Starting phenix.real_space_refine on Sat Jul 4 03:04:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqv_26073/07_2026/7tqv_26073.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.74, per 1000 atoms: 0.21 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: 1.62 Conformation dependent library (CDL) restraints added in 744.3 milliseconds 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: 2.08 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: 3.13 Time building geometry restraints manager: 2.13 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: 10536 18.94 - 37.87: 219 37.87 - 56.81: 32 56.81 - 75.75: 4 75.75 - 94.68: 1 Dihedral angle restraints: 10792 sinusoidal: 4761 harmonic: 6031 Sorted by residual: dihedral pdb=" O5' A G 19 " pdb=" C5' A G 19 " pdb=" C4' A G 19 " pdb=" C3' A G 19 " ideal model delta sinusoidal sigma weight residual -65.00 -122.89 57.89 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" O5' U H 43 " pdb=" C5' U H 43 " pdb=" C4' U H 43 " pdb=" C3' U H 43 " ideal model delta sinusoidal sigma weight residual 55.00 112.78 -57.78 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN E 310 " pdb=" CA GLN E 310 " pdb=" CB GLN E 310 " pdb=" CG GLN E 310 " ideal model delta sinusoidal sigma weight residual -180.00 -131.87 -48.13 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 10789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1742 0.025 - 0.051: 674 0.051 - 0.076: 257 0.076 - 0.101: 135 0.101 - 0.126: 126 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE F 28 " pdb=" N ILE F 28 " pdb=" C ILE F 28 " pdb=" CB ILE F 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 2931 not shown) Planarity restraints: 2989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 51 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO B 51 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 50 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO E 51 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " 0.016 5.00e-02 4.00e+02 ... (remaining 2986 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 541 2.71 - 3.26: 16653 3.26 - 3.80: 28201 3.80 - 4.35: 36417 4.35 - 4.90: 60871 Nonbonded interactions: 142683 Sorted by model distance: nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.162 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18291 Z= 0.107 Angle : 0.383 7.561 25123 Z= 0.208 Chirality : 0.040 0.126 2934 Planarity : 0.003 0.028 2989 Dihedral : 7.789 94.682 6904 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG F 199 TYR 0.008 0.001 TYR A 325 PHE 0.006 0.001 PHE D 44 TRP 0.004 0.001 TRP D 87 HIS 0.002 0.001 HIS D 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (18291) covalent geometry : angle 0.38338 / 0.21 (25123) hydrogen bonds : bond 0.25034 / 16.81 ( 685) hydrogen bonds : angle 9.08032 / 6.60 ( 1873) *********************** 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 : 0.690 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: 0.7938 (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: B 331 MET cc_start: 0.5518 (tpp) cc_final: 0.5221 (mtt) 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: 0.7729 (t0) REVERT: D 110 LYS cc_start: 0.7443 (mttt) cc_final: 0.6708 (tptp) REVERT: D 205 LYS cc_start: 0.7621 (mttm) cc_final: 0.7209 (ptpp) REVERT: D 331 MET cc_start: 0.4884 (tpp) cc_final: 0.4250 (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: 0.8128 (m) REVERT: E 92 ASP cc_start: 0.7803 (m-30) cc_final: 0.7139 (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: 0.3386 (t-170) REVERT: F 220 ASP cc_start: 0.6944 (m-30) cc_final: 0.6629 (p0) REVERT: F 312 LEU cc_start: 0.0666 (OUTLIER) cc_final: 0.0448 (pt) outliers start: 15 outliers final: 2 residues processed: 365 average time/residue: 0.1409 time to fit residues: 75.9991 Evaluate side-chains 155 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 140 ASN A 176 GLN ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS B 176 GLN C 5 ASN C 164 ASN C 176 GLN D 176 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 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.156018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.122831 restraints weight = 27096.490| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.71 r_work: 0.3608 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18291 Z= 0.221 Angle : 0.604 9.625 25123 Z= 0.323 Chirality : 0.046 0.177 2934 Planarity : 0.004 0.042 2989 Dihedral : 6.896 93.776 2989 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.16 % Allowed : 8.11 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2070 helix: -0.04 (0.21), residues: 552 sheet: 0.01 (0.30), residues: 360 loop : -0.73 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.018 0.002 TYR F 343 PHE 0.023 0.002 PHE C 214 TRP 0.018 0.002 TRP F 333 HIS 0.007 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (18291) covalent geometry : angle 0.60379 / 0.32 (25123) hydrogen bonds : bond 0.04222 / 2.91 ( 685) hydrogen bonds : angle 6.03861 / 4.36 ( 1873) *********************** 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 236 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8173 (mttm) cc_final: 0.7953 (pttt) REVERT: A 331 MET cc_start: 0.7798 (mmm) cc_final: 0.7391 (tpt) REVERT: B 92 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7423 (t70) REVERT: C 31 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7580 (p) REVERT: C 225 ARG cc_start: 0.8311 (ttm170) cc_final: 0.8015 (ttm110) REVERT: D 12 ASN cc_start: 0.8145 (m-40) cc_final: 0.7839 (t0) REVERT: D 205 LYS cc_start: 0.7464 (mttm) cc_final: 0.6847 (ptpp) REVERT: D 258 ARG cc_start: 0.5797 (tpt170) cc_final: 0.5558 (tpt-90) REVERT: D 343 TYR cc_start: 0.7243 (p90) cc_final: 0.6493 (p90) REVERT: E 116 ILE cc_start: 0.7311 (tt) cc_final: 0.7005 (tp) REVERT: E 270 ILE cc_start: 0.8004 (mt) cc_final: 0.7747 (tt) REVERT: E 338 HIS cc_start: 0.4085 (OUTLIER) cc_final: 0.3198 (t-170) REVERT: F 136 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7489 (tpt170) REVERT: F 226 TYR cc_start: 0.6975 (m-80) cc_final: 0.6685 (m-80) outliers start: 58 outliers final: 34 residues processed: 228 average time/residue: 0.1217 time to fit residues: 43.2998 Evaluate side-chains 158 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 300 LEU 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 B residue 296 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 92 ASP 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 269 PHE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 293 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 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 0.0980 chunk 207 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 153 optimal weight: 0.0050 chunk 13 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 176 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.157943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124616 restraints weight = 27342.403| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.49 r_work: 0.3663 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18291 Z= 0.125 Angle : 0.503 9.278 25123 Z= 0.264 Chirality : 0.043 0.190 2934 Planarity : 0.004 0.035 2989 Dihedral : 6.668 95.600 2987 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.85 % Allowed : 10.83 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2070 helix: 0.34 (0.22), residues: 552 sheet: -0.09 (0.29), residues: 360 loop : -0.79 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.019 0.001 TYR C 343 PHE 0.027 0.001 PHE F 222 TRP 0.012 0.001 TRP C 87 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (18291) covalent geometry : angle 0.50251 / 0.26 (25123) hydrogen bonds : bond 0.03453 / 2.35 ( 685) hydrogen bonds : angle 5.39274 / 3.89 ( 1873) *********************** 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 167 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.555 Fit side-chains REVERT: A 186 VAL cc_start: 0.7383 (t) cc_final: 0.7127 (p) REVERT: A 205 LYS cc_start: 0.8198 (mttm) cc_final: 0.7967 (pttt) REVERT: A 331 MET cc_start: 0.7722 (mmm) cc_final: 0.7443 (tpt) REVERT: C 225 ARG cc_start: 0.8338 (ttm170) cc_final: 0.8030 (ttm110) REVERT: D 205 LYS cc_start: 0.7508 (mttm) cc_final: 0.6865 (ptpp) REVERT: D 343 TYR cc_start: 0.7388 (p90) cc_final: 0.6649 (p90) REVERT: E 116 ILE cc_start: 0.7490 (tt) cc_final: 0.7237 (tp) REVERT: E 216 GLU cc_start: 0.7159 (tt0) cc_final: 0.6885 (pt0) REVERT: E 233 PHE cc_start: 0.7632 (m-80) cc_final: 0.7202 (m-10) REVERT: E 338 HIS cc_start: 0.3994 (OUTLIER) cc_final: 0.3231 (t-170) REVERT: F 180 TYR cc_start: 0.7298 (m-80) cc_final: 0.6584 (m-80) REVERT: F 194 TYR cc_start: 0.7462 (m-80) cc_final: 0.7139 (m-80) REVERT: F 258 ARG cc_start: 0.7506 (tpt170) cc_final: 0.6840 (tpp-160) outliers start: 34 outliers final: 25 residues processed: 159 average time/residue: 0.1044 time to fit residues: 26.2472 Evaluate side-chains 139 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 208 SER 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 122 VAL 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 85 VAL Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 312 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 173 VAL Chi-restraints excluded: chain F residue 193 THR 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 207 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.156718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.123784 restraints weight = 27413.888| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.63 r_work: 0.3631 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18291 Z= 0.168 Angle : 0.538 10.752 25123 Z= 0.282 Chirality : 0.044 0.146 2934 Planarity : 0.004 0.033 2989 Dihedral : 6.790 93.753 2986 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.21 % Allowed : 10.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2070 helix: 0.34 (0.22), residues: 552 sheet: -0.34 (0.28), residues: 360 loop : -0.93 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 136 TYR 0.016 0.002 TYR C 343 PHE 0.024 0.002 PHE D 241 TRP 0.017 0.002 TRP C 87 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (18291) covalent geometry : angle 0.53845 / 0.28 (25123) hydrogen bonds : bond 0.03583 / 2.45 ( 685) hydrogen bonds : angle 5.29360 / 3.81 ( 1873) *********************** 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 187 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.593 Fit side-chains REVERT: A 186 VAL cc_start: 0.7453 (t) cc_final: 0.7181 (p) REVERT: A 205 LYS cc_start: 0.8250 (mttm) cc_final: 0.7991 (pttt) REVERT: A 233 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8051 (t80) REVERT: B 92 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7437 (t70) REVERT: C 215 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6222 (mp) REVERT: C 225 ARG cc_start: 0.8359 (ttm170) cc_final: 0.8034 (ttm110) REVERT: C 279 TYR cc_start: 0.8156 (m-80) cc_final: 0.7910 (m-10) REVERT: D 205 LYS cc_start: 0.7547 (mttm) cc_final: 0.6824 (ptpp) REVERT: D 331 MET cc_start: 0.4767 (tmm) cc_final: 0.4520 (tmm) REVERT: D 343 TYR cc_start: 0.7309 (p90) cc_final: 0.6733 (p90) REVERT: E 80 ILE cc_start: 0.8510 (tt) cc_final: 0.8217 (tt) REVERT: E 105 MET cc_start: 0.7301 (tpp) cc_final: 0.6936 (tpp) REVERT: E 116 ILE cc_start: 0.7657 (tt) cc_final: 0.7402 (tp) REVERT: E 173 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8001 (m) REVERT: E 216 GLU cc_start: 0.7381 (tt0) cc_final: 0.7126 (pt0) REVERT: E 233 PHE cc_start: 0.7673 (m-80) cc_final: 0.7097 (m-10) REVERT: E 270 ILE cc_start: 0.7976 (mt) cc_final: 0.7708 (tt) REVERT: E 338 HIS cc_start: 0.3662 (OUTLIER) cc_final: 0.3139 (t-170) REVERT: F 194 TYR cc_start: 0.7295 (m-80) cc_final: 0.6843 (m-80) REVERT: F 258 ARG cc_start: 0.7610 (tpt170) cc_final: 0.6739 (mmt180) outliers start: 59 outliers final: 41 residues processed: 175 average time/residue: 0.1136 time to fit residues: 31.6809 Evaluate side-chains 159 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 265 GLU 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 219 MET Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 29 ASN 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 115 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 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 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 52 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.159467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.126538 restraints weight = 27657.503| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.52 r_work: 0.3681 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18291 Z= 0.108 Angle : 0.485 9.568 25123 Z= 0.252 Chirality : 0.043 0.137 2934 Planarity : 0.003 0.031 2989 Dihedral : 6.628 94.779 2986 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.61 % Allowed : 12.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2070 helix: 0.51 (0.22), residues: 552 sheet: -0.35 (0.27), residues: 360 loop : -0.86 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.024 0.001 TYR D 238 PHE 0.022 0.001 PHE E 222 TRP 0.012 0.001 TRP C 87 HIS 0.003 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (18291) covalent geometry : angle 0.48475 / 0.25 (25123) hydrogen bonds : bond 0.03057 / 2.08 ( 685) hydrogen bonds : angle 4.96672 / 3.59 ( 1873) *********************** 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 176 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7427 (t) cc_final: 0.7197 (p) REVERT: A 205 LYS cc_start: 0.8235 (mttm) cc_final: 0.7957 (pttt) REVERT: A 233 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (t80) REVERT: C 215 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6146 (mp) REVERT: C 225 ARG cc_start: 0.8351 (ttm170) cc_final: 0.8044 (ttm110) REVERT: D 205 LYS cc_start: 0.7557 (mttm) cc_final: 0.6821 (ptpp) REVERT: D 331 MET cc_start: 0.4764 (tmm) cc_final: 0.4483 (tmm) REVERT: D 343 TYR cc_start: 0.7212 (p90) cc_final: 0.6558 (p90) REVERT: E 105 MET cc_start: 0.7119 (tpp) cc_final: 0.6798 (tpp) REVERT: E 116 ILE cc_start: 0.7618 (tt) cc_final: 0.7383 (tp) REVERT: E 173 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7957 (m) REVERT: E 216 GLU cc_start: 0.7576 (tt0) cc_final: 0.7301 (pt0) REVERT: E 233 PHE cc_start: 0.7619 (m-80) cc_final: 0.7065 (m-10) REVERT: E 270 ILE cc_start: 0.7906 (mt) cc_final: 0.7651 (tt) REVERT: E 338 HIS cc_start: 0.3593 (OUTLIER) cc_final: 0.3233 (t-170) REVERT: F 180 TYR cc_start: 0.7281 (m-80) cc_final: 0.6678 (m-80) REVERT: F 194 TYR cc_start: 0.7183 (m-80) cc_final: 0.6206 (m-10) outliers start: 48 outliers final: 32 residues processed: 167 average time/residue: 0.1162 time to fit residues: 30.7983 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 : 0.621 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 265 GLU 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 219 MET Chi-restraints excluded: chain C residue 251 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 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 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 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 182 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 338 HIS ** 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 = 0.4410 r_free = 0.4410 target = 0.162817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.127900 restraints weight = 28940.629| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.57 r_work: 0.3751 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18291 Z= 0.176 Angle : 0.536 9.218 25123 Z= 0.281 Chirality : 0.045 0.207 2934 Planarity : 0.004 0.034 2989 Dihedral : 6.828 93.226 2986 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.89 % Allowed : 12.90 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2070 helix: 0.38 (0.22), residues: 552 sheet: -0.51 (0.27), residues: 360 loop : -0.94 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 136 TYR 0.017 0.002 TYR F 325 PHE 0.020 0.002 PHE F 222 TRP 0.017 0.002 TRP C 87 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (18291) covalent geometry : angle 0.53619 / 0.28 (25123) hydrogen bonds : bond 0.03538 / 2.43 ( 685) hydrogen bonds : angle 5.13400 / 3.71 ( 1873) *********************** 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: 53 poor density : 119 time to evaluate : 0.571 Fit side-chains REVERT: A 186 VAL cc_start: 0.7529 (t) cc_final: 0.7273 (p) REVERT: A 205 LYS cc_start: 0.8291 (mttm) cc_final: 0.8017 (pttt) REVERT: A 233 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8012 (t80) REVERT: C 215 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6108 (mp) REVERT: C 225 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7949 (ttm110) REVERT: C 279 TYR cc_start: 0.8137 (m-10) cc_final: 0.7873 (m-10) REVERT: D 205 LYS cc_start: 0.7610 (mttm) cc_final: 0.6915 (ptpp) REVERT: D 331 MET cc_start: 0.4875 (tmm) cc_final: 0.4578 (tmm) REVERT: D 343 TYR cc_start: 0.7313 (p90) cc_final: 0.6737 (p90) REVERT: E 105 MET cc_start: 0.7017 (tpp) cc_final: 0.6756 (tpp) REVERT: E 116 ILE cc_start: 0.7691 (tt) cc_final: 0.7420 (tp) REVERT: E 173 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8112 (m) REVERT: E 216 GLU cc_start: 0.7683 (tt0) cc_final: 0.7315 (pt0) REVERT: E 233 PHE cc_start: 0.7641 (m-80) cc_final: 0.7067 (m-10) REVERT: E 270 ILE cc_start: 0.8032 (mt) cc_final: 0.7784 (tt) REVERT: E 338 HIS cc_start: 0.3425 (OUTLIER) cc_final: 0.3156 (t-170) REVERT: F 258 ARG cc_start: 0.7601 (tpt170) cc_final: 0.6738 (mmt180) outliers start: 53 outliers final: 39 residues processed: 162 average time/residue: 0.1147 time to fit residues: 30.0711 Evaluate side-chains 153 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 265 GLU 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 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 189 optimal weight: 0.0370 chunk 140 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS E 96 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.160811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.127407 restraints weight = 28062.840| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.40 r_work: 0.3722 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18291 Z= 0.090 Angle : 0.481 12.242 25123 Z= 0.249 Chirality : 0.042 0.181 2934 Planarity : 0.003 0.032 2989 Dihedral : 6.587 94.940 2986 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.56 % Allowed : 13.83 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2070 helix: 0.60 (0.22), residues: 552 sheet: -0.52 (0.27), residues: 360 loop : -0.85 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.013 0.001 TYR F 325 PHE 0.017 0.001 PHE F 222 TRP 0.010 0.001 TRP C 87 HIS 0.003 0.000 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (18291) covalent geometry : angle 0.48132 / 0.25 (25123) hydrogen bonds : bond 0.02738 / 1.88 ( 685) hydrogen bonds : angle 4.77912 / 3.47 ( 1873) *********************** 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 175 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.535 Fit side-chains REVERT: A 186 VAL cc_start: 0.7478 (t) cc_final: 0.7276 (p) REVERT: A 205 LYS cc_start: 0.8357 (mttm) cc_final: 0.8034 (pttt) REVERT: A 233 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7872 (t80) REVERT: C 215 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6042 (mp) REVERT: C 225 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7958 (ttm110) REVERT: C 265 GLU cc_start: 0.7315 (pm20) cc_final: 0.6861 (pm20) REVERT: D 205 LYS cc_start: 0.7646 (mttm) cc_final: 0.6918 (ptpp) REVERT: D 249 LEU cc_start: 0.6671 (mt) cc_final: 0.5997 (mm) REVERT: D 325 TYR cc_start: 0.7906 (m-10) cc_final: 0.7646 (m-10) REVERT: D 331 MET cc_start: 0.4841 (tmm) cc_final: 0.4577 (tmm) REVERT: D 343 TYR cc_start: 0.7243 (p90) cc_final: 0.6732 (p90) REVERT: E 42 GLU cc_start: 0.7555 (tt0) cc_final: 0.7201 (tt0) REVERT: E 105 MET cc_start: 0.7261 (tpp) cc_final: 0.7008 (tpp) REVERT: E 173 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8010 (m) REVERT: E 216 GLU cc_start: 0.7807 (tt0) cc_final: 0.7428 (pt0) REVERT: E 233 PHE cc_start: 0.7601 (m-80) cc_final: 0.6979 (m-10) REVERT: E 270 ILE cc_start: 0.7918 (mt) cc_final: 0.7688 (tt) REVERT: E 338 HIS cc_start: 0.3573 (OUTLIER) cc_final: 0.3163 (t-170) REVERT: F 258 ARG cc_start: 0.7576 (tpt170) cc_final: 0.6672 (mmt180) outliers start: 47 outliers final: 32 residues processed: 166 average time/residue: 0.1119 time to fit residues: 29.9213 Evaluate side-chains 153 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 296 ILE 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 C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 197 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 208 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 338 HIS ** 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 = 0.4412 r_free = 0.4412 target = 0.163882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.128908 restraints weight = 29287.763| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.50 r_work: 0.3798 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18291 Z= 0.117 Angle : 0.494 8.752 25123 Z= 0.256 Chirality : 0.043 0.224 2934 Planarity : 0.003 0.032 2989 Dihedral : 6.591 93.708 2985 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.61 % Allowed : 13.94 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2070 helix: 0.60 (0.23), residues: 552 sheet: -0.59 (0.27), residues: 360 loop : -0.85 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 225 TYR 0.014 0.001 TYR F 325 PHE 0.027 0.001 PHE C 222 TRP 0.011 0.001 TRP C 87 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (18291) covalent geometry : angle 0.49430 / 0.26 (25123) hydrogen bonds : bond 0.02912 / 2.00 ( 685) hydrogen bonds : angle 4.82457 / 3.50 ( 1873) *********************** 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 168 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 0.606 Fit side-chains REVERT: A 205 LYS cc_start: 0.8265 (mttm) cc_final: 0.8001 (pttt) REVERT: A 233 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 215 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6309 (mp) REVERT: C 225 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7965 (ttm110) REVERT: D 205 LYS cc_start: 0.7553 (mttm) cc_final: 0.6850 (ptpp) REVERT: D 249 LEU cc_start: 0.6620 (mt) cc_final: 0.5916 (mm) REVERT: D 331 MET cc_start: 0.4899 (tmm) cc_final: 0.4621 (tmm) REVERT: D 343 TYR cc_start: 0.7207 (p90) cc_final: 0.6730 (p90) REVERT: E 105 MET cc_start: 0.6967 (tpp) cc_final: 0.6757 (tpp) REVERT: E 173 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8029 (m) REVERT: E 216 GLU cc_start: 0.7622 (tt0) cc_final: 0.7283 (pt0) REVERT: E 219 MET cc_start: 0.7344 (pmm) cc_final: 0.6652 (ptm) REVERT: E 233 PHE cc_start: 0.7647 (m-80) cc_final: 0.7059 (m-10) REVERT: E 270 ILE cc_start: 0.7975 (mt) cc_final: 0.7712 (tt) REVERT: E 338 HIS cc_start: 0.3431 (OUTLIER) cc_final: 0.3219 (t-170) REVERT: F 258 ARG cc_start: 0.7530 (tpt170) cc_final: 0.6671 (mmt180) outliers start: 48 outliers final: 39 residues processed: 158 average time/residue: 0.1107 time to fit residues: 28.5066 Evaluate side-chains 156 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 GLU 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 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 85 VAL 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 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 0.0170 chunk 156 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.165221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.130545 restraints weight = 29111.838| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.40 r_work: 0.3835 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18291 Z= 0.096 Angle : 0.487 11.674 25123 Z= 0.249 Chirality : 0.042 0.182 2934 Planarity : 0.003 0.032 2989 Dihedral : 6.492 94.160 2985 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.23 % Allowed : 14.59 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2070 helix: 0.67 (0.23), residues: 552 sheet: -0.59 (0.27), residues: 360 loop : -0.83 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.013 0.001 TYR F 325 PHE 0.028 0.001 PHE C 222 TRP 0.010 0.001 TRP C 87 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (18291) covalent geometry : angle 0.48728 / 0.25 (25123) hydrogen bonds : bond 0.02690 / 1.86 ( 685) hydrogen bonds : angle 4.70085 / 3.41 ( 1873) *********************** 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: 41 poor density : 116 time to evaluate : 0.545 Fit side-chains REVERT: A 205 LYS cc_start: 0.8249 (mttm) cc_final: 0.8035 (pttt) REVERT: A 233 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7835 (t80) REVERT: C 215 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6436 (mp) REVERT: C 225 ARG cc_start: 0.8316 (ttm170) cc_final: 0.8098 (ttm110) REVERT: D 205 LYS cc_start: 0.7604 (mttm) cc_final: 0.6906 (ptpp) REVERT: D 249 LEU cc_start: 0.6555 (mt) cc_final: 0.5851 (mm) REVERT: D 331 MET cc_start: 0.4937 (tmm) cc_final: 0.4676 (tmm) REVERT: D 343 TYR cc_start: 0.7231 (p90) cc_final: 0.6714 (p90) REVERT: E 42 GLU cc_start: 0.7038 (tt0) cc_final: 0.6732 (tt0) REVERT: E 173 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (m) REVERT: E 216 GLU cc_start: 0.7617 (tt0) cc_final: 0.7255 (pt0) REVERT: E 219 MET cc_start: 0.7343 (pmm) cc_final: 0.6634 (ptm) REVERT: E 233 PHE cc_start: 0.7678 (m-80) cc_final: 0.7099 (m-10) REVERT: E 270 ILE cc_start: 0.7872 (mt) cc_final: 0.7631 (tt) REVERT: F 258 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6573 (mmt180) outliers start: 41 outliers final: 34 residues processed: 149 average time/residue: 0.1130 time to fit residues: 27.2119 Evaluate side-chains 150 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 GLU 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 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 43 optimal weight: 0.0170 chunk 132 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 338 HIS F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.164053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129188 restraints weight = 29127.094| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.44 r_work: 0.3809 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4962 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= 0.111 Angle : 0.499 12.707 25123 Z= 0.254 Chirality : 0.043 0.184 2934 Planarity : 0.003 0.032 2989 Dihedral : 6.506 93.510 2983 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 14.43 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 2070 helix: 0.67 (0.23), residues: 552 sheet: -0.61 (0.27), residues: 360 loop : -0.82 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 225 TYR 0.014 0.001 TYR F 325 PHE 0.030 0.001 PHE C 222 TRP 0.010 0.001 TRP C 87 HIS 0.006 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (18291) covalent geometry : angle 0.49869 / 0.25 (25123) hydrogen bonds : bond 0.02820 / 1.96 ( 685) hydrogen bonds : angle 4.75268 / 3.44 ( 1873) ********************** 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 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.691 Fit side-chains REVERT: A 205 LYS cc_start: 0.8245 (mttm) cc_final: 0.8038 (pttt) REVERT: A 233 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7834 (t80) REVERT: C 215 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6436 (mp) REVERT: C 225 ARG cc_start: 0.8305 (ttm170) cc_final: 0.7999 (ttm110) REVERT: C 265 GLU cc_start: 0.6833 (pm20) cc_final: 0.6523 (pm20) REVERT: D 205 LYS cc_start: 0.7579 (mttm) cc_final: 0.6902 (ptpp) REVERT: D 249 LEU cc_start: 0.6509 (mt) cc_final: 0.5800 (mm) REVERT: D 331 MET cc_start: 0.4872 (tmm) cc_final: 0.4614 (tmm) REVERT: D 343 TYR cc_start: 0.7216 (p90) cc_final: 0.6705 (p90) REVERT: E 173 VAL cc_start: 0.8312 (OUTLIER) cc_final: 0.8004 (m) REVERT: E 216 GLU cc_start: 0.7635 (tt0) cc_final: 0.7251 (pt0) REVERT: E 219 MET cc_start: 0.7321 (pmm) cc_final: 0.6604 (ptm) REVERT: E 233 PHE cc_start: 0.7737 (m-80) cc_final: 0.7241 (m-10) REVERT: E 270 ILE cc_start: 0.7928 (mt) cc_final: 0.7673 (tt) REVERT: F 258 ARG cc_start: 0.7464 (tpt170) cc_final: 0.6560 (mmt180) outliers start: 43 outliers final: 36 residues processed: 148 average time/residue: 0.1192 time to fit residues: 28.5440 Evaluate side-chains 151 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 GLU 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 215 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS 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 193 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 143 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.161266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.128028 restraints weight = 28473.675| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.38 r_work: 0.3789 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5089 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= 0.141 Angle : 0.525 13.096 25123 Z= 0.268 Chirality : 0.044 0.178 2934 Planarity : 0.004 0.032 2989 Dihedral : 6.635 92.978 2983 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.34 % Allowed : 14.64 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2070 helix: 0.55 (0.23), residues: 552 sheet: -0.98 (0.31), residues: 264 loop : -0.83 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 225 TYR 0.015 0.002 TYR F 325 PHE 0.031 0.001 PHE C 222 TRP 0.012 0.001 TRP C 87 HIS 0.006 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (18291) covalent geometry : angle 0.52509 / 0.27 (25123) hydrogen bonds : bond 0.03086 / 2.14 ( 685) hydrogen bonds : angle 4.87710 / 3.53 ( 1873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3546.00 seconds wall clock time: 61 minutes 40.33 seconds (3700.33 seconds total)