Starting phenix.real_space_refine on Sat Sep 28 02:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/09_2024/7tqv_26073.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/09_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_26073/09_2024/7tqv_26073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/09_2024/7tqv_26073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/09_2024/7tqv_26073.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqv_26073/09_2024/7tqv_26073.cif" } 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. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 10.64, per 1000 atoms: 0.60 Number of scatterers: 17792 At special positions: 0 Unit cell: (111.187, 133.786, 140.114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 66 15.00 O 3606 8.00 N 2899 7.00 C 11160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.2 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: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.619A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 77 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.619A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 227 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 299 through 309 removed outlier: 3.513A pdb=" N GLU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 77 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.785A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.683A pdb=" N GLU A 265 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.349A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 343 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU B 265 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 316 through 323 Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU C 265 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323 Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267 removed outlier: 3.681A pdb=" N GLU D 265 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 316 through 323 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'E' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU E 265 " --> pdb=" O THR E 282 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 316 through 323 Processing sheet with id=AD9, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AE5, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.683A pdb=" N GLU F 265 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323 662 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 5.21 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: 0.00 - 1.51: 24891 1.51 - 3.02: 205 3.02 - 4.54: 26 4.54 - 6.05: 0 6.05 - 7.56: 1 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 3.040 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.163 3.040 nonbonded pdb=" O GLY D 77 " pdb=" OG1 THR D 121 " model vdw 2.164 3.040 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.164 3.040 nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.164 3.040 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = (chain 'C' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C \ or name O or name CB )) or resid 2 through 345)) selection = chain '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: 1.000 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: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 45.770 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.500 ------------------------------------------------------------------------------- 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 : 1.857 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: 0.3174 time to fit residues: 169.5191 Evaluate side-chains 156 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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: 0.9980 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.0050 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 overall best weight: 2.0598 ------------------------------------------------------------------------------- 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 176 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS B 5 ASN B 176 GLN C 5 ASN C 164 ASN C 176 GLN D 176 GLN D 209 GLN D 338 HIS E 5 ASN ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN F 75 ASN F 164 ASN F 176 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18291 Z= 0.222 Angle : 0.532 9.369 25123 Z= 0.283 Chirality : 0.044 0.176 2934 Planarity : 0.004 0.047 2989 Dihedral : 12.761 94.819 3211 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.83 % Allowed : 8.06 % Favored : 89.11 % 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: -0.39 (0.19), residues: 2070 helix: 0.29 (0.21), residues: 546 sheet: 0.23 (0.31), residues: 360 loop : -0.64 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 333 HIS 0.009 0.001 HIS B 338 PHE 0.021 0.002 PHE C 214 TYR 0.015 0.002 TYR C 343 ARG 0.005 0.001 ARG F 136 *********************** 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 228 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7224 (t) cc_final: 0.6929 (p) REVERT: A 205 LYS cc_start: 0.8413 (mttm) cc_final: 0.7926 (pttt) REVERT: B 92 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7308 (t0) REVERT: C 34 THR cc_start: 0.8551 (t) cc_final: 0.8327 (m) REVERT: C 111 LYS cc_start: 0.8392 (mttt) cc_final: 0.8177 (mtpt) REVERT: C 225 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8159 (ttm110) REVERT: D 12 ASN cc_start: 0.8037 (m-40) cc_final: 0.7645 (t0) REVERT: D 13 LYS cc_start: 0.7695 (mttm) cc_final: 0.7094 (tptt) REVERT: D 205 LYS cc_start: 0.7621 (mttm) cc_final: 0.7137 (ptpp) REVERT: D 343 TYR cc_start: 0.7323 (p90) cc_final: 0.6645 (p90) REVERT: E 34 THR cc_start: 0.8503 (t) cc_final: 0.8250 (m) REVERT: E 116 ILE cc_start: 0.7138 (tt) cc_final: 0.6825 (tp) REVERT: E 338 HIS cc_start: 0.4126 (OUTLIER) cc_final: 0.3275 (t-170) REVERT: F 180 TYR cc_start: 0.7080 (m-80) cc_final: 0.6556 (m-80) REVERT: F 226 TYR cc_start: 0.6827 (m-80) cc_final: 0.6484 (m-80) outliers start: 52 outliers final: 25 residues processed: 218 average time/residue: 0.2914 time to fit residues: 99.5627 Evaluate side-chains 151 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 31 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 217 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 312 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 31 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** 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 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18291 Z= 0.350 Angle : 0.610 10.667 25123 Z= 0.322 Chirality : 0.046 0.171 2934 Planarity : 0.004 0.040 2989 Dihedral : 12.959 93.565 3209 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.05 % Allowed : 10.67 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2070 helix: 0.01 (0.22), residues: 552 sheet: -0.23 (0.29), residues: 360 loop : -0.94 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 87 HIS 0.010 0.001 HIS F 96 PHE 0.032 0.002 PHE F 222 TYR 0.022 0.002 TYR C 343 ARG 0.005 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 193 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8484 (mttm) cc_final: 0.7952 (pttt) REVERT: A 233 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 297 ASP cc_start: 0.7716 (t70) cc_final: 0.7468 (p0) REVERT: A 331 MET cc_start: 0.7495 (mmm) cc_final: 0.7016 (tpt) REVERT: B 92 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7251 (t70) REVERT: C 225 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8045 (ttm110) REVERT: D 205 LYS cc_start: 0.7617 (mttm) cc_final: 0.7051 (ptpp) REVERT: D 343 TYR cc_start: 0.7328 (p90) cc_final: 0.6693 (p90) REVERT: E 116 ILE cc_start: 0.7484 (tt) cc_final: 0.7230 (tp) REVERT: E 173 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7797 (m) REVERT: E 270 ILE cc_start: 0.7929 (mt) cc_final: 0.7720 (tt) REVERT: E 338 HIS cc_start: 0.3753 (OUTLIER) cc_final: 0.2976 (t-170) REVERT: F 30 ASN cc_start: 0.8531 (m-40) cc_final: 0.8016 (t0) REVERT: F 180 TYR cc_start: 0.7245 (m-80) cc_final: 0.6423 (m-80) REVERT: F 194 TYR cc_start: 0.7121 (m-80) cc_final: 0.6403 (m-80) REVERT: F 226 TYR cc_start: 0.7150 (m-80) cc_final: 0.6861 (m-10) outliers start: 56 outliers final: 37 residues processed: 182 average time/residue: 0.2695 time to fit residues: 77.3167 Evaluate side-chains 155 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 114 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 79 ASP 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 295 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL 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 291 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 106 THR 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 31 THR Chi-restraints excluded: chain F residue 102 VAL 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 Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 0.0170 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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** ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18291 Z= 0.166 Angle : 0.489 9.319 25123 Z= 0.255 Chirality : 0.043 0.136 2934 Planarity : 0.004 0.035 2989 Dihedral : 12.795 95.391 3208 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.23 % Allowed : 11.98 % 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: -0.68 (0.18), residues: 2070 helix: 0.40 (0.22), residues: 552 sheet: -0.29 (0.28), residues: 360 loop : -0.90 (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 250 PHE 0.018 0.001 PHE C 214 TYR 0.014 0.001 TYR C 343 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 173 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 1.741 Fit side-chains REVERT: A 186 VAL cc_start: 0.7370 (t) cc_final: 0.7073 (p) REVERT: A 205 LYS cc_start: 0.8473 (mttm) cc_final: 0.7941 (pttt) REVERT: A 331 MET cc_start: 0.7558 (mmm) cc_final: 0.7184 (tpt) REVERT: B 240 ASP cc_start: 0.5056 (p0) cc_final: 0.4728 (p0) REVERT: C 111 LYS cc_start: 0.8402 (mttt) cc_final: 0.8044 (mtpp) REVERT: C 215 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6208 (mp) REVERT: C 225 ARG cc_start: 0.8457 (ttm170) cc_final: 0.8138 (ttm110) REVERT: D 205 LYS cc_start: 0.7628 (mttm) cc_final: 0.7031 (ptpp) REVERT: D 331 MET cc_start: 0.4882 (tmm) cc_final: 0.4521 (tmm) REVERT: D 343 TYR cc_start: 0.7316 (p90) cc_final: 0.6797 (p90) REVERT: E 34 THR cc_start: 0.8586 (t) cc_final: 0.8302 (m) REVERT: E 105 MET cc_start: 0.7270 (tpp) cc_final: 0.6943 (tpp) REVERT: E 116 ILE cc_start: 0.7442 (tt) cc_final: 0.7204 (tp) REVERT: E 338 HIS cc_start: 0.3505 (OUTLIER) cc_final: 0.3102 (t-170) REVERT: F 30 ASN cc_start: 0.8432 (m-40) cc_final: 0.7965 (t0) REVERT: F 37 ASP cc_start: 0.7174 (t70) cc_final: 0.6947 (t0) REVERT: F 180 TYR cc_start: 0.7225 (m-80) cc_final: 0.6524 (m-80) REVERT: F 194 TYR cc_start: 0.6966 (m-80) cc_final: 0.6287 (m-80) outliers start: 41 outliers final: 27 residues processed: 162 average time/residue: 0.2658 time to fit residues: 68.4074 Evaluate side-chains 144 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 99 THR 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 296 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 92 ASP 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 312 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 151 optimal weight: 0.0870 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** E 96 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4202 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= 0.126 Angle : 0.472 10.434 25123 Z= 0.245 Chirality : 0.043 0.396 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.708 95.588 3208 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.34 % Allowed : 11.87 % 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: -0.52 (0.18), residues: 2070 helix: 0.62 (0.22), residues: 552 sheet: -0.29 (0.28), residues: 360 loop : -0.81 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 87 HIS 0.004 0.000 HIS C 250 PHE 0.018 0.001 PHE F 222 TYR 0.025 0.001 TYR D 238 ARG 0.005 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 180 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7353 (t) cc_final: 0.7088 (p) REVERT: A 205 LYS cc_start: 0.8469 (mttm) cc_final: 0.7962 (pttt) REVERT: B 240 ASP cc_start: 0.5130 (p0) cc_final: 0.4686 (p0) REVERT: C 111 LYS cc_start: 0.8365 (mttt) cc_final: 0.8032 (mtpp) REVERT: C 215 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6341 (mp) REVERT: C 225 ARG cc_start: 0.8429 (ttm170) cc_final: 0.7989 (ttm110) REVERT: D 205 LYS cc_start: 0.7634 (mttm) cc_final: 0.7014 (ptpp) REVERT: D 210 MET cc_start: 0.6475 (mtp) cc_final: 0.6265 (mtp) REVERT: D 331 MET cc_start: 0.4766 (tmm) cc_final: 0.4409 (tmm) REVERT: D 343 TYR cc_start: 0.7257 (p90) cc_final: 0.6724 (p90) REVERT: E 34 THR cc_start: 0.8515 (t) cc_final: 0.8283 (m) REVERT: E 80 ILE cc_start: 0.8459 (tt) cc_final: 0.8169 (pt) REVERT: E 116 ILE cc_start: 0.7341 (tt) cc_final: 0.7135 (tp) REVERT: E 338 HIS cc_start: 0.3480 (OUTLIER) cc_final: 0.3148 (t-170) REVERT: F 30 ASN cc_start: 0.8438 (m-40) cc_final: 0.8047 (t0) REVERT: F 37 ASP cc_start: 0.7182 (t70) cc_final: 0.6965 (t0) REVERT: F 180 TYR cc_start: 0.7121 (m-80) cc_final: 0.6513 (m-80) outliers start: 43 outliers final: 29 residues processed: 171 average time/residue: 0.2634 time to fit residues: 71.5964 Evaluate side-chains 155 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 99 THR 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 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET 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 E residue 106 THR Chi-restraints excluded: chain E residue 113 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 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL 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: 2.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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** D 338 HIS ** 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: 0.7019 moved from start: 0.4414 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= 0.193 Angle : 0.493 10.203 25123 Z= 0.256 Chirality : 0.044 0.351 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.738 94.193 3207 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 12.85 % Favored : 84.76 % 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: 0.63 (0.23), residues: 552 sheet: -0.37 (0.28), residues: 360 loop : -0.82 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS C 96 PHE 0.023 0.001 PHE E 222 TYR 0.014 0.001 TYR D 238 ARG 0.004 0.000 ARG D 258 *********************** 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 169 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7378 (t) cc_final: 0.7095 (p) REVERT: A 205 LYS cc_start: 0.8481 (mttm) cc_final: 0.7951 (pttt) REVERT: B 240 ASP cc_start: 0.5207 (p0) cc_final: 0.4710 (p0) REVERT: C 215 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6319 (mp) REVERT: C 225 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8086 (ttm110) REVERT: D 205 LYS cc_start: 0.7633 (mttm) cc_final: 0.7024 (ptpp) REVERT: D 249 LEU cc_start: 0.6801 (mt) cc_final: 0.6227 (mm) REVERT: D 331 MET cc_start: 0.4778 (tmm) cc_final: 0.4401 (tmm) REVERT: D 343 TYR cc_start: 0.7246 (p90) cc_final: 0.6756 (p90) REVERT: E 105 MET cc_start: 0.7254 (tpp) cc_final: 0.6989 (tpp) REVERT: E 116 ILE cc_start: 0.7483 (tt) cc_final: 0.7231 (tp) REVERT: E 333 TRP cc_start: 0.5295 (m100) cc_final: 0.4991 (m100) REVERT: E 338 HIS cc_start: 0.3422 (OUTLIER) cc_final: 0.3180 (t-170) REVERT: F 30 ASN cc_start: 0.8428 (m-40) cc_final: 0.8033 (t0) REVERT: F 37 ASP cc_start: 0.7123 (t70) cc_final: 0.6893 (t0) REVERT: F 180 TYR cc_start: 0.7168 (m-80) cc_final: 0.6560 (m-80) REVERT: F 194 TYR cc_start: 0.7079 (m-10) cc_final: 0.6233 (m-80) outliers start: 44 outliers final: 34 residues processed: 160 average time/residue: 0.2509 time to fit residues: 64.8018 Evaluate side-chains 150 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 99 THR 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 122 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET 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 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 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 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS 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: 1.9990 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 0.0040 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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** D 338 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18291 Z= 0.190 Angle : 0.499 9.200 25123 Z= 0.259 Chirality : 0.044 0.332 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.754 94.163 3207 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.40 % Allowed : 13.45 % 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: -0.57 (0.18), residues: 2070 helix: 0.57 (0.23), residues: 552 sheet: -0.44 (0.27), residues: 378 loop : -0.80 (0.18), residues: 1140 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 0.014 0.001 TYR F 325 ARG 0.003 0.000 ARG F 136 *********************** 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 163 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 1.865 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7365 (t) cc_final: 0.7085 (p) REVERT: A 205 LYS cc_start: 0.8497 (mttm) cc_final: 0.7964 (pttt) REVERT: A 233 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 331 MET cc_start: 0.7253 (tpp) cc_final: 0.7026 (tpp) REVERT: B 240 ASP cc_start: 0.5174 (p0) cc_final: 0.4640 (p0) REVERT: C 215 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6372 (mp) REVERT: C 225 ARG cc_start: 0.8403 (ttm170) cc_final: 0.8021 (ttm110) REVERT: D 205 LYS cc_start: 0.7585 (mttm) cc_final: 0.6994 (ptpp) REVERT: D 249 LEU cc_start: 0.6724 (mt) cc_final: 0.6160 (mm) REVERT: D 331 MET cc_start: 0.4848 (tmm) cc_final: 0.4483 (tmm) REVERT: D 343 TYR cc_start: 0.7291 (p90) cc_final: 0.6789 (p90) REVERT: E 105 MET cc_start: 0.7241 (tpp) cc_final: 0.6995 (tpp) REVERT: E 116 ILE cc_start: 0.7478 (tt) cc_final: 0.7222 (tp) REVERT: E 173 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7797 (m) REVERT: E 333 TRP cc_start: 0.5286 (m100) cc_final: 0.4999 (m100) REVERT: E 338 HIS cc_start: 0.3433 (OUTLIER) cc_final: 0.3217 (t-170) REVERT: F 30 ASN cc_start: 0.8414 (m-40) cc_final: 0.7999 (t0) REVERT: F 37 ASP cc_start: 0.7131 (t70) cc_final: 0.6887 (t0) outliers start: 44 outliers final: 35 residues processed: 154 average time/residue: 0.2539 time to fit residues: 63.5166 Evaluate side-chains 150 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 99 THR 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 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET 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 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 VAL 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 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS 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: 20.0000 chunk 80 optimal weight: 0.0980 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 338 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18291 Z= 0.264 Angle : 0.538 9.061 25123 Z= 0.281 Chirality : 0.045 0.320 2934 Planarity : 0.004 0.030 2989 Dihedral : 12.869 93.359 3207 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.67 % Allowed : 13.77 % Favored : 83.56 % 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: -0.79 (0.18), residues: 2070 helix: 0.36 (0.22), residues: 552 sheet: -0.62 (0.27), residues: 360 loop : -0.90 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 87 HIS 0.006 0.001 HIS C 96 PHE 0.028 0.002 PHE E 233 TYR 0.017 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 159 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 110 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7441 (t) cc_final: 0.7123 (p) REVERT: A 205 LYS cc_start: 0.8473 (mttm) cc_final: 0.7901 (pttt) REVERT: A 233 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8056 (t80) REVERT: B 240 ASP cc_start: 0.5375 (p0) cc_final: 0.4845 (p0) REVERT: C 215 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6326 (mp) REVERT: C 225 ARG cc_start: 0.8427 (ttm170) cc_final: 0.7999 (ttm110) REVERT: D 12 ASN cc_start: 0.7613 (m-40) cc_final: 0.7164 (t0) REVERT: D 205 LYS cc_start: 0.7606 (mttm) cc_final: 0.7021 (ptpp) REVERT: D 249 LEU cc_start: 0.6820 (mt) cc_final: 0.6305 (mt) REVERT: D 331 MET cc_start: 0.4866 (tmm) cc_final: 0.4476 (tmm) REVERT: D 343 TYR cc_start: 0.7248 (p90) cc_final: 0.6763 (p90) REVERT: E 105 MET cc_start: 0.7274 (tpp) cc_final: 0.7031 (tpp) REVERT: E 116 ILE cc_start: 0.7489 (tt) cc_final: 0.7220 (tp) REVERT: E 173 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7956 (m) REVERT: E 219 MET cc_start: 0.7238 (pmm) cc_final: 0.6708 (ptm) REVERT: E 333 TRP cc_start: 0.5433 (m100) cc_final: 0.5137 (m-10) REVERT: F 30 ASN cc_start: 0.8412 (m-40) cc_final: 0.7967 (t0) REVERT: F 37 ASP cc_start: 0.7283 (t70) cc_final: 0.6984 (t0) outliers start: 49 outliers final: 34 residues processed: 149 average time/residue: 0.2577 time to fit residues: 62.4772 Evaluate side-chains 145 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 99 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 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR 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 E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL 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 F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18291 Z= 0.274 Angle : 0.546 8.854 25123 Z= 0.284 Chirality : 0.045 0.306 2934 Planarity : 0.004 0.031 2989 Dihedral : 12.932 93.479 3205 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.61 % Allowed : 13.72 % Favored : 83.67 % 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: -0.91 (0.18), residues: 2070 helix: 0.28 (0.22), residues: 552 sheet: -0.70 (0.27), residues: 360 loop : -0.98 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 87 HIS 0.010 0.001 HIS E 338 PHE 0.020 0.002 PHE E 222 TYR 0.015 0.002 TYR F 325 ARG 0.003 0.000 ARG D 258 *********************** 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 162 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 2.002 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8576 (m) cc_final: 0.8261 (p) REVERT: A 186 VAL cc_start: 0.7467 (t) cc_final: 0.7143 (p) REVERT: A 205 LYS cc_start: 0.8480 (mttm) cc_final: 0.7903 (pttt) REVERT: A 233 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8014 (t80) REVERT: A 331 MET cc_start: 0.7118 (tpp) cc_final: 0.6777 (tpp) REVERT: B 240 ASP cc_start: 0.5413 (p0) cc_final: 0.4753 (p0) REVERT: C 215 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6242 (mp) REVERT: C 225 ARG cc_start: 0.8459 (ttm170) cc_final: 0.8050 (ttm110) REVERT: D 12 ASN cc_start: 0.7596 (m-40) cc_final: 0.7192 (t0) REVERT: D 205 LYS cc_start: 0.7592 (mttm) cc_final: 0.7041 (ptpp) REVERT: D 249 LEU cc_start: 0.6755 (mt) cc_final: 0.6233 (mt) REVERT: D 331 MET cc_start: 0.4953 (tmm) cc_final: 0.4558 (tmm) REVERT: D 343 TYR cc_start: 0.7256 (p90) cc_final: 0.6771 (p90) REVERT: E 105 MET cc_start: 0.7282 (tpp) cc_final: 0.7036 (tpp) REVERT: E 116 ILE cc_start: 0.7516 (tt) cc_final: 0.7243 (tp) REVERT: E 173 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8075 (m) REVERT: E 219 MET cc_start: 0.7202 (pmm) cc_final: 0.6603 (ptm) REVERT: E 333 TRP cc_start: 0.5542 (m100) cc_final: 0.5294 (m-10) REVERT: F 30 ASN cc_start: 0.8399 (m-40) cc_final: 0.7951 (t0) outliers start: 48 outliers final: 37 residues processed: 154 average time/residue: 0.2523 time to fit residues: 63.2702 Evaluate side-chains 150 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 99 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 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET 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 84 THR 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 291 CYS Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL 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 F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 209 optimal weight: 40.0000 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 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 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18291 Z= 0.168 Angle : 0.500 9.437 25123 Z= 0.258 Chirality : 0.043 0.291 2934 Planarity : 0.004 0.043 2989 Dihedral : 12.837 94.720 3205 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.23 % Allowed : 14.21 % Favored : 83.56 % 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: -0.81 (0.18), residues: 2070 helix: 0.47 (0.23), residues: 552 sheet: -0.70 (0.27), residues: 360 loop : -0.96 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.003 0.001 HIS C 96 PHE 0.022 0.001 PHE E 222 TYR 0.013 0.001 TYR F 325 ARG 0.002 0.000 ARG E 139 ********************** 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 154 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8332 (m) cc_final: 0.8055 (p) REVERT: A 186 VAL cc_start: 0.7380 (t) cc_final: 0.7112 (p) REVERT: A 205 LYS cc_start: 0.8469 (mttm) cc_final: 0.7888 (pttt) REVERT: A 233 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 331 MET cc_start: 0.7095 (tpp) cc_final: 0.6785 (tpp) REVERT: C 215 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6353 (mp) REVERT: C 225 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8055 (ttm110) REVERT: D 205 LYS cc_start: 0.7568 (mttm) cc_final: 0.7012 (ptpp) REVERT: D 249 LEU cc_start: 0.6721 (mt) cc_final: 0.6146 (mt) REVERT: D 331 MET cc_start: 0.4944 (tmm) cc_final: 0.4562 (tmm) REVERT: D 343 TYR cc_start: 0.7244 (p90) cc_final: 0.6766 (p90) REVERT: E 105 MET cc_start: 0.7238 (tpp) cc_final: 0.7002 (tpp) REVERT: E 116 ILE cc_start: 0.7473 (tt) cc_final: 0.7216 (tp) REVERT: E 173 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (m) REVERT: E 231 TYR cc_start: 0.5600 (m-10) cc_final: 0.5306 (m-10) REVERT: E 333 TRP cc_start: 0.5540 (m100) cc_final: 0.5304 (m100) REVERT: F 30 ASN cc_start: 0.8419 (m-40) cc_final: 0.7991 (t0) outliers start: 41 outliers final: 34 residues processed: 146 average time/residue: 0.2577 time to fit residues: 60.8278 Evaluate side-chains 146 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 99 THR 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 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET 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 106 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 VAL 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 F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** C 164 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126807 restraints weight = 27647.399| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.28 r_work: 0.3721 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5166 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= 0.154 Angle : 0.499 9.405 25123 Z= 0.258 Chirality : 0.043 0.286 2934 Planarity : 0.004 0.038 2989 Dihedral : 12.825 94.513 3205 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2070 helix: 0.58 (0.23), residues: 552 sheet: -0.58 (0.27), residues: 354 loop : -0.96 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 87 HIS 0.003 0.001 HIS C 250 PHE 0.028 0.001 PHE B 241 TYR 0.013 0.001 TYR F 325 ARG 0.003 0.000 ARG F 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.03 seconds wall clock time: 58 minutes 38.08 seconds (3518.08 seconds total)