tp) REVERT: E 338 HIS cc_start: 0.4238 (OUTLIER) cc_final: 0.3388 (t-170) REVERT: F 220 ASP cc_start: 0.6944 (m-30) cc_final: 0.6630 (p0) REVERT: F 312 LEU cc_start: 0.0666 (OUTLIER) cc_final: 0.0447 (pt) outliers start: 15 outliers final: 2 residues processed: 365 average time/residue: 0.3213 time to fit residues: 170.9727 Evaluate side-chains 156 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 312 LEU 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: 5.9990 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: 10.0000 chunk 100 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS B 5 ASN B 176 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 75 ASN F 164 ASN F 176 GLN F 310 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18291 Z= 0.175 Angle : 0.500 9.627 25123 Z= 0.264 Chirality : 0.043 0.179 2934 Planarity : 0.004 0.046 2989 Dihedral : 12.719 92.054 3211 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.45 % Allowed : 8.55 % Favored : 89.00 % 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: 0.33 (0.22), residues: 552 sheet: 0.34 (0.31), residues: 360 loop : -0.54 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 333 HIS 0.009 0.001 HIS B 338 PHE 0.021 0.001 PHE C 214 TYR 0.012 0.001 TYR A 226 ARG 0.008 0.001 ARG C 139 *********************** 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 216 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7262 (t) cc_final: 0.6972 (p) REVERT: A 205 LYS cc_start: 0.8370 (mttm) cc_final: 0.7917 (pttt) REVERT: B 92 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7292 (t0) REVERT: C 34 THR cc_start: 0.8480 (t) cc_final: 0.8264 (m) REVERT: C 105 MET cc_start: 0.7361 (tmm) cc_final: 0.7044 (tmm) REVERT: C 111 LYS cc_start: 0.8393 (mttt) cc_final: 0.8186 (mtpt) REVERT: C 225 ARG cc_start: 0.8468 (ttm170) cc_final: 0.8162 (ttm110) REVERT: D 85 VAL cc_start: 0.8214 (t) cc_final: 0.7981 (p) REVERT: D 205 LYS cc_start: 0.7603 (mttm) cc_final: 0.7133 (ptpp) REVERT: D 343 TYR cc_start: 0.7278 (p90) cc_final: 0.6678 (p90) REVERT: E 34 THR cc_start: 0.8452 (t) cc_final: 0.8155 (m) REVERT: E 42 GLU cc_start: 0.7356 (tt0) cc_final: 0.7093 (tt0) REVERT: E 116 ILE cc_start: 0.7088 (tt) cc_final: 0.6778 (tp) REVERT: E 338 HIS cc_start: 0.4228 (OUTLIER) cc_final: 0.3335 (t-170) REVERT: F 180 TYR cc_start: 0.6907 (m-80) cc_final: 0.6647 (m-80) REVERT: F 226 TYR cc_start: 0.6759 (m-80) cc_final: 0.6409 (m-80) REVERT: F 325 TYR cc_start: 0.6292 (m-80) cc_final: 0.5914 (m-80) outliers start: 45 outliers final: 21 residues processed: 209 average time/residue: 0.2770 time to fit residues: 89.6299 Evaluate side-chains 147 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 206 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 209 GLN D 75 ASN D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 18291 Z= 0.463 Angle : 0.678 10.242 25123 Z= 0.360 Chirality : 0.049 0.155 2934 Planarity : 0.005 0.057 2989 Dihedral : 13.116 89.423 3209 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.54 % Allowed : 10.67 % Favored : 85.79 % 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: -0.96 (0.18), residues: 2070 helix: -0.30 (0.21), residues: 552 sheet: -0.25 (0.28), residues: 378 loop : -0.90 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 87 HIS 0.012 0.001 HIS F 96 PHE 0.028 0.003 PHE F 222 TYR 0.026 0.003 TYR D 325 ARG 0.006 0.001 ARG A 207 *********************** 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 197 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 132 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8460 (mttm) cc_final: 0.7910 (pttt) REVERT: A 233 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 331 MET cc_start: 0.7478 (mmm) cc_final: 0.7067 (tpt) REVERT: B 92 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7270 (t70) REVERT: C 34 THR cc_start: 0.8740 (t) cc_final: 0.8522 (m) REVERT: C 105 MET cc_start: 0.7784 (tmm) cc_final: 0.7400 (tmm) REVERT: C 225 ARG cc_start: 0.8490 (ttm170) cc_final: 0.8120 (ttm110) REVERT: D 205 LYS cc_start: 0.7585 (mttm) cc_final: 0.7029 (ptpp) REVERT: D 343 TYR cc_start: 0.7327 (p90) cc_final: 0.6827 (p90) REVERT: E 92 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8157 (t0) REVERT: E 116 ILE cc_start: 0.7449 (tt) cc_final: 0.7160 (tp) REVERT: E 338 HIS cc_start: 0.3511 (OUTLIER) cc_final: 0.2899 (t-170) REVERT: F 139 ARG cc_start: 0.7795 (ttt90) cc_final: 0.7416 (ttt-90) outliers start: 65 outliers final: 37 residues processed: 186 average time/residue: 0.2788 time to fit residues: 83.4318 Evaluate side-chains 151 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 209 GLN D 189 GLN E 176 GLN ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18291 Z= 0.149 Angle : 0.488 9.536 25123 Z= 0.255 Chirality : 0.043 0.193 2934 Planarity : 0.003 0.039 2989 Dihedral : 12.826 93.345 3209 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.61 % Allowed : 11.87 % Favored : 85.52 % 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: -0.71 (0.18), residues: 2070 helix: 0.25 (0.22), residues: 552 sheet: -0.27 (0.28), residues: 360 loop : -0.86 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.005 0.001 HIS C 250 PHE 0.020 0.001 PHE C 214 TYR 0.018 0.001 TYR D 238 ARG 0.004 0.000 ARG E 139 *********************** 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 180 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8452 (mttm) cc_final: 0.7956 (pttt) REVERT: C 31 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7392 (p) REVERT: C 105 MET cc_start: 0.7480 (tmm) cc_final: 0.7075 (tmm) REVERT: C 211 GLU cc_start: 0.7783 (tp30) cc_final: 0.7208 (mp0) REVERT: C 215 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6105 (mp) REVERT: C 225 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8085 (ttm110) REVERT: D 205 LYS cc_start: 0.7613 (mttm) cc_final: 0.7043 (ptpp) REVERT: D 331 MET cc_start: 0.4600 (tmm) cc_final: 0.4261 (tmm) REVERT: D 343 TYR cc_start: 0.7307 (p90) cc_final: 0.6880 (p90) REVERT: E 105 MET cc_start: 0.7240 (tpp) cc_final: 0.6835 (tpp) REVERT: E 116 ILE cc_start: 0.7424 (tt) cc_final: 0.7137 (tp) REVERT: E 338 HIS cc_start: 0.3454 (OUTLIER) cc_final: 0.3007 (t-170) REVERT: F 37 ASP cc_start: 0.7065 (t70) cc_final: 0.6851 (t0) REVERT: F 180 TYR cc_start: 0.7234 (m-80) cc_final: 0.6586 (m-80) REVERT: F 194 TYR cc_start: 0.7014 (m-80) cc_final: 0.6678 (m-10) REVERT: F 258 ARG cc_start: 0.7354 (tpt170) cc_final: 0.7088 (tpp-160) outliers start: 48 outliers final: 26 residues processed: 168 average time/residue: 0.2634 time to fit residues: 71.1435 Evaluate side-chains 142 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 2 optimal weight: 0.2980 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 182 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN B 137 ASN C 310 GLN D 189 GLN ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6994 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18291 Z= 0.139 Angle : 0.471 9.003 25123 Z= 0.245 Chirality : 0.043 0.453 2934 Planarity : 0.003 0.034 2989 Dihedral : 12.731 93.601 3208 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 12.47 % Favored : 84.98 % 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: -0.56 (0.18), residues: 2070 helix: 0.55 (0.22), residues: 552 sheet: -0.40 (0.28), residues: 348 loop : -0.78 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS C 96 PHE 0.018 0.001 PHE F 222 TYR 0.019 0.001 TYR F 325 ARG 0.006 0.000 ARG F 136 *********************** 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 182 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6961 (t0) REVERT: A 186 VAL cc_start: 0.7334 (t) cc_final: 0.7048 (p) REVERT: A 205 LYS cc_start: 0.8451 (mttm) cc_final: 0.7961 (pttt) REVERT: C 31 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 105 MET cc_start: 0.7456 (tmm) cc_final: 0.7162 (tpp) REVERT: C 215 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6234 (mp) REVERT: C 225 ARG cc_start: 0.8465 (ttm170) cc_final: 0.8047 (ttm110) REVERT: D 205 LYS cc_start: 0.7634 (mttm) cc_final: 0.7029 (ptpp) REVERT: D 258 ARG cc_start: 0.6359 (tpt170) cc_final: 0.6020 (tpt170) REVERT: D 331 MET cc_start: 0.4549 (tmm) cc_final: 0.4196 (tmm) REVERT: D 343 TYR cc_start: 0.7283 (p90) cc_final: 0.6793 (p90) REVERT: E 80 ILE cc_start: 0.8408 (tt) cc_final: 0.8111 (tt) REVERT: E 92 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7984 (t70) REVERT: E 105 MET cc_start: 0.7138 (tpp) cc_final: 0.6837 (tpp) REVERT: E 116 ILE cc_start: 0.7360 (tt) cc_final: 0.7091 (tp) REVERT: F 30 ASN cc_start: 0.8436 (m-40) cc_final: 0.7815 (t0) REVERT: F 180 TYR cc_start: 0.7163 (m-80) cc_final: 0.6617 (m-80) REVERT: F 258 ARG cc_start: 0.7395 (tpt170) cc_final: 0.6793 (mmt180) outliers start: 47 outliers final: 33 residues processed: 171 average time/residue: 0.2735 time to fit residues: 74.3581 Evaluate side-chains 154 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU 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: 0.1980 chunk 40 optimal weight: 0.0970 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- 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 ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18291 Z= 0.206 Angle : 0.502 9.836 25123 Z= 0.260 Chirality : 0.044 0.359 2934 Planarity : 0.003 0.031 2989 Dihedral : 12.782 92.383 3205 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.72 % Allowed : 13.12 % Favored : 84.16 % 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: 0.51 (0.23), residues: 552 sheet: -0.36 (0.27), residues: 360 loop : -0.84 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 87 HIS 0.004 0.001 HIS C 96 PHE 0.018 0.001 PHE F 222 TYR 0.015 0.001 TYR C 343 ARG 0.005 0.000 ARG F 136 *********************** 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 175 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8426 (m) cc_final: 0.8176 (p) REVERT: A 186 VAL cc_start: 0.7446 (t) cc_final: 0.7149 (p) REVERT: A 205 LYS cc_start: 0.8460 (mttm) cc_final: 0.7959 (pttt) REVERT: A 233 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7892 (t80) REVERT: A 331 MET cc_start: 0.7178 (tpp) cc_final: 0.6710 (tpp) REVERT: C 31 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7338 (p) REVERT: C 105 MET cc_start: 0.7538 (tmm) cc_final: 0.7258 (tpp) REVERT: C 215 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6196 (mp) REVERT: C 225 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8037 (ttm110) REVERT: D 205 LYS cc_start: 0.7642 (mttm) cc_final: 0.7022 (ptpp) REVERT: D 249 LEU cc_start: 0.6866 (mt) cc_final: 0.6476 (mt) REVERT: D 325 TYR cc_start: 0.7515 (m-80) cc_final: 0.7215 (m-10) REVERT: D 331 MET cc_start: 0.4692 (tmm) cc_final: 0.4336 (tmm) REVERT: D 343 TYR cc_start: 0.7256 (p90) cc_final: 0.6814 (p90) REVERT: E 80 ILE cc_start: 0.8536 (tt) cc_final: 0.8258 (tt) REVERT: E 105 MET cc_start: 0.7219 (tpp) cc_final: 0.6957 (tpp) REVERT: E 116 ILE cc_start: 0.7392 (tt) cc_final: 0.7096 (tp) REVERT: F 30 ASN cc_start: 0.8461 (m-40) cc_final: 0.7831 (t0) outliers start: 50 outliers final: 39 residues processed: 164 average time/residue: 0.2600 time to fit residues: 69.3866 Evaluate side-chains 156 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ** 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: 0.7014 moved from start: 0.4608 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= 0.158 Angle : 0.478 11.164 25123 Z= 0.246 Chirality : 0.043 0.317 2934 Planarity : 0.003 0.032 2989 Dihedral : 12.747 93.304 3205 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.67 % Allowed : 13.83 % Favored : 83.51 % 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: -0.54 (0.18), residues: 2070 helix: 0.61 (0.23), residues: 552 sheet: -0.36 (0.27), residues: 360 loop : -0.81 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.003 0.001 HIS C 96 PHE 0.026 0.001 PHE C 222 TYR 0.014 0.001 TYR F 325 ARG 0.003 0.000 ARG D 258 *********************** 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 177 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8352 (m) cc_final: 0.8078 (p) REVERT: A 186 VAL cc_start: 0.7397 (t) cc_final: 0.7125 (p) REVERT: A 205 LYS cc_start: 0.8448 (mttm) cc_final: 0.7939 (pttt) REVERT: A 233 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7835 (t80) REVERT: C 31 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7336 (p) REVERT: C 105 MET cc_start: 0.7459 (tmm) cc_final: 0.7166 (tpp) REVERT: C 215 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6342 (mp) REVERT: C 225 ARG cc_start: 0.8414 (ttm170) cc_final: 0.7963 (ttm110) REVERT: D 205 LYS cc_start: 0.7637 (mttm) cc_final: 0.7011 (ptpp) REVERT: D 249 LEU cc_start: 0.6725 (mt) cc_final: 0.6155 (mm) REVERT: D 325 TYR cc_start: 0.7429 (m-80) cc_final: 0.7200 (m-10) REVERT: D 331 MET cc_start: 0.4653 (tmm) cc_final: 0.4313 (tmm) REVERT: D 343 TYR cc_start: 0.7207 (p90) cc_final: 0.6778 (p90) REVERT: E 92 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7984 (t70) REVERT: E 105 MET cc_start: 0.7287 (tpp) cc_final: 0.7067 (tpp) REVERT: E 116 ILE cc_start: 0.7379 (tt) cc_final: 0.7080 (tp) REVERT: F 30 ASN cc_start: 0.8421 (m-40) cc_final: 0.7854 (t0) REVERT: F 180 TYR cc_start: 0.7175 (m-80) cc_final: 0.6637 (m-80) REVERT: F 258 ARG cc_start: 0.7316 (tpt170) cc_final: 0.6739 (mmt180) outliers start: 49 outliers final: 40 residues processed: 164 average time/residue: 0.2577 time to fit residues: 68.2250 Evaluate side-chains 162 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN D 310 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18291 Z= 0.328 Angle : 0.571 12.158 25123 Z= 0.297 Chirality : 0.046 0.308 2934 Planarity : 0.004 0.038 2989 Dihedral : 12.925 90.722 3205 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.83 % Allowed : 14.37 % Favored : 82.80 % 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: -0.78 (0.18), residues: 2070 helix: 0.27 (0.22), residues: 552 sheet: -0.45 (0.27), residues: 366 loop : -0.89 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 87 HIS 0.007 0.001 HIS C 96 PHE 0.031 0.002 PHE E 233 TYR 0.018 0.002 TYR F 325 ARG 0.003 0.000 ARG F 136 *********************** 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 169 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 117 time to evaluate : 1.967 Fit side-chains REVERT: A 107 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7145 (t70) REVERT: A 186 VAL cc_start: 0.7400 (t) cc_final: 0.7086 (p) REVERT: A 205 LYS cc_start: 0.8470 (mttm) cc_final: 0.7864 (pttt) REVERT: A 233 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 331 MET cc_start: 0.7375 (tpp) cc_final: 0.6860 (tpp) REVERT: C 31 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7352 (p) REVERT: C 105 MET cc_start: 0.7768 (tmm) cc_final: 0.7457 (tpp) REVERT: C 215 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6261 (mp) REVERT: C 225 ARG cc_start: 0.8442 (ttm170) cc_final: 0.7963 (ttm110) REVERT: D 205 LYS cc_start: 0.7624 (mttm) cc_final: 0.7057 (ptpp) REVERT: D 331 MET cc_start: 0.4687 (tmm) cc_final: 0.4322 (tmm) REVERT: D 343 TYR cc_start: 0.7303 (p90) cc_final: 0.6928 (p90) REVERT: E 105 MET cc_start: 0.7276 (tpp) cc_final: 0.7058 (tpp) REVERT: E 116 ILE cc_start: 0.7442 (tt) cc_final: 0.7137 (tp) REVERT: F 30 ASN cc_start: 0.8458 (m-40) cc_final: 0.7813 (t0) outliers start: 52 outliers final: 39 residues processed: 156 average time/residue: 0.2615 time to fit residues: 66.1276 Evaluate side-chains 153 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** 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: 0.7070 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18291 Z= 0.217 Angle : 0.519 13.428 25123 Z= 0.267 Chirality : 0.044 0.283 2934 Planarity : 0.003 0.036 2989 Dihedral : 12.865 91.895 3205 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.83 % Allowed : 14.64 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2070 helix: 0.36 (0.22), residues: 552 sheet: -0.64 (0.28), residues: 348 loop : -0.88 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.005 0.001 HIS C 96 PHE 0.029 0.002 PHE C 222 TYR 0.015 0.001 TYR F 325 ARG 0.003 0.000 ARG F 136 *********************** 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 168 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7440 (t) cc_final: 0.7145 (p) REVERT: A 205 LYS cc_start: 0.8454 (mttm) cc_final: 0.7868 (pttt) REVERT: A 233 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 31 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7370 (p) REVERT: C 215 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6344 (mp) REVERT: C 225 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8001 (ttm110) REVERT: D 205 LYS cc_start: 0.7601 (mttm) cc_final: 0.7016 (ptpp) REVERT: D 249 LEU cc_start: 0.6792 (mt) cc_final: 0.6166 (mm) REVERT: D 331 MET cc_start: 0.4677 (tmm) cc_final: 0.4298 (tmm) REVERT: D 343 TYR cc_start: 0.7303 (p90) cc_final: 0.6890 (p90) REVERT: E 105 MET cc_start: 0.7338 (tpp) cc_final: 0.7133 (tpp) REVERT: E 116 ILE cc_start: 0.7420 (tt) cc_final: 0.7120 (tp) REVERT: F 30 ASN cc_start: 0.8488 (m-40) cc_final: 0.7859 (t0) outliers start: 52 outliers final: 46 residues processed: 157 average time/residue: 0.2496 time to fit residues: 63.6275 Evaluate side-chains 161 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 209 optimal weight: 40.0000 chunk 192 optimal weight: 0.0270 chunk 166 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 0.0060 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 96 HIS C 164 ASN 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: 0.6983 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18291 Z= 0.125 Angle : 0.482 14.244 25123 Z= 0.247 Chirality : 0.042 0.282 2934 Planarity : 0.003 0.038 2989 Dihedral : 12.737 94.059 3205 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 15.24 % Favored : 82.47 % 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: -0.58 (0.18), residues: 2070 helix: 0.68 (0.23), residues: 552 sheet: -0.38 (0.27), residues: 354 loop : -0.90 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 87 HIS 0.003 0.000 HIS B 250 PHE 0.027 0.001 PHE C 222 TYR 0.013 0.001 TYR F 325 ARG 0.003 0.000 ARG D 258 ********************** 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 163 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7218 (t0) REVERT: A 186 VAL cc_start: 0.7353 (t) cc_final: 0.7108 (p) REVERT: A 205 LYS cc_start: 0.8436 (mttm) cc_final: 0.7914 (pttt) REVERT: A 210 MET cc_start: 0.6021 (mtt) cc_final: 0.5809 (ttp) REVERT: A 300 LEU cc_start: 0.7387 (tp) cc_final: 0.6971 (tp) REVERT: A 331 MET cc_start: 0.7423 (tpp) cc_final: 0.6801 (tpp) REVERT: C 31 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7384 (p) REVERT: C 215 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6383 (mp) REVERT: C 225 ARG cc_start: 0.8379 (ttm170) cc_final: 0.8009 (ttm110) REVERT: D 205 LYS cc_start: 0.7606 (mttm) cc_final: 0.7010 (ptpp) REVERT: D 331 MET cc_start: 0.4633 (tmm) cc_final: 0.4302 (tmm) REVERT: D 343 TYR cc_start: 0.7272 (p90) cc_final: 0.6867 (p90) REVERT: E 92 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7851 (t70) REVERT: E 116 ILE cc_start: 0.7379 (tt) cc_final: 0.7096 (tp) REVERT: F 30 ASN cc_start: 0.8463 (m-40) cc_final: 0.7913 (t0) outliers start: 42 outliers final: 33 residues processed: 153 average time/residue: 0.2580 time to fit residues: 63.8185 Evaluate side-chains 153 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0808 > 50: distance: 57 - 78: 29.879 distance: 60 - 75: 31.479 distance: 70 - 75: 32.522 distance: 75 - 76: 54.173 distance: 76 - 77: 44.857 distance: 76 - 79: 43.814 distance: 77 - 78: 31.874 distance: 77 - 83: 32.503 distance: 79 - 80: 15.366 distance: 80 - 81: 40.416 distance: 80 - 82: 56.983 distance: 83 - 84: 21.639 distance: 84 - 85: 54.393 distance: 84 - 87: 45.277 distance: 85 - 86: 26.692 distance: 85 - 91: 45.176 distance: 87 - 88: 54.230 distance: 87 - 89: 26.334 distance: 88 - 90: 38.876 distance: 91 - 92: 30.782 distance: 92 - 93: 22.902 distance: 93 - 94: 23.903 distance: 93 - 95: 14.378 distance: 95 - 96: 5.780 distance: 96 - 97: 50.650 distance: 96 - 99: 24.178 distance: 97 - 98: 38.703 distance: 97 - 104: 20.834 distance: 99 - 100: 26.735 distance: 100 - 101: 18.130 distance: 101 - 102: 18.060 distance: 101 - 103: 10.091 distance: 104 - 105: 16.073 distance: 105 - 106: 22.314 distance: 105 - 108: 16.072 distance: 106 - 107: 20.402 distance: 106 - 109: 16.316 distance: 109 - 110: 18.864 distance: 110 - 111: 38.048 distance: 110 - 113: 16.231 distance: 111 - 112: 50.760 distance: 111 - 116: 21.324 distance: 113 - 114: 47.212 distance: 113 - 115: 47.060 distance: 116 - 117: 27.645 distance: 117 - 118: 18.410 distance: 117 - 120: 42.283 distance: 118 - 119: 41.288 distance: 118 - 125: 32.814 distance: 120 - 121: 47.103 distance: 121 - 122: 32.258 distance: 122 - 123: 9.153 distance: 123 - 124: 13.610 distance: 125 - 126: 13.819 distance: 126 - 127: 40.172 distance: 126 - 129: 35.278 distance: 127 - 128: 23.439 distance: 127 - 132: 47.291 distance: 129 - 130: 44.475 distance: 129 - 131: 13.479 distance: 132 - 133: 30.678 distance: 133 - 134: 22.125 distance: 133 - 136: 20.648 distance: 134 - 135: 23.745 distance: 134 - 141: 26.041 distance: 136 - 137: 22.444 distance: 137 - 138: 25.647 distance: 138 - 139: 25.449 distance: 138 - 140: 24.233 distance: 141 - 142: 16.780 distance: 142 - 143: 16.801 distance: 142 - 145: 10.567 distance: 143 - 144: 19.767 distance: 143 - 152: 15.095 distance: 145 - 146: 22.787 distance: 146 - 147: 32.799 distance: 146 - 148: 23.281 distance: 147 - 149: 14.144 distance: 148 - 150: 25.303 distance: 149 - 151: 4.439 distance: 150 - 151: 11.531