Starting phenix.real_space_refine on Sun Jun 15 23:41:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_26073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_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/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_26073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_26073.map" model { file = "/net/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_26073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqv_26073/06_2025/7tqv_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-5710/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: 11.28, per 1000 atoms: 0.63 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: 4.88 Conformation dependent library (CDL) restraints added in 2.3 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: 7.19 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: 7.26 Time building geometry restraints manager: 5.80 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.040 Find NCS groups from input model: 0.880 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.550 ------------------------------------------------------------------------------- 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= 0.107 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 Details of bonding type rmsd hydrogen bonds : bond 0.25034 ( 685) hydrogen bonds : angle 9.08032 ( 1873) covalent geometry : bond 0.00238 (18291) covalent geometry : angle 0.38338 (25123) *********************** 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 to be fit. rotamer outliers: 15 poor density : 350 time to evaluate : 1.926 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: 0.3186 time to fit residues: 170.4600 Evaluate side-chains 156 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.158502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.122991 restraints weight = 27361.256| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.74 r_work: 0.3629 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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= 0.149 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 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 685) hydrogen bonds : angle 5.89553 ( 1873) covalent geometry : bond 0.00343 (18291) covalent geometry : angle 0.53226 (25123) *********************** 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 to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7230 (t) cc_final: 0.6956 (p) REVERT: A 205 LYS cc_start: 0.8240 (mttm) cc_final: 0.7836 (pttt) REVERT: B 92 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 137 ASN cc_start: 0.6253 (m110) cc_final: 0.6036 (m110) REVERT: C 224 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8034 (pt0) REVERT: C 225 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8030 (ttm110) REVERT: D 12 ASN cc_start: 0.8240 (m-40) cc_final: 0.7802 (t0) REVERT: D 13 LYS cc_start: 0.8010 (mttm) cc_final: 0.7476 (tptt) REVERT: D 205 LYS cc_start: 0.7520 (mttm) cc_final: 0.6778 (ptpp) REVERT: D 343 TYR cc_start: 0.6982 (p90) cc_final: 0.6296 (p90) REVERT: E 34 THR cc_start: 0.8536 (t) cc_final: 0.8310 (m) REVERT: E 116 ILE cc_start: 0.7201 (tt) cc_final: 0.6884 (tp) REVERT: E 338 HIS cc_start: 0.4239 (OUTLIER) cc_final: 0.3289 (t-170) REVERT: F 180 TYR cc_start: 0.7302 (m-80) cc_final: 0.6645 (m-80) REVERT: F 226 TYR cc_start: 0.6934 (m-80) cc_final: 0.6414 (m-80) outliers start: 52 outliers final: 25 residues processed: 218 average time/residue: 0.2796 time to fit residues: 95.4343 Evaluate side-chains 150 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 155 optimal weight: 0.0050 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 156 optimal weight: 0.1980 chunk 119 optimal weight: 0.0980 chunk 171 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 5 ASN F 9 ASN F 164 ASN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.161419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126140 restraints weight = 27182.816| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.60 r_work: 0.3692 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3108 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= 0.087 Angle : 0.477 9.821 25123 Z= 0.248 Chirality : 0.042 0.179 2934 Planarity : 0.003 0.028 2989 Dihedral : 12.682 96.535 3209 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.74 % Allowed : 10.29 % Favored : 87.97 % 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: -0.29 (0.18), residues: 2070 helix: 0.60 (0.22), residues: 552 sheet: 0.10 (0.29), residues: 360 loop : -0.64 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 333 HIS 0.003 0.000 HIS B 338 PHE 0.027 0.001 PHE F 222 TYR 0.016 0.001 TYR C 343 ARG 0.004 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 685) hydrogen bonds : angle 5.22256 ( 1873) covalent geometry : bond 0.00191 (18291) covalent geometry : angle 0.47708 (25123) *********************** 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 177 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 2.043 Fit side-chains REVERT: A 186 VAL cc_start: 0.7315 (t) cc_final: 0.7074 (p) REVERT: A 205 LYS cc_start: 0.8231 (mttm) cc_final: 0.7878 (pttt) REVERT: A 331 MET cc_start: 0.7419 (mmm) cc_final: 0.7063 (tpt) REVERT: B 137 ASN cc_start: 0.6070 (m110) cc_final: 0.5845 (m110) REVERT: C 225 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8017 (ttm110) REVERT: C 238 TYR cc_start: 0.6342 (m-80) cc_final: 0.5972 (m-80) REVERT: D 12 ASN cc_start: 0.8006 (m-40) cc_final: 0.7797 (t0) REVERT: D 205 LYS cc_start: 0.7490 (mttm) cc_final: 0.6744 (ptpp) REVERT: D 343 TYR cc_start: 0.7117 (p90) cc_final: 0.6512 (p90) REVERT: E 34 THR cc_start: 0.8406 (t) cc_final: 0.8179 (m) REVERT: E 116 ILE cc_start: 0.7267 (tt) cc_final: 0.7019 (tp) REVERT: E 216 GLU cc_start: 0.7161 (tt0) cc_final: 0.6733 (pt0) REVERT: E 338 HIS cc_start: 0.4256 (OUTLIER) cc_final: 0.3394 (t-170) REVERT: F 37 ASP cc_start: 0.7237 (t70) cc_final: 0.7012 (t0) REVERT: F 180 TYR cc_start: 0.7047 (m-80) cc_final: 0.6561 (m-80) REVERT: F 194 TYR cc_start: 0.6991 (m-80) cc_final: 0.6288 (m-80) REVERT: F 258 ARG cc_start: 0.7460 (tpt170) cc_final: 0.6653 (tpp-160) outliers start: 32 outliers final: 20 residues processed: 167 average time/residue: 0.3013 time to fit residues: 79.2719 Evaluate side-chains 145 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 29 ASN 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 97 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 31 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 D residue 332 LEU 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 338 HIS Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 196 THR 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 154 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN F 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.160625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.125269 restraints weight = 27174.908| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.74 r_work: 0.3672 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3439 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= 0.089 Angle : 0.462 8.523 25123 Z= 0.240 Chirality : 0.042 0.134 2934 Planarity : 0.003 0.028 2989 Dihedral : 12.631 95.521 3208 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 10.07 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2070 helix: 0.78 (0.23), residues: 552 sheet: 0.00 (0.28), residues: 360 loop : -0.63 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 333 HIS 0.002 0.000 HIS B 338 PHE 0.024 0.001 PHE D 241 TYR 0.011 0.001 TYR F 325 ARG 0.003 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 685) hydrogen bonds : angle 4.92896 ( 1873) covalent geometry : bond 0.00200 (18291) covalent geometry : angle 0.46165 (25123) *********************** 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 178 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 2.137 Fit side-chains REVERT: A 12 ASN cc_start: 0.7586 (m-40) cc_final: 0.7374 (m-40) REVERT: A 186 VAL cc_start: 0.7308 (t) cc_final: 0.7061 (p) REVERT: A 205 LYS cc_start: 0.8283 (mttm) cc_final: 0.7896 (pttt) REVERT: A 331 MET cc_start: 0.7500 (mmm) cc_final: 0.7210 (tpt) REVERT: B 137 ASN cc_start: 0.6124 (m110) cc_final: 0.5891 (m110) REVERT: B 240 ASP cc_start: 0.5429 (p0) cc_final: 0.4893 (p0) REVERT: C 215 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6162 (mp) REVERT: C 225 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7937 (ttm110) REVERT: D 205 LYS cc_start: 0.7509 (mttm) cc_final: 0.6736 (ptpp) REVERT: D 331 MET cc_start: 0.4201 (tmm) cc_final: 0.3912 (tmm) REVERT: D 343 TYR cc_start: 0.7129 (p90) cc_final: 0.6667 (p90) REVERT: E 105 MET cc_start: 0.7223 (tpp) cc_final: 0.6846 (tpp) REVERT: E 116 ILE cc_start: 0.7367 (tt) cc_final: 0.7113 (tp) REVERT: E 216 GLU cc_start: 0.7254 (tt0) cc_final: 0.6836 (pt0) REVERT: E 338 HIS cc_start: 0.3918 (OUTLIER) cc_final: 0.3299 (t-170) REVERT: F 37 ASP cc_start: 0.7075 (t70) cc_final: 0.6787 (t0) REVERT: F 180 TYR cc_start: 0.7057 (m-80) cc_final: 0.6499 (m-80) REVERT: F 194 TYR cc_start: 0.6829 (m-80) cc_final: 0.6241 (m-80) REVERT: F 258 ARG cc_start: 0.7464 (tpt170) cc_final: 0.6649 (tpp-160) REVERT: F 325 TYR cc_start: 0.6246 (m-80) cc_final: 0.5824 (m-80) outliers start: 50 outliers final: 31 residues processed: 168 average time/residue: 0.2849 time to fit residues: 75.7042 Evaluate side-chains 149 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 296 ILE Chi-restraints excluded: chain C residue 9 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 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 312 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 92 ASP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 203 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 110 optimal weight: 0.0030 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.0000 chunk 63 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 159 optimal weight: 0.2980 overall best weight: 2.2598 ------------------------------------------------------------------------------- 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 338 HIS ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.120656 restraints weight = 27451.959| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.75 r_work: 0.3597 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3888 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= 0.146 Angle : 0.504 8.894 25123 Z= 0.264 Chirality : 0.043 0.140 2934 Planarity : 0.003 0.028 2989 Dihedral : 12.723 94.228 3208 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.34 % Allowed : 10.83 % Favored : 86.83 % 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: -0.41 (0.18), residues: 2070 helix: 0.61 (0.23), residues: 552 sheet: -0.15 (0.28), residues: 360 loop : -0.71 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 87 HIS 0.004 0.001 HIS F 96 PHE 0.019 0.002 PHE E 222 TYR 0.014 0.001 TYR C 343 ARG 0.006 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 685) hydrogen bonds : angle 4.98625 ( 1873) covalent geometry : bond 0.00345 (18291) covalent geometry : angle 0.50377 (25123) *********************** 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 172 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7926 (m-40) cc_final: 0.7665 (m-40) REVERT: A 186 VAL cc_start: 0.7322 (t) cc_final: 0.7033 (p) REVERT: A 205 LYS cc_start: 0.8296 (mttm) cc_final: 0.7863 (pttt) REVERT: A 331 MET cc_start: 0.7527 (mmm) cc_final: 0.7214 (tpt) REVERT: B 92 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7430 (t70) REVERT: B 137 ASN cc_start: 0.6366 (m110) cc_final: 0.6129 (m110) REVERT: B 240 ASP cc_start: 0.5706 (p0) cc_final: 0.5037 (p0) REVERT: C 215 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5991 (mp) REVERT: C 225 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7924 (ttm110) REVERT: C 279 TYR cc_start: 0.8154 (m-80) cc_final: 0.7882 (m-10) REVERT: C 297 ASP cc_start: 0.7458 (t0) cc_final: 0.7157 (t0) REVERT: D 12 ASN cc_start: 0.7713 (m-40) cc_final: 0.7416 (t0) REVERT: D 205 LYS cc_start: 0.7519 (mttm) cc_final: 0.6725 (ptpp) REVERT: D 331 MET cc_start: 0.4220 (tmm) cc_final: 0.3972 (tmm) REVERT: D 343 TYR cc_start: 0.6948 (p90) cc_final: 0.6135 (p90) REVERT: E 105 MET cc_start: 0.7294 (tpp) cc_final: 0.6943 (tpp) REVERT: E 116 ILE cc_start: 0.7532 (tt) cc_final: 0.7279 (tp) REVERT: E 216 GLU cc_start: 0.7271 (tt0) cc_final: 0.6893 (pt0) REVERT: E 270 ILE cc_start: 0.7696 (mt) cc_final: 0.7466 (tt) REVERT: E 338 HIS cc_start: 0.3900 (OUTLIER) cc_final: 0.3247 (t-170) REVERT: F 37 ASP cc_start: 0.7296 (t70) cc_final: 0.6935 (t0) REVERT: F 180 TYR cc_start: 0.7298 (m-80) cc_final: 0.6558 (m-80) REVERT: F 194 TYR cc_start: 0.6920 (m-80) cc_final: 0.6719 (m-10) outliers start: 43 outliers final: 34 residues processed: 164 average time/residue: 0.2534 time to fit residues: 67.8038 Evaluate side-chains 152 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 208 SER 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 210 MET 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 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 312 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 332 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 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 251 LEU 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 122 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 130 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 207 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 117 optimal weight: 0.0010 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.160991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.127493 restraints weight = 27012.838| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.53 r_work: 0.3715 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18291 Z= 0.087 Angle : 0.460 12.073 25123 Z= 0.239 Chirality : 0.042 0.134 2934 Planarity : 0.003 0.028 2989 Dihedral : 12.658 95.607 3208 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.01 % Allowed : 11.43 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2070 helix: 0.77 (0.23), residues: 552 sheet: -0.18 (0.28), residues: 360 loop : -0.69 (0.18), residues: 1158 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 0.027 0.001 PHE C 222 TYR 0.012 0.001 TYR F 325 ARG 0.004 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.02733 ( 685) hydrogen bonds : angle 4.69793 ( 1873) covalent geometry : bond 0.00195 (18291) covalent geometry : angle 0.45992 (25123) *********************** 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 172 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.963 Fit side-chains REVERT: A 12 ASN cc_start: 0.7577 (m-40) cc_final: 0.7309 (m-40) REVERT: B 240 ASP cc_start: 0.5608 (p0) cc_final: 0.4971 (p0) REVERT: C 215 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6400 (mp) REVERT: C 225 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7958 (ttm110) REVERT: D 205 LYS cc_start: 0.7627 (mttm) cc_final: 0.6927 (ptpp) REVERT: D 216 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6333 (tm-30) REVERT: D 331 MET cc_start: 0.4771 (tmm) cc_final: 0.4517 (tmm) REVERT: D 343 TYR cc_start: 0.7284 (p90) cc_final: 0.6914 (p90) REVERT: E 105 MET cc_start: 0.7212 (tpp) cc_final: 0.6867 (tpp) REVERT: E 116 ILE cc_start: 0.7514 (tt) cc_final: 0.7294 (tp) REVERT: E 216 GLU cc_start: 0.7223 (tt0) cc_final: 0.6995 (pt0) REVERT: E 233 PHE cc_start: 0.7649 (m-10) cc_final: 0.7293 (m-10) REVERT: E 338 HIS cc_start: 0.3576 (OUTLIER) cc_final: 0.3203 (t-170) REVERT: F 37 ASP cc_start: 0.6997 (t70) cc_final: 0.6719 (t0) REVERT: F 180 TYR cc_start: 0.7094 (m-80) cc_final: 0.6521 (m-80) REVERT: F 194 TYR cc_start: 0.7025 (m-80) cc_final: 0.6343 (m-80) REVERT: F 258 ARG cc_start: 0.7551 (tpt170) cc_final: 0.6797 (mmt180) outliers start: 37 outliers final: 27 residues processed: 164 average time/residue: 0.2633 time to fit residues: 69.5154 Evaluate side-chains 148 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 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 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 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 332 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 173 VAL 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 102 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 91 optimal weight: 0.0010 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 201 optimal weight: 0.0040 chunk 202 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.161932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.128737 restraints weight = 27207.608| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.46 r_work: 0.3730 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18291 Z= 0.092 Angle : 0.469 12.772 25123 Z= 0.241 Chirality : 0.042 0.141 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.639 94.856 3208 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.12 % Allowed : 11.98 % Favored : 85.90 % 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: -0.35 (0.18), residues: 2070 helix: 0.83 (0.23), residues: 552 sheet: -0.29 (0.27), residues: 360 loop : -0.70 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS C 15 PHE 0.026 0.001 PHE C 214 TYR 0.012 0.001 TYR F 325 ARG 0.003 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 685) hydrogen bonds : angle 4.64169 ( 1873) covalent geometry : bond 0.00210 (18291) covalent geometry : angle 0.46906 (25123) *********************** 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 165 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 2.254 Fit side-chains REVERT: B 240 ASP cc_start: 0.5609 (p0) cc_final: 0.4980 (p0) REVERT: C 215 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6313 (mp) REVERT: C 225 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7910 (ttm110) REVERT: D 12 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7258 (t0) REVERT: D 205 LYS cc_start: 0.7609 (mttm) cc_final: 0.6901 (ptpp) REVERT: D 216 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6417 (tm-30) REVERT: D 331 MET cc_start: 0.4741 (tmm) cc_final: 0.4498 (tmm) REVERT: D 343 TYR cc_start: 0.7287 (p90) cc_final: 0.6978 (p90) REVERT: E 116 ILE cc_start: 0.7490 (tt) cc_final: 0.7281 (tp) REVERT: E 216 GLU cc_start: 0.7288 (tt0) cc_final: 0.7016 (pt0) REVERT: E 233 PHE cc_start: 0.7657 (m-80) cc_final: 0.7194 (m-10) REVERT: E 338 HIS cc_start: 0.3596 (OUTLIER) cc_final: 0.3241 (t-170) REVERT: F 37 ASP cc_start: 0.6960 (t70) cc_final: 0.6682 (t0) REVERT: F 180 TYR cc_start: 0.7081 (m-80) cc_final: 0.6504 (m-80) REVERT: F 258 ARG cc_start: 0.7551 (tpt170) cc_final: 0.6781 (mmt180) outliers start: 39 outliers final: 30 residues processed: 157 average time/residue: 0.2936 time to fit residues: 73.4895 Evaluate side-chains 144 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 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 210 MET 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 D residue 12 ASN 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 312 LEU Chi-restraints excluded: chain D residue 332 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 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 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR 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 158 optimal weight: 10.0000 chunk 16 optimal weight: 0.0670 chunk 71 optimal weight: 0.0040 chunk 111 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 overall best weight: 0.7534 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.162766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.129676 restraints weight = 27110.160| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.42 r_work: 0.3751 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4394 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= 0.086 Angle : 0.472 12.249 25123 Z= 0.241 Chirality : 0.042 0.149 2934 Planarity : 0.003 0.028 2989 Dihedral : 12.617 94.937 3208 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.29 % Allowed : 12.25 % Favored : 85.47 % 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: -0.34 (0.18), residues: 2070 helix: 0.86 (0.23), residues: 552 sheet: -0.38 (0.27), residues: 360 loop : -0.68 (0.18), residues: 1158 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 0.026 0.001 PHE C 222 TYR 0.012 0.001 TYR F 325 ARG 0.003 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 685) hydrogen bonds : angle 4.56583 ( 1873) covalent geometry : bond 0.00195 (18291) covalent geometry : angle 0.47228 (25123) *********************** 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 162 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.988 Fit side-chains REVERT: B 240 ASP cc_start: 0.5788 (p0) cc_final: 0.5045 (p0) REVERT: C 215 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6352 (mp) REVERT: C 225 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7851 (ttm110) REVERT: D 205 LYS cc_start: 0.7706 (mttm) cc_final: 0.7032 (ptpp) REVERT: D 216 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6376 (tm-30) REVERT: D 331 MET cc_start: 0.4749 (tmm) cc_final: 0.4508 (tmm) REVERT: D 343 TYR cc_start: 0.7278 (p90) cc_final: 0.7015 (p90) REVERT: E 216 GLU cc_start: 0.7502 (tt0) cc_final: 0.7150 (pt0) REVERT: E 233 PHE cc_start: 0.7605 (m-80) cc_final: 0.7127 (m-10) REVERT: E 338 HIS cc_start: 0.3507 (OUTLIER) cc_final: 0.3257 (t-170) REVERT: F 37 ASP cc_start: 0.7056 (t70) cc_final: 0.6737 (t0) REVERT: F 180 TYR cc_start: 0.7260 (m-80) cc_final: 0.6683 (m-80) REVERT: F 258 ARG cc_start: 0.7644 (tpt170) cc_final: 0.6846 (mmt180) outliers start: 42 outliers final: 35 residues processed: 153 average time/residue: 0.2583 time to fit residues: 64.3903 Evaluate side-chains 149 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 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 210 MET 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 296 ILE 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 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 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 251 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 199 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.163369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.130716 restraints weight = 27306.807| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.46 r_work: 0.3753 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18291 Z= 0.083 Angle : 0.479 13.417 25123 Z= 0.242 Chirality : 0.042 0.213 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.610 95.140 3208 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.18 % Allowed : 12.41 % Favored : 85.41 % 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: -0.31 (0.18), residues: 2070 helix: 0.88 (0.23), residues: 552 sheet: -0.43 (0.27), residues: 360 loop : -0.62 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.004 0.000 HIS B 250 PHE 0.027 0.001 PHE C 222 TYR 0.012 0.001 TYR F 325 ARG 0.003 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 685) hydrogen bonds : angle 4.51133 ( 1873) covalent geometry : bond 0.00189 (18291) covalent geometry : angle 0.47927 (25123) *********************** 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 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 2.200 Fit side-chains revert: symmetry clash REVERT: B 240 ASP cc_start: 0.5341 (p0) cc_final: 0.4551 (p0) REVERT: C 215 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6463 (mp) REVERT: C 225 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7956 (ttm110) REVERT: D 205 LYS cc_start: 0.7588 (mttm) cc_final: 0.6845 (ptpp) REVERT: D 216 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6362 (tm-30) REVERT: D 331 MET cc_start: 0.4719 (tmm) cc_final: 0.4507 (tmm) REVERT: D 343 TYR cc_start: 0.7270 (p90) cc_final: 0.7016 (p90) REVERT: E 216 GLU cc_start: 0.7352 (tt0) cc_final: 0.7050 (pt0) REVERT: E 233 PHE cc_start: 0.7611 (m-80) cc_final: 0.7152 (m-10) REVERT: E 333 TRP cc_start: 0.5180 (m100) cc_final: 0.4977 (m100) REVERT: F 37 ASP cc_start: 0.6804 (t70) cc_final: 0.6548 (t0) REVERT: F 180 TYR cc_start: 0.7073 (m-80) cc_final: 0.6559 (m-80) REVERT: F 258 ARG cc_start: 0.7541 (tpt170) cc_final: 0.6740 (mmt180) outliers start: 40 outliers final: 35 residues processed: 149 average time/residue: 0.2631 time to fit residues: 63.4190 Evaluate side-chains 150 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 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 210 MET Chi-restraints excluded: chain B residue 281 ILE 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 296 ILE 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 0.7980 chunk 190 optimal weight: 0.0370 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.0170 chunk 95 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.131271 restraints weight = 27271.098| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.45 r_work: 0.3763 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18291 Z= 0.081 Angle : 0.485 15.152 25123 Z= 0.245 Chirality : 0.042 0.189 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.570 94.766 3206 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.96 % Allowed : 12.52 % 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: -0.29 (0.18), residues: 2070 helix: 0.92 (0.23), residues: 552 sheet: -0.48 (0.27), residues: 360 loop : -0.60 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 87 HIS 0.005 0.001 HIS E 338 PHE 0.028 0.001 PHE E 222 TYR 0.012 0.001 TYR F 325 ARG 0.003 0.000 ARG F 225 Details of bonding type rmsd hydrogen bonds : bond 0.02574 ( 685) hydrogen bonds : angle 4.47101 ( 1873) covalent geometry : bond 0.00184 (18291) covalent geometry : angle 0.48537 (25123) ********************** 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 to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: C 215 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6362 (mp) REVERT: C 225 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7921 (ttm110) REVERT: D 205 LYS cc_start: 0.7634 (mttm) cc_final: 0.6899 (ptpp) REVERT: D 209 GLN cc_start: 0.6589 (tm-30) cc_final: 0.6329 (mp10) REVERT: D 216 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6375 (tm-30) REVERT: D 343 TYR cc_start: 0.7227 (p90) cc_final: 0.6984 (p90) REVERT: E 105 MET cc_start: 0.7282 (tpp) cc_final: 0.7052 (tpt) REVERT: E 216 GLU cc_start: 0.7488 (tt0) cc_final: 0.7163 (pt0) REVERT: E 233 PHE cc_start: 0.7604 (m-80) cc_final: 0.7220 (m-10) REVERT: F 37 ASP cc_start: 0.6973 (t70) cc_final: 0.6670 (t0) REVERT: F 180 TYR cc_start: 0.7198 (m-80) cc_final: 0.6710 (m-80) REVERT: F 258 ARG cc_start: 0.7587 (tpt170) cc_final: 0.6701 (mmt180) outliers start: 36 outliers final: 32 residues processed: 146 average time/residue: 0.2977 time to fit residues: 70.4040 Evaluate side-chains 144 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 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 281 ILE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 ILE 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 296 ILE 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 190 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 80 optimal weight: 6.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 310 GLN D 310 GLN D 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.162858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.130169 restraints weight = 27403.712| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.44 r_work: 0.3741 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4744 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= 0.094 Angle : 0.500 13.944 25123 Z= 0.251 Chirality : 0.042 0.186 2934 Planarity : 0.003 0.029 2989 Dihedral : 12.552 94.409 3206 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.01 % Allowed : 12.79 % Favored : 85.19 % 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: -0.31 (0.18), residues: 2070 helix: 0.90 (0.23), residues: 552 sheet: -0.49 (0.27), residues: 360 loop : -0.62 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 87 HIS 0.002 0.000 HIS C 96 PHE 0.029 0.001 PHE E 222 TYR 0.012 0.001 TYR F 325 ARG 0.003 0.000 ARG F 225 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 685) hydrogen bonds : angle 4.49647 ( 1873) covalent geometry : bond 0.00218 (18291) covalent geometry : angle 0.50044 (25123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9443.35 seconds wall clock time: 166 minutes 31.14 seconds (9991.14 seconds total)