Starting phenix.real_space_refine on Sat Sep 12 19:35:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqv_26073/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2026/7tqv_26073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 33} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 20} Link IDs: {'rna3p': 32} Time building chain proxies: 3.43, per 1000 atoms: 0.19 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: 1.79 Conformation dependent library (CDL) restraints added in 775.1 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: 1.71 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: 2.90 Time building geometry restraints manager: 2.32 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: 24752 1.51 - 3.02: 337 3.02 - 4.54: 32 4.54 - 6.05: 1 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 - 14.26: 10327 14.26 - 28.52: 293 28.52 - 42.78: 112 42.78 - 57.04: 53 57.04 - 71.30: 7 Dihedral angle restraints: 10792 sinusoidal: 4761 harmonic: 6031 Sorted by residual: dihedral pdb=" C4' U G 24 " pdb=" C3' U G 24 " pdb=" C2' U G 24 " pdb=" C1' U G 24 " ideal model delta sinusoidal sigma weight residual 36.34 -34.95 71.30 1 3.10e+00 1.04e-01 6.79e+02 dihedral pdb=" O4' U G 24 " pdb=" C4' U G 24 " pdb=" C3' U G 24 " pdb=" C2' U G 24 " ideal model delta sinusoidal sigma weight residual -35.15 23.91 -59.06 1 4.00e+00 6.25e-02 2.92e+02 dihedral pdb=" O4' U G 24 " pdb=" C2' U G 24 " pdb=" C1' U G 24 " pdb=" C3' U G 24 " ideal model delta sinusoidal sigma weight residual -94.41 -34.79 -59.62 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 10789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2568 0.068 - 0.137: 298 0.137 - 0.205: 0 0.205 - 0.273: 66 0.273 - 0.342: 2 Chirality restraints: 2934 Sorted by residual: chirality pdb=" P G H 17 " pdb=" OP1 G H 17 " pdb=" OP2 G H 17 " pdb=" O5' G H 17 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C2' U G 24 " pdb=" C3' U G 24 " pdb=" O2' U G 24 " pdb=" C1' U G 24 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" P A G 25 " pdb=" OP1 A G 25 " pdb=" OP2 A G 25 " pdb=" O5' A G 25 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (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: 1.100 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.410 Find NCS groups from input model: 0.340 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- 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= 0.111 Angle : 0.442 7.561 25123 Z= 0.221 Chirality : 0.054 0.342 2934 Planarity : 0.003 0.028 2989 Dihedral : 8.934 71.298 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 0.00245 / 0.11 (18291) covalent geometry : angle 0.44169 / 0.22 (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 : 0.693 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: 0.1498 time to fit residues: 81.2019 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 : 0.915 ------------------------------------------------------------------------------- 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 5 ASN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.156205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.122787 restraints weight = 27042.019| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.69 r_work: 0.3611 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18291 Z= 0.222 Angle : 0.662 12.899 25123 Z= 0.333 Chirality : 0.050 0.263 2934 Planarity : 0.005 0.049 2989 Dihedral : 8.837 93.932 2989 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.21 % Allowed : 8.17 % Favored : 88.62 % 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: -0.03 (0.21), residues: 552 sheet: -0.02 (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 0.009 0.002 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (18291) covalent geometry : angle 0.66188 / 0.33 (25123) hydrogen bonds : bond 0.04262 / 2.94 ( 685) hydrogen bonds : angle 6.05817 / 4.37 ( 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 237 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.7812 (mmm) cc_final: 0.7444 (tpt) REVERT: B 92 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7425 (t70) REVERT: B 137 ASN cc_start: 0.6299 (m110) cc_final: 0.6084 (m110) REVERT: C 31 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7582 (p) REVERT: C 225 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8003 (ttm110) REVERT: D 12 ASN cc_start: 0.8159 (m-40) cc_final: 0.7852 (t0) REVERT: D 205 LYS cc_start: 0.7458 (mttm) cc_final: 0.6843 (ptpp) REVERT: D 258 ARG cc_start: 0.5734 (tpt170) cc_final: 0.5501 (tpt-90) REVERT: D 343 TYR cc_start: 0.7275 (p90) cc_final: 0.6509 (p90) REVERT: E 116 ILE cc_start: 0.7318 (tt) cc_final: 0.7019 (tp) REVERT: E 270 ILE cc_start: 0.7985 (mt) cc_final: 0.7726 (tt) REVERT: E 338 HIS cc_start: 0.4178 (OUTLIER) cc_final: 0.3301 (t-170) REVERT: F 226 TYR cc_start: 0.7024 (m-80) cc_final: 0.6687 (m-80) outliers start: 59 outliers final: 34 residues processed: 228 average time/residue: 0.1223 time to fit residues: 44.2048 Evaluate side-chains 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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: 10.0000 chunk 207 optimal weight: 30.0000 chunk 209 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 153 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.157189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123854 restraints weight = 27364.269| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.54 r_work: 0.3641 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18291 Z= 0.140 Angle : 0.554 9.169 25123 Z= 0.278 Chirality : 0.047 0.221 2934 Planarity : 0.004 0.035 2989 Dihedral : 8.541 72.391 2987 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 10.94 % Favored : 86.66 % 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: -0.63 (0.18), residues: 2070 helix: 0.30 (0.22), residues: 552 sheet: -0.16 (0.29), residues: 360 loop : -0.83 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.020 0.001 TYR C 343 PHE 0.024 0.001 PHE F 222 TRP 0.013 0.001 TRP C 87 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (18291) covalent geometry : angle 0.55445 / 0.28 (25123) hydrogen bonds : bond 0.03611 / 2.47 ( 685) hydrogen bonds : angle 5.44667 / 3.93 ( 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 179 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7399 (t) cc_final: 0.7138 (p) REVERT: A 331 MET cc_start: 0.7714 (mmm) cc_final: 0.7429 (tpt) REVERT: B 137 ASN cc_start: 0.6279 (m110) cc_final: 0.6073 (m110) REVERT: C 225 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8006 (ttm110) REVERT: D 205 LYS cc_start: 0.7523 (mttm) cc_final: 0.6872 (ptpp) REVERT: D 343 TYR cc_start: 0.7351 (p90) cc_final: 0.6602 (p90) REVERT: E 116 ILE cc_start: 0.7512 (tt) cc_final: 0.7262 (tp) REVERT: E 216 GLU cc_start: 0.7196 (tt0) cc_final: 0.6869 (pt0) REVERT: E 233 PHE cc_start: 0.7662 (m-80) cc_final: 0.7208 (m-10) REVERT: E 338 HIS cc_start: 0.4021 (OUTLIER) cc_final: 0.3218 (t-170) REVERT: F 180 TYR cc_start: 0.7302 (m-80) cc_final: 0.6584 (m-80) REVERT: F 194 TYR cc_start: 0.7462 (m-80) cc_final: 0.7144 (m-80) outliers start: 44 outliers final: 29 residues processed: 166 average time/residue: 0.1211 time to fit residues: 32.1749 Evaluate side-chains 145 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 B residue 296 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 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 29 ASN 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 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 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 194 optimal weight: 0.0010 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** 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 = 0.4356 r_free = 0.4356 target = 0.158937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126738 restraints weight = 27459.868| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.35 r_work: 0.3691 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4093 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= 0.143 Angle : 0.551 9.869 25123 Z= 0.274 Chirality : 0.047 0.221 2934 Planarity : 0.004 0.034 2989 Dihedral : 8.475 71.497 2986 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.94 % Allowed : 11.11 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.68 (0.18), residues: 2070 helix: 0.43 (0.22), residues: 552 sheet: -0.36 (0.28), residues: 360 loop : -0.89 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 136 TYR 0.015 0.001 TYR F 325 PHE 0.021 0.001 PHE D 241 TRP 0.014 0.001 TRP C 87 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (18291) covalent geometry : angle 0.55130 / 0.27 (25123) hydrogen bonds : bond 0.03296 / 2.26 ( 685) hydrogen bonds : angle 5.17938 / 3.73 ( 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 186 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 0.676 Fit side-chains REVERT: A 186 VAL cc_start: 0.7553 (t) cc_final: 0.7306 (p) REVERT: A 233 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 92 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7587 (t70) REVERT: B 240 ASP cc_start: 0.5572 (p0) cc_final: 0.4965 (p0) REVERT: C 215 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6287 (mp) REVERT: C 225 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7946 (ttm110) REVERT: C 282 THR cc_start: 0.8447 (m) cc_final: 0.8208 (m) REVERT: D 12 ASN cc_start: 0.8057 (m-40) cc_final: 0.7707 (t0) REVERT: D 205 LYS cc_start: 0.7561 (mttm) cc_final: 0.6960 (ptpp) REVERT: D 331 MET cc_start: 0.4862 (tmm) cc_final: 0.4618 (tmm) REVERT: D 343 TYR cc_start: 0.7389 (p90) cc_final: 0.6825 (p90) REVERT: E 80 ILE cc_start: 0.8508 (tt) cc_final: 0.8224 (tt) REVERT: E 105 MET cc_start: 0.7398 (tpp) cc_final: 0.6996 (tpp) REVERT: E 116 ILE cc_start: 0.7670 (tt) cc_final: 0.7449 (tp) REVERT: E 173 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8023 (m) REVERT: E 216 GLU cc_start: 0.7494 (tt0) cc_final: 0.7209 (pt0) REVERT: E 233 PHE cc_start: 0.7650 (m-80) cc_final: 0.7097 (m-10) REVERT: E 270 ILE cc_start: 0.8043 (mt) cc_final: 0.7800 (tt) REVERT: E 338 HIS cc_start: 0.3733 (OUTLIER) cc_final: 0.3202 (t-170) REVERT: F 194 TYR cc_start: 0.7448 (m-80) cc_final: 0.7053 (m-80) REVERT: F 258 ARG cc_start: 0.7705 (tpt170) cc_final: 0.6767 (mmt180) outliers start: 54 outliers final: 37 residues processed: 175 average time/residue: 0.1281 time to fit residues: 35.8585 Evaluate side-chains 158 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 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 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 52 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 101 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.157636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.125230 restraints weight = 27415.845| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.36 r_work: 0.3675 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4383 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= 0.163 Angle : 0.568 11.442 25123 Z= 0.282 Chirality : 0.047 0.215 2934 Planarity : 0.004 0.031 2989 Dihedral : 8.480 71.085 2986 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.38 % Allowed : 11.81 % Favored : 84.81 % 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: -0.75 (0.18), residues: 2070 helix: 0.39 (0.22), residues: 552 sheet: -0.46 (0.27), residues: 360 loop : -0.92 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.015 0.001 TYR F 325 PHE 0.020 0.002 PHE E 222 TRP 0.016 0.001 TRP C 87 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (18291) covalent geometry : angle 0.56780 / 0.28 (25123) hydrogen bonds : bond 0.03436 / 2.36 ( 685) hydrogen bonds : angle 5.13372 / 3.71 ( 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 182 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7583 (t) cc_final: 0.7321 (p) REVERT: A 233 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 240 ASP cc_start: 0.5613 (p0) cc_final: 0.4858 (p0) REVERT: C 215 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6184 (mp) REVERT: C 225 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7864 (ttm110) REVERT: C 251 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8243 (mp) REVERT: C 265 GLU cc_start: 0.7256 (pm20) cc_final: 0.6911 (pm20) REVERT: D 12 ASN cc_start: 0.8029 (m-40) cc_final: 0.7656 (t0) REVERT: D 205 LYS cc_start: 0.7562 (mttm) cc_final: 0.6943 (ptpp) REVERT: D 331 MET cc_start: 0.4909 (tmm) cc_final: 0.4624 (tmm) REVERT: D 343 TYR cc_start: 0.7297 (p90) cc_final: 0.6690 (p90) REVERT: E 80 ILE cc_start: 0.8539 (tt) cc_final: 0.8267 (tt) REVERT: E 105 MET cc_start: 0.7329 (tpp) cc_final: 0.7003 (tpp) REVERT: E 116 ILE cc_start: 0.7686 (tt) cc_final: 0.7450 (tp) REVERT: E 173 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8108 (m) REVERT: E 216 GLU cc_start: 0.7762 (tt0) cc_final: 0.7402 (pt0) REVERT: E 233 PHE cc_start: 0.7623 (m-80) cc_final: 0.7057 (m-10) REVERT: E 270 ILE cc_start: 0.8071 (mt) cc_final: 0.7840 (tt) REVERT: E 338 HIS cc_start: 0.3673 (OUTLIER) cc_final: 0.3230 (t-170) REVERT: F 258 ARG cc_start: 0.7722 (tpt170) cc_final: 0.6814 (mmt180) outliers start: 62 outliers final: 47 residues processed: 171 average time/residue: 0.1240 time to fit residues: 34.1732 Evaluate side-chains 168 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 107 ASP 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 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 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 84 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 D residue 193 THR 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 107 ASP Chi-restraints excluded: chain E residue 113 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 261 GLU 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 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: 5.9990 chunk 29 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN 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 = 0.4365 r_free = 0.4365 target = 0.160025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127495 restraints weight = 27286.666| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.35 r_work: 0.3721 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4500 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= 0.099 Angle : 0.509 9.316 25123 Z= 0.252 Chirality : 0.046 0.198 2934 Planarity : 0.003 0.031 2989 Dihedral : 8.325 69.305 2986 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 13.28 % Favored : 84.38 % 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: -0.59 (0.18), residues: 2070 helix: 0.61 (0.23), residues: 552 sheet: -0.48 (0.27), residues: 360 loop : -0.83 (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 0.018 0.001 PHE F 222 TRP 0.011 0.001 TRP C 87 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (18291) covalent geometry : angle 0.50916 / 0.25 (25123) hydrogen bonds : bond 0.02859 / 1.96 ( 685) hydrogen bonds : angle 4.82529 / 3.51 ( 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 176 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.730 Fit side-chains REVERT: A 186 VAL cc_start: 0.7487 (t) cc_final: 0.7277 (p) REVERT: A 233 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 240 ASP cc_start: 0.5569 (p0) cc_final: 0.4779 (p0) REVERT: C 215 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6187 (mp) REVERT: C 225 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7940 (ttm110) REVERT: C 251 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7927 (mp) REVERT: C 265 GLU cc_start: 0.7174 (pm20) cc_final: 0.6852 (pm20) REVERT: D 205 LYS cc_start: 0.7622 (mttm) cc_final: 0.6894 (ptpp) REVERT: D 325 TYR cc_start: 0.7904 (m-80) cc_final: 0.7664 (m-10) REVERT: D 331 MET cc_start: 0.4816 (tmm) cc_final: 0.4539 (tmm) REVERT: D 343 TYR cc_start: 0.7200 (p90) cc_final: 0.6674 (p90) REVERT: E 105 MET cc_start: 0.7283 (tpp) cc_final: 0.6976 (tpp) REVERT: E 116 ILE cc_start: 0.7639 (tt) cc_final: 0.7400 (tp) REVERT: E 173 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7978 (m) REVERT: E 216 GLU cc_start: 0.7771 (tt0) cc_final: 0.7393 (pt0) REVERT: E 233 PHE cc_start: 0.7637 (m-80) cc_final: 0.7017 (m-10) REVERT: E 270 ILE cc_start: 0.7963 (mt) cc_final: 0.7728 (tt) REVERT: E 338 HIS cc_start: 0.3697 (OUTLIER) cc_final: 0.3265 (t-170) REVERT: F 180 TYR cc_start: 0.7412 (m-80) cc_final: 0.6840 (m-80) REVERT: F 258 ARG cc_start: 0.7639 (tpt170) cc_final: 0.6729 (mmt180) outliers start: 43 outliers final: 31 residues processed: 167 average time/residue: 0.1247 time to fit residues: 33.4832 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 288 SER 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 132 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 182 optimal weight: 4.9990 chunk 58 optimal weight: 0.0050 chunk 42 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 178 optimal weight: 2.9990 overall best weight: 0.7094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 96 HIS D 338 HIS F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.161262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.129824 restraints weight = 27651.826| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.42 r_work: 0.3746 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18291 Z= 0.088 Angle : 0.511 11.659 25123 Z= 0.250 Chirality : 0.045 0.175 2934 Planarity : 0.003 0.030 2989 Dihedral : 8.227 68.213 2985 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.18 % Allowed : 14.04 % Favored : 83.78 % 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: -0.51 (0.18), residues: 2070 helix: 0.74 (0.23), residues: 552 sheet: -0.50 (0.27), residues: 360 loop : -0.78 (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 0.026 0.001 PHE C 222 TRP 0.009 0.001 TRP C 87 HIS 0.002 0.000 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (18291) covalent geometry : angle 0.51052 / 0.25 (25123) hydrogen bonds : bond 0.02664 / 1.83 ( 685) hydrogen bonds : angle 4.71009 / 3.42 ( 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 168 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.673 Fit side-chains REVERT: A 233 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 240 ASP cc_start: 0.5275 (p0) cc_final: 0.4704 (p0) REVERT: C 215 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6461 (mp) REVERT: C 225 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7894 (ttm110) REVERT: C 251 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7778 (mp) REVERT: D 205 LYS cc_start: 0.7565 (mttm) cc_final: 0.6911 (ptpp) REVERT: D 249 LEU cc_start: 0.6690 (mt) cc_final: 0.6042 (mm) REVERT: D 331 MET cc_start: 0.5014 (tmm) cc_final: 0.4776 (tmm) REVERT: D 343 TYR cc_start: 0.7344 (p90) cc_final: 0.6802 (p90) REVERT: E 105 MET cc_start: 0.7001 (tpp) cc_final: 0.6753 (tpp) REVERT: E 113 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7400 (p) REVERT: E 116 ILE cc_start: 0.7539 (tt) cc_final: 0.7320 (tp) REVERT: E 216 GLU cc_start: 0.7593 (tt0) cc_final: 0.7284 (pt0) REVERT: E 219 MET cc_start: 0.7328 (pmm) cc_final: 0.6680 (ptm) REVERT: E 233 PHE cc_start: 0.7607 (m-80) cc_final: 0.7109 (m-10) REVERT: E 270 ILE cc_start: 0.7855 (mt) cc_final: 0.7626 (tt) REVERT: F 180 TYR cc_start: 0.7135 (m-80) cc_final: 0.6563 (m-80) REVERT: F 258 ARG cc_start: 0.7528 (tpt170) cc_final: 0.6665 (mmt180) outliers start: 40 outliers final: 30 residues processed: 161 average time/residue: 0.1210 time to fit residues: 31.9765 Evaluate side-chains 148 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 288 SER 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 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 THR 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 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 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: 10.0000 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4415 r_free = 0.4415 target = 0.163325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.129215 restraints weight = 29394.255| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.54 r_work: 0.3760 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18291 Z= 0.173 Angle : 0.582 10.640 25123 Z= 0.289 Chirality : 0.048 0.202 2934 Planarity : 0.004 0.030 2989 Dihedral : 8.410 69.631 2983 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.94 % Allowed : 13.99 % Favored : 83.07 % 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: -0.76 (0.18), residues: 2070 helix: 0.44 (0.22), residues: 552 sheet: -0.64 (0.27), residues: 360 loop : -0.89 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.017 0.002 TYR F 325 PHE 0.029 0.002 PHE C 222 TRP 0.014 0.001 TRP C 87 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (18291) covalent geometry : angle 0.58176 / 0.29 (25123) hydrogen bonds : bond 0.03412 / 2.36 ( 685) hydrogen bonds : angle 5.00300 / 3.62 ( 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 172 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.775 Fit side-chains REVERT: A 233 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 240 ASP cc_start: 0.5495 (p0) cc_final: 0.4751 (p0) REVERT: C 215 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6259 (mp) REVERT: C 225 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7875 (ttm110) REVERT: D 12 ASN cc_start: 0.7587 (m-40) cc_final: 0.7171 (t0) REVERT: D 205 LYS cc_start: 0.7607 (mttm) cc_final: 0.6927 (ptpp) REVERT: D 331 MET cc_start: 0.4874 (tmm) cc_final: 0.4594 (tmm) REVERT: D 343 TYR cc_start: 0.7188 (p90) cc_final: 0.6634 (p90) REVERT: E 80 ILE cc_start: 0.8465 (tt) cc_final: 0.8188 (tt) REVERT: E 105 MET cc_start: 0.6973 (tpp) cc_final: 0.6724 (tpp) REVERT: E 113 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7542 (p) REVERT: E 116 ILE cc_start: 0.7615 (tt) cc_final: 0.7384 (tp) REVERT: E 173 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8096 (m) REVERT: E 216 GLU cc_start: 0.7692 (tt0) cc_final: 0.7345 (pt0) REVERT: E 219 MET cc_start: 0.7314 (pmm) cc_final: 0.6572 (ptm) REVERT: E 233 PHE cc_start: 0.7693 (m-80) cc_final: 0.7218 (m-10) REVERT: E 270 ILE cc_start: 0.8029 (mt) cc_final: 0.7781 (tt) REVERT: F 258 ARG cc_start: 0.7560 (tpt170) cc_final: 0.6707 (mmt180) outliers start: 54 outliers final: 42 residues processed: 161 average time/residue: 0.1216 time to fit residues: 32.2556 Evaluate side-chains 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 107 ASP 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 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 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 173 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 29 ASN 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 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 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS 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 = 0.4383 r_free = 0.4383 target = 0.160531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126725 restraints weight = 29138.532| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.41 r_work: 0.3725 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18291 Z= 0.239 Angle : 0.651 9.531 25123 Z= 0.326 Chirality : 0.050 0.228 2934 Planarity : 0.004 0.047 2989 Dihedral : 8.700 70.204 2983 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.83 % Allowed : 14.32 % Favored : 82.85 % 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: -1.10 (0.18), residues: 2070 helix: 0.02 (0.22), residues: 552 sheet: -0.91 (0.28), residues: 348 loop : -1.01 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 91 TYR 0.022 0.002 TYR F 325 PHE 0.031 0.002 PHE C 222 TRP 0.018 0.002 TRP C 87 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (18291) covalent geometry : angle 0.65062 / 0.33 (25123) hydrogen bonds : bond 0.03990 / 2.76 ( 685) hydrogen bonds : angle 5.29300 / 3.82 ( 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 165 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: B 240 ASP cc_start: 0.5990 (p0) cc_final: 0.4992 (p0) REVERT: C 225 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7860 (ttm110) REVERT: C 279 TYR cc_start: 0.8257 (m-10) cc_final: 0.7982 (m-10) REVERT: D 12 ASN cc_start: 0.7904 (m-40) cc_final: 0.7547 (t0) REVERT: D 205 LYS cc_start: 0.7683 (mttm) cc_final: 0.6990 (ptpp) REVERT: D 343 TYR cc_start: 0.7275 (p90) cc_final: 0.6485 (p90) REVERT: E 80 ILE cc_start: 0.8605 (tt) cc_final: 0.8300 (tt) REVERT: E 105 MET cc_start: 0.7268 (tpp) cc_final: 0.7036 (tpp) REVERT: E 113 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7635 (p) REVERT: E 116 ILE cc_start: 0.7735 (tt) cc_final: 0.7473 (tp) REVERT: E 173 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8322 (m) REVERT: E 216 GLU cc_start: 0.7662 (tt0) cc_final: 0.7224 (pt0) REVERT: E 219 MET cc_start: 0.7383 (pmm) cc_final: 0.6583 (ptm) REVERT: E 233 PHE cc_start: 0.7806 (m-80) cc_final: 0.7199 (m-10) REVERT: E 270 ILE cc_start: 0.8121 (mt) cc_final: 0.7847 (tt) REVERT: F 258 ARG cc_start: 0.7665 (tpt170) cc_final: 0.6629 (mmt180) outliers start: 52 outliers final: 39 residues processed: 156 average time/residue: 0.1214 time to fit residues: 31.1466 Evaluate side-chains 148 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 107 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 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 219 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 106 THR 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 29 ASN 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 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 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 164 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 338 HIS F 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.163805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.129327 restraints weight = 29207.744| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.58 r_work: 0.3798 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18291 Z= 0.105 Angle : 0.559 14.943 25123 Z= 0.273 Chirality : 0.046 0.200 2934 Planarity : 0.004 0.032 2989 Dihedral : 8.387 68.325 2983 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.18 % Allowed : 14.97 % Favored : 82.85 % 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: -0.81 (0.18), residues: 2070 helix: 0.38 (0.22), residues: 552 sheet: -0.56 (0.27), residues: 348 loop : -0.96 (0.17), residues: 1170 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 0.027 0.001 PHE C 222 TRP 0.011 0.001 TRP C 87 HIS 0.009 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (18291) covalent geometry : angle 0.55857 / 0.27 (25123) hydrogen bonds : bond 0.02953 / 2.02 ( 685) hydrogen bonds : angle 4.83361 / 3.51 ( 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 148 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: C 225 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7880 (ttm110) REVERT: D 12 ASN cc_start: 0.7507 (m-40) cc_final: 0.7160 (t0) REVERT: D 205 LYS cc_start: 0.7581 (mttm) cc_final: 0.6896 (ptpp) REVERT: D 343 TYR cc_start: 0.6850 (p90) cc_final: 0.6272 (p90) REVERT: E 113 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7578 (p) REVERT: E 116 ILE cc_start: 0.7601 (tt) cc_final: 0.7374 (tp) REVERT: E 173 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8166 (m) REVERT: E 216 GLU cc_start: 0.7488 (tt0) cc_final: 0.7068 (pt0) REVERT: E 219 MET cc_start: 0.7254 (pmm) cc_final: 0.6499 (ptm) REVERT: E 233 PHE cc_start: 0.7716 (m-80) cc_final: 0.7210 (m-10) REVERT: E 270 ILE cc_start: 0.7924 (mt) cc_final: 0.7661 (tt) REVERT: F 258 ARG cc_start: 0.7459 (tpt170) cc_final: 0.6454 (mmt180) outliers start: 40 outliers final: 36 residues processed: 138 average time/residue: 0.1217 time to fit residues: 27.5096 Evaluate side-chains 140 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 243 HIS 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 173 VAL Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 29 ASN 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 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 164 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN C 164 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.162550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.128743 restraints weight = 29251.662| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.52 r_work: 0.3762 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18291 Z= 0.164 Angle : 0.587 14.702 25123 Z= 0.289 Chirality : 0.048 0.202 2934 Planarity : 0.004 0.031 2989 Dihedral : 8.420 68.434 2983 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.40 % Allowed : 15.02 % Favored : 82.58 % 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: -0.97 (0.18), residues: 2070 helix: 0.36 (0.22), residues: 552 sheet: -1.16 (0.31), residues: 264 loop : -0.98 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 225 TYR 0.015 0.002 TYR C 343 PHE 0.033 0.002 PHE B 241 TRP 0.014 0.001 TRP C 87 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (18291) covalent geometry : angle 0.58704 / 0.29 (25123) hydrogen bonds : bond 0.03345 / 2.30 ( 685) hydrogen bonds : angle 4.94615 / 3.59 ( 1873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.94 seconds wall clock time: 71 minutes 9.80 seconds (4269.80 seconds total)