Starting phenix.real_space_refine on Thu Sep 18 15:28:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_26073.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_26073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_26073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_26073.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_26073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tqv_26073/09_2025/7tqv_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17792 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2733 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 333} Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2734 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2731 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 710 Classifications: {'RNA': 33} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 31} Chain: "H" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 691 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 20} Link IDs: {'rna3p': 32} Time building chain proxies: 4.73, per 1000 atoms: 0.27 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: 1.60 Conformation dependent library (CDL) restraints added in 843.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4140 Ramachandran restraints generated. 2070 Oldfield, 0 Emsley, 2070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 42 sheets defined 26.1% alpha, 21.9% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.619A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 77 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.619A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 227 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 299 through 309 removed outlier: 3.513A pdb=" N GLU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 77 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 227 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.618A pdb=" N VAL F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.785A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.683A pdb=" N GLU A 265 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 323 removed outlier: 4.349A pdb=" N SER A 329 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 343 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB4, first strand: chain 'B' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU B 265 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 316 through 323 Processing sheet with id=AB6, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC1, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AC2, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU C 265 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 316 through 323 Processing sheet with id=AC4, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 267 removed outlier: 3.681A pdb=" N GLU D 265 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 316 through 323 Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.243A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AD6, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'E' and resid 264 through 267 removed outlier: 3.682A pdb=" N GLU E 265 " --> pdb=" O THR E 282 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 316 through 323 Processing sheet with id=AD9, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.784A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.242A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AE5, first strand: chain 'F' and resid 264 through 267 removed outlier: 3.683A pdb=" N GLU F 265 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 316 through 323 662 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5452 1.34 - 1.45: 2792 1.45 - 1.57: 9825 1.57 - 1.69: 130 1.69 - 1.81: 92 Bond restraints: 18291 Sorted by residual: bond pdb=" C GLN A 189 " pdb=" N LEU A 190 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.83e-02 1.25e+03 2.54e+00 bond pdb=" C ALA F 118 " pdb=" N PRO F 119 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.38e-01 bond pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 1.524 1.515 0.010 1.05e-02 9.07e+03 8.28e-01 bond pdb=" C ALA E 118 " pdb=" N PRO E 119 " ideal model delta sigma weight residual 1.339 1.370 -0.031 3.40e-02 8.65e+02 8.17e-01 bond pdb=" C ALA C 118 " pdb=" N PRO C 119 " ideal model delta sigma weight residual 1.339 1.370 -0.030 3.40e-02 8.65e+02 8.03e-01 ... (remaining 18286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 24891 1.51 - 3.02: 205 3.02 - 4.54: 26 4.54 - 6.05: 0 6.05 - 7.56: 1 Bond angle restraints: 25123 Sorted by residual: angle pdb=" C THR F 49 " pdb=" N LEU F 50 " pdb=" CA LEU F 50 " ideal model delta sigma weight residual 121.48 129.04 -7.56 2.04e+00 2.40e-01 1.37e+01 angle pdb=" C ASP E 336 " pdb=" N GLY E 337 " pdb=" CA GLY E 337 " ideal model delta sigma weight residual 123.30 121.34 1.96 1.06e+00 8.90e-01 3.40e+00 angle pdb=" C ASP D 336 " pdb=" N GLY D 337 " pdb=" CA GLY D 337 " ideal model delta sigma weight residual 123.30 121.35 1.95 1.06e+00 8.90e-01 3.38e+00 angle pdb=" C ASP F 336 " pdb=" N GLY F 337 " pdb=" CA GLY F 337 " ideal model delta sigma weight residual 123.30 121.36 1.94 1.06e+00 8.90e-01 3.35e+00 angle pdb=" C ASP C 336 " pdb=" N GLY C 337 " pdb=" CA GLY C 337 " ideal model delta sigma weight residual 123.30 121.36 1.94 1.06e+00 8.90e-01 3.34e+00 ... (remaining 25118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.94: 10607 18.94 - 37.87: 254 37.87 - 56.81: 76 56.81 - 75.75: 76 75.75 - 94.68: 1 Dihedral angle restraints: 11014 sinusoidal: 4983 harmonic: 6031 Sorted by residual: dihedral pdb=" O5' A G 19 " pdb=" C5' A G 19 " pdb=" C4' A G 19 " pdb=" C3' A G 19 " ideal model delta sinusoidal sigma weight residual -65.00 -122.89 57.89 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" O5' U H 43 " pdb=" C5' U H 43 " pdb=" C4' U H 43 " pdb=" C3' U H 43 " ideal model delta sinusoidal sigma weight residual 55.00 112.78 -57.78 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLN E 310 " pdb=" CA GLN E 310 " pdb=" CB GLN E 310 " pdb=" CG GLN E 310 " ideal model delta sinusoidal sigma weight residual -180.00 -131.87 -48.13 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 11011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1742 0.025 - 0.051: 674 0.051 - 0.076: 257 0.076 - 0.101: 135 0.101 - 0.126: 126 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE F 28 " pdb=" N ILE F 28 " pdb=" C ILE F 28 " pdb=" CB ILE F 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 2931 not shown) Planarity restraints: 2989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 50 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 51 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO B 51 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 50 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.26e+00 pdb=" N PRO E 51 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " 0.016 5.00e-02 4.00e+02 ... (remaining 2986 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 541 2.71 - 3.26: 16653 3.26 - 3.80: 28201 3.80 - 4.35: 36417 4.35 - 4.90: 60871 Nonbonded interactions: 142683 Sorted by model distance: nonbonded pdb=" O GLY C 77 " pdb=" OG1 THR C 121 " model vdw 2.162 3.040 nonbonded pdb=" O GLY A 77 " pdb=" OG1 THR A 121 " model vdw 2.163 3.040 nonbonded pdb=" O GLY D 77 " pdb=" OG1 THR D 121 " model vdw 2.164 3.040 nonbonded pdb=" O GLY E 77 " pdb=" OG1 THR E 121 " model vdw 2.164 3.040 nonbonded pdb=" O GLY B 77 " pdb=" OG1 THR B 121 " model vdw 2.164 3.040 ... (remaining 142678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid -1 through 345) selection = chain 'B' selection = (chain 'C' and (resid -1 through 0 or (resid 1 and (name N or name CA or name C \ or name O or name CB )) or resid 2 through 345)) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18291 Z= 0.107 Angle : 0.383 7.561 25123 Z= 0.208 Chirality : 0.040 0.126 2934 Planarity : 0.003 0.028 2989 Dihedral : 10.867 94.682 7126 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.82 % Allowed : 4.14 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00238 (18291) covalent geometry : angle 0.38338 (25123) hydrogen bonds : bond 0.25034 ( 685) hydrogen bonds : angle 9.08032 ( 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 : 0.555 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: 0.1484 time to fit residues: 79.5677 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 : 0.657 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4297 r_free = 0.4297 target = 0.156046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122953 restraints weight = 27098.039| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.79 r_work: 0.3606 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18291 Z= 0.221 Angle : 0.604 9.534 25123 Z= 0.322 Chirality : 0.046 0.173 2934 Planarity : 0.005 0.043 2989 Dihedral : 12.900 93.592 3211 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.16 % Allowed : 8.22 % 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 aren not related in a simple way. whole: -0.66 (0.18), residues: 2070 helix: -0.06 (0.21), residues: 552 sheet: 0.01 (0.30), residues: 360 loop : -0.72 (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 0.017 0.002 TRP F 333 HIS 0.008 0.002 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00515 (18291) covalent geometry : angle 0.60368 (25123) hydrogen bonds : bond 0.04277 ( 685) hydrogen bonds : angle 6.05853 ( 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: 58 poor density : 179 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8160 (mttm) cc_final: 0.7954 (pttt) REVERT: A 331 MET cc_start: 0.7805 (mmm) cc_final: 0.7437 (tpt) REVERT: B 92 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7425 (t70) REVERT: B 137 ASN cc_start: 0.6318 (m110) cc_final: 0.6104 (m110) REVERT: C 31 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7587 (p) REVERT: C 225 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8022 (ttm110) REVERT: D 12 ASN cc_start: 0.8158 (m-40) cc_final: 0.7849 (t0) REVERT: D 205 LYS cc_start: 0.7484 (mttm) cc_final: 0.6858 (ptpp) REVERT: D 258 ARG cc_start: 0.5842 (tpt170) cc_final: 0.5607 (tpt-90) REVERT: D 343 TYR cc_start: 0.7246 (p90) cc_final: 0.6492 (p90) REVERT: E 116 ILE cc_start: 0.7329 (tt) cc_final: 0.7006 (tp) REVERT: E 270 ILE cc_start: 0.7981 (mt) cc_final: 0.7725 (tt) REVERT: E 338 HIS cc_start: 0.4186 (OUTLIER) cc_final: 0.3288 (t-170) REVERT: F 136 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7484 (tpt170) REVERT: F 226 TYR cc_start: 0.6964 (m-80) cc_final: 0.6640 (m-80) outliers start: 58 outliers final: 33 residues processed: 227 average time/residue: 0.1351 time to fit residues: 47.2040 Evaluate side-chains 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 C residue 306 ILE 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 312 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 0.7980 chunk 207 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4308 r_free = 0.4308 target = 0.157168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.123553 restraints weight = 27377.270| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.47 r_work: 0.3652 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3596 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= 0.135 Angle : 0.511 9.202 25123 Z= 0.269 Chirality : 0.043 0.141 2934 Planarity : 0.004 0.035 2989 Dihedral : 12.822 95.442 3209 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.34 % Allowed : 10.72 % Favored : 86.94 % 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 aren not related in a simple way. whole: -0.60 (0.18), residues: 2070 helix: 0.30 (0.22), residues: 552 sheet: -0.12 (0.29), residues: 360 loop : -0.81 (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 0.023 0.001 PHE E 222 TRP 0.013 0.001 TRP C 87 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00313 (18291) covalent geometry : angle 0.51145 (25123) hydrogen bonds : bond 0.03588 ( 685) hydrogen bonds : angle 5.44530 ( 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 177 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7387 (t) cc_final: 0.7127 (p) REVERT: A 205 LYS cc_start: 0.8191 (mttm) cc_final: 0.7977 (pttt) REVERT: A 331 MET cc_start: 0.7701 (mmm) cc_final: 0.7373 (tpt) REVERT: B 137 ASN cc_start: 0.6252 (m110) cc_final: 0.6046 (m110) REVERT: C 225 ARG cc_start: 0.8357 (ttm170) cc_final: 0.7997 (ttm110) REVERT: D 205 LYS cc_start: 0.7517 (mttm) cc_final: 0.6870 (ptpp) REVERT: D 343 TYR cc_start: 0.7359 (p90) cc_final: 0.6612 (p90) REVERT: E 116 ILE cc_start: 0.7518 (tt) cc_final: 0.7268 (tp) REVERT: E 216 GLU cc_start: 0.7169 (tt0) cc_final: 0.6900 (pt0) REVERT: E 233 PHE cc_start: 0.7649 (m-80) cc_final: 0.7202 (m-10) REVERT: E 338 HIS cc_start: 0.3991 (OUTLIER) cc_final: 0.3229 (t-170) REVERT: F 180 TYR cc_start: 0.7294 (m-80) cc_final: 0.6575 (m-80) REVERT: F 194 TYR cc_start: 0.7461 (m-80) cc_final: 0.7137 (m-80) outliers start: 43 outliers final: 27 residues processed: 166 average time/residue: 0.1228 time to fit residues: 32.5845 Evaluate side-chains 144 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS 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 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: 0.9980 chunk 194 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 = 0.4312 r_free = 0.4312 target = 0.156445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123925 restraints weight = 27461.720| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.51 r_work: 0.3648 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4132 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= 0.164 Angle : 0.533 9.414 25123 Z= 0.280 Chirality : 0.044 0.145 2934 Planarity : 0.004 0.034 2989 Dihedral : 12.852 93.990 3208 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.16 % Allowed : 11.16 % Favored : 85.68 % 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 aren not related in a simple way. whole: -0.76 (0.18), residues: 2070 helix: 0.33 (0.22), residues: 552 sheet: -0.36 (0.28), residues: 360 loop : -0.94 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 136 TYR 0.015 0.002 TYR F 325 PHE 0.021 0.002 PHE D 241 TRP 0.016 0.002 TRP C 87 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00388 (18291) covalent geometry : angle 0.53288 (25123) hydrogen bonds : bond 0.03529 ( 685) hydrogen bonds : angle 5.29032 ( 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 188 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 186 VAL cc_start: 0.7480 (t) cc_final: 0.7231 (p) REVERT: A 233 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7974 (t80) REVERT: B 92 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7441 (t70) REVERT: C 215 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6229 (mp) REVERT: C 225 ARG cc_start: 0.8335 (ttm170) cc_final: 0.8029 (ttm110) REVERT: C 279 TYR cc_start: 0.8070 (m-80) cc_final: 0.7864 (m-10) REVERT: C 282 THR cc_start: 0.8391 (m) cc_final: 0.8168 (m) REVERT: D 12 ASN cc_start: 0.7811 (m-40) cc_final: 0.7498 (t0) REVERT: D 205 LYS cc_start: 0.7560 (mttm) cc_final: 0.6896 (ptpp) REVERT: D 331 MET cc_start: 0.4905 (tmm) cc_final: 0.4662 (tmm) REVERT: D 343 TYR cc_start: 0.7387 (p90) cc_final: 0.6820 (p90) REVERT: E 80 ILE cc_start: 0.8498 (tt) cc_final: 0.8203 (tt) REVERT: E 105 MET cc_start: 0.7243 (tpp) cc_final: 0.6835 (tpp) REVERT: E 116 ILE cc_start: 0.7637 (tt) cc_final: 0.7394 (tp) REVERT: E 173 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8019 (m) REVERT: E 216 GLU cc_start: 0.7347 (tt0) cc_final: 0.7144 (pt0) REVERT: E 233 PHE cc_start: 0.7647 (m-80) cc_final: 0.7127 (m-10) REVERT: E 270 ILE cc_start: 0.8005 (mt) cc_final: 0.7735 (tt) REVERT: E 338 HIS cc_start: 0.3630 (OUTLIER) cc_final: 0.3143 (t-170) REVERT: F 194 TYR cc_start: 0.7350 (m-80) cc_final: 0.6912 (m-80) outliers start: 58 outliers final: 41 residues processed: 176 average time/residue: 0.1316 time to fit residues: 36.5625 Evaluate side-chains 158 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain 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 251 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN F 310 GLN 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 = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.125671 restraints weight = 27324.545| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.49 r_work: 0.3683 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4267 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= 0.107 Angle : 0.485 10.120 25123 Z= 0.253 Chirality : 0.043 0.137 2934 Planarity : 0.003 0.032 2989 Dihedral : 12.783 95.032 3208 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.83 % Allowed : 12.03 % Favored : 85.14 % 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 aren not related in a simple way. whole: -0.64 (0.18), residues: 2070 helix: 0.50 (0.22), residues: 552 sheet: -0.36 (0.28), residues: 360 loop : -0.88 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.024 0.001 TYR D 238 PHE 0.022 0.001 PHE D 241 TRP 0.012 0.001 TRP C 87 HIS 0.003 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00246 (18291) covalent geometry : angle 0.48546 (25123) hydrogen bonds : bond 0.03027 ( 685) hydrogen bonds : angle 4.96270 ( 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: 52 poor density : 130 time to evaluate : 0.695 Fit side-chains REVERT: A 186 VAL cc_start: 0.7423 (t) cc_final: 0.7196 (p) REVERT: A 233 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7921 (t80) REVERT: C 215 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6191 (mp) REVERT: C 225 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7940 (ttm110) REVERT: D 205 LYS cc_start: 0.7579 (mttm) cc_final: 0.6844 (ptpp) REVERT: D 331 MET cc_start: 0.4810 (tmm) cc_final: 0.4528 (tmm) REVERT: D 343 TYR cc_start: 0.7236 (p90) cc_final: 0.6578 (p90) REVERT: E 105 MET cc_start: 0.7110 (tpp) cc_final: 0.6756 (tpp) REVERT: E 116 ILE cc_start: 0.7625 (tt) cc_final: 0.7383 (tp) REVERT: E 173 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7947 (m) REVERT: E 216 GLU cc_start: 0.7556 (tt0) cc_final: 0.7309 (pt0) REVERT: E 233 PHE cc_start: 0.7634 (m-80) cc_final: 0.7084 (m-10) REVERT: E 270 ILE cc_start: 0.7910 (mt) cc_final: 0.7653 (tt) REVERT: E 338 HIS cc_start: 0.3584 (OUTLIER) cc_final: 0.3232 (t-170) REVERT: F 180 TYR cc_start: 0.7269 (m-80) cc_final: 0.6671 (m-80) REVERT: F 194 TYR cc_start: 0.7185 (m-80) cc_final: 0.6215 (m-10) REVERT: F 258 ARG cc_start: 0.7584 (tpt170) cc_final: 0.6717 (mmt180) outliers start: 52 outliers final: 36 residues processed: 172 average time/residue: 0.1259 time to fit residues: 34.6757 Evaluate side-chains 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain 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 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 182 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN 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 = 0.4408 r_free = 0.4408 target = 0.162705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.127751 restraints weight = 28983.327| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.49 r_work: 0.3759 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18291 Z= 0.172 Angle : 0.530 9.280 25123 Z= 0.279 Chirality : 0.044 0.216 2934 Planarity : 0.004 0.032 2989 Dihedral : 12.864 93.568 3208 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.94 % Allowed : 13.01 % Favored : 84.05 % 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 aren not related in a simple way. whole: -0.78 (0.18), residues: 2070 helix: 0.39 (0.22), residues: 552 sheet: -0.52 (0.27), residues: 360 loop : -0.94 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.017 0.002 TYR F 325 PHE 0.027 0.002 PHE C 222 TRP 0.016 0.002 TRP C 87 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00408 (18291) covalent geometry : angle 0.52957 (25123) hydrogen bonds : bond 0.03465 ( 685) hydrogen bonds : angle 5.10491 ( 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 174 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.661 Fit side-chains REVERT: A 186 VAL cc_start: 0.7552 (t) cc_final: 0.7287 (p) REVERT: A 233 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8017 (t80) REVERT: C 215 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6345 (mp) REVERT: C 225 ARG cc_start: 0.8385 (ttm170) cc_final: 0.8029 (ttm110) REVERT: C 279 TYR cc_start: 0.8092 (m-10) cc_final: 0.7858 (m-10) REVERT: D 12 ASN cc_start: 0.7777 (m-40) cc_final: 0.7400 (t0) REVERT: D 205 LYS cc_start: 0.7607 (mttm) cc_final: 0.6914 (ptpp) REVERT: D 331 MET cc_start: 0.4840 (tmm) cc_final: 0.4537 (tmm) REVERT: D 343 TYR cc_start: 0.7267 (p90) cc_final: 0.6679 (p90) REVERT: E 105 MET cc_start: 0.7013 (tpp) cc_final: 0.6741 (tpp) REVERT: E 116 ILE cc_start: 0.7660 (tt) cc_final: 0.7409 (tp) REVERT: E 173 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8105 (m) REVERT: E 216 GLU cc_start: 0.7717 (tt0) cc_final: 0.7376 (pt0) REVERT: E 233 PHE cc_start: 0.7685 (m-80) cc_final: 0.7098 (m-10) REVERT: E 270 ILE cc_start: 0.8050 (mt) cc_final: 0.7803 (tt) REVERT: E 338 HIS cc_start: 0.3450 (OUTLIER) cc_final: 0.3152 (t-170) REVERT: F 258 ARG cc_start: 0.7613 (tpt170) cc_final: 0.6737 (mmt180) outliers start: 54 outliers final: 41 residues processed: 164 average time/residue: 0.1199 time to fit residues: 32.0480 Evaluate side-chains 156 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS E 96 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.160896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.127368 restraints weight = 28031.247| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.41 r_work: 0.3720 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18291 Z= 0.090 Angle : 0.468 8.793 25123 Z= 0.245 Chirality : 0.042 0.176 2934 Planarity : 0.003 0.032 2989 Dihedral : 12.751 95.477 3208 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.34 % Allowed : 14.04 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.18), residues: 2070 helix: 0.62 (0.23), residues: 552 sheet: -0.53 (0.27), residues: 360 loop : -0.85 (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 0.025 0.001 PHE C 222 TRP 0.010 0.001 TRP C 87 HIS 0.003 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00203 (18291) covalent geometry : angle 0.46844 (25123) hydrogen bonds : bond 0.02738 ( 685) hydrogen bonds : angle 4.77059 ( 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 169 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.654 Fit side-chains REVERT: A 233 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7874 (t80) REVERT: C 215 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6401 (mp) REVERT: C 225 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7932 (ttm110) REVERT: D 205 LYS cc_start: 0.7599 (mttm) cc_final: 0.6870 (ptpp) REVERT: D 331 MET cc_start: 0.4888 (tmm) cc_final: 0.4629 (tmm) REVERT: D 343 TYR cc_start: 0.7273 (p90) cc_final: 0.6732 (p90) REVERT: E 105 MET cc_start: 0.7063 (tpp) cc_final: 0.6805 (tpp) REVERT: E 116 ILE cc_start: 0.7549 (tt) cc_final: 0.7345 (tp) REVERT: E 173 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7994 (m) REVERT: E 216 GLU cc_start: 0.7671 (tt0) cc_final: 0.7342 (pt0) REVERT: E 233 PHE cc_start: 0.7634 (m-80) cc_final: 0.7065 (m-10) REVERT: E 270 ILE cc_start: 0.7876 (mt) cc_final: 0.7643 (tt) REVERT: E 338 HIS cc_start: 0.3413 (OUTLIER) cc_final: 0.3168 (t-170) REVERT: F 258 ARG cc_start: 0.7519 (tpt170) cc_final: 0.6622 (mmt180) outliers start: 43 outliers final: 33 residues processed: 159 average time/residue: 0.1270 time to fit residues: 32.1790 Evaluate side-chains 149 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 219 MET 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 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 48 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 197 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 208 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 overall best weight: 2.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.163845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.129836 restraints weight = 29223.480| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.48 r_work: 0.3781 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18291 Z= 0.135 Angle : 0.510 11.192 25123 Z= 0.265 Chirality : 0.044 0.200 2934 Planarity : 0.003 0.033 2989 Dihedral : 12.792 93.430 3207 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 14.43 % 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 aren not related in a simple way. whole: -0.67 (0.18), residues: 2070 helix: 0.59 (0.23), residues: 552 sheet: -0.60 (0.27), residues: 360 loop : -0.88 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.015 0.001 TYR F 325 PHE 0.028 0.001 PHE C 222 TRP 0.013 0.001 TRP C 87 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00320 (18291) covalent geometry : angle 0.50992 (25123) hydrogen bonds : bond 0.03062 ( 685) hydrogen bonds : angle 4.88070 ( 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 157 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.656 Fit side-chains REVERT: A 233 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 215 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6437 (mp) REVERT: C 225 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7954 (ttm110) REVERT: D 205 LYS cc_start: 0.7554 (mttm) cc_final: 0.6878 (ptpp) REVERT: D 249 LEU cc_start: 0.6618 (mt) cc_final: 0.5911 (mm) REVERT: D 331 MET cc_start: 0.4933 (tmm) cc_final: 0.4642 (tmm) REVERT: D 343 TYR cc_start: 0.7199 (p90) cc_final: 0.6727 (p90) REVERT: E 105 MET cc_start: 0.6969 (tpp) cc_final: 0.6745 (tpp) REVERT: E 116 ILE cc_start: 0.7624 (tt) cc_final: 0.7399 (tp) REVERT: E 173 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8084 (m) REVERT: E 216 GLU cc_start: 0.7642 (tt0) cc_final: 0.7302 (pt0) REVERT: E 219 MET cc_start: 0.7346 (pmm) cc_final: 0.6658 (ptm) REVERT: E 233 PHE cc_start: 0.7652 (m-80) cc_final: 0.7069 (m-10) REVERT: E 270 ILE cc_start: 0.7991 (mt) cc_final: 0.7745 (tt) REVERT: F 258 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6693 (mmt180) outliers start: 46 outliers final: 36 residues processed: 146 average time/residue: 0.1244 time to fit residues: 29.5985 Evaluate side-chains 146 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 177 PHE Chi-restraints excluded: chain B residue 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 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 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 243 HIS 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: 3.9990 chunk 156 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 338 HIS F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.163262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.129266 restraints weight = 29124.467| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.47 r_work: 0.3770 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18291 Z= 0.151 Angle : 0.531 11.698 25123 Z= 0.275 Chirality : 0.044 0.201 2934 Planarity : 0.004 0.033 2989 Dihedral : 12.858 93.515 3205 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.67 % Allowed : 14.48 % 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 aren not related in a simple way. whole: -0.77 (0.18), residues: 2070 helix: 0.48 (0.23), residues: 552 sheet: -0.80 (0.28), residues: 348 loop : -0.88 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.015 0.002 TYR F 325 PHE 0.029 0.002 PHE C 222 TRP 0.013 0.001 TRP C 87 HIS 0.007 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00358 (18291) covalent geometry : angle 0.53123 (25123) hydrogen bonds : bond 0.03195 ( 685) hydrogen bonds : angle 4.93503 ( 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 162 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.698 Fit side-chains REVERT: A 233 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7975 (t80) REVERT: C 215 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6372 (mp) REVERT: C 225 ARG cc_start: 0.8301 (ttm170) cc_final: 0.7986 (ttm110) REVERT: D 12 ASN cc_start: 0.7483 (m-40) cc_final: 0.7099 (t0) REVERT: D 205 LYS cc_start: 0.7571 (mttm) cc_final: 0.6938 (ptpp) REVERT: D 249 LEU cc_start: 0.6609 (mt) cc_final: 0.5890 (mm) REVERT: D 331 MET cc_start: 0.4931 (tmm) cc_final: 0.4638 (tmm) REVERT: D 343 TYR cc_start: 0.7246 (p90) cc_final: 0.6776 (p90) REVERT: E 105 MET cc_start: 0.6996 (tpp) cc_final: 0.6773 (tpp) REVERT: E 116 ILE cc_start: 0.7656 (tt) cc_final: 0.7434 (tp) REVERT: E 173 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8169 (m) REVERT: E 216 GLU cc_start: 0.7507 (tt0) cc_final: 0.7195 (pt0) REVERT: E 233 PHE cc_start: 0.7677 (m-80) cc_final: 0.7222 (m-10) REVERT: E 270 ILE cc_start: 0.8014 (mt) cc_final: 0.7761 (tt) REVERT: F 258 ARG cc_start: 0.7527 (tpt170) cc_final: 0.6631 (mmt180) outliers start: 49 outliers final: 39 residues processed: 151 average time/residue: 0.1250 time to fit residues: 30.6934 Evaluate side-chains 149 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 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 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 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 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 43 optimal weight: 0.0570 chunk 132 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS F 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.163790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.128794 restraints weight = 29198.107| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.49 r_work: 0.3799 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18291 Z= 0.108 Angle : 0.494 9.987 25123 Z= 0.255 Chirality : 0.043 0.185 2934 Planarity : 0.003 0.034 2989 Dihedral : 12.803 94.285 3205 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.34 % Allowed : 14.86 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.18), residues: 2070 helix: 0.62 (0.23), residues: 552 sheet: -0.70 (0.27), residues: 360 loop : -0.91 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.014 0.001 TYR F 325 PHE 0.029 0.001 PHE C 222 TRP 0.012 0.001 TRP C 87 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00252 (18291) covalent geometry : angle 0.49388 (25123) hydrogen bonds : bond 0.02853 ( 685) hydrogen bonds : angle 4.78185 ( 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 155 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7850 (t80) REVERT: C 215 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6341 (mp) REVERT: C 225 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7982 (ttm110) REVERT: D 12 ASN cc_start: 0.7427 (m-40) cc_final: 0.7028 (t0) REVERT: D 205 LYS cc_start: 0.7559 (mttm) cc_final: 0.6901 (ptpp) REVERT: D 249 LEU cc_start: 0.6537 (mt) cc_final: 0.5757 (mm) REVERT: D 331 MET cc_start: 0.4911 (tmm) cc_final: 0.4624 (tmm) REVERT: D 343 TYR cc_start: 0.7230 (p90) cc_final: 0.6716 (p90) REVERT: E 105 MET cc_start: 0.6967 (tpp) cc_final: 0.6762 (tpp) REVERT: E 116 ILE cc_start: 0.7623 (tt) cc_final: 0.7377 (tp) REVERT: E 173 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8099 (m) REVERT: E 216 GLU cc_start: 0.7591 (tt0) cc_final: 0.7189 (pt0) REVERT: E 219 MET cc_start: 0.7318 (pmm) cc_final: 0.6583 (ptm) REVERT: E 233 PHE cc_start: 0.7686 (m-80) cc_final: 0.7215 (m-10) REVERT: E 270 ILE cc_start: 0.7950 (mt) cc_final: 0.7683 (tt) REVERT: F 258 ARG cc_start: 0.7519 (tpt170) cc_final: 0.6535 (mmt180) outliers start: 43 outliers final: 36 residues processed: 147 average time/residue: 0.1237 time to fit residues: 29.3624 Evaluate side-chains 149 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 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 215 LEU Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 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 106 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 243 HIS Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 143 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS F 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.163285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.128460 restraints weight = 29248.479| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.53 r_work: 0.3778 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18291 Z= 0.118 Angle : 0.507 15.161 25123 Z= 0.259 Chirality : 0.043 0.193 2934 Planarity : 0.003 0.034 2989 Dihedral : 12.815 93.752 3205 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.50 % Allowed : 14.81 % Favored : 82.69 % 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 aren not related in a simple way. whole: -0.71 (0.18), residues: 2070 helix: 0.63 (0.23), residues: 552 sheet: -0.60 (0.31), residues: 264 loop : -0.95 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.015 0.001 TYR E 226 PHE 0.030 0.001 PHE C 222 TRP 0.012 0.001 TRP C 87 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00279 (18291) covalent geometry : angle 0.50652 (25123) hydrogen bonds : bond 0.02953 ( 685) hydrogen bonds : angle 4.79424 ( 1873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.73 seconds wall clock time: 63 minutes 57.87 seconds (3837.87 seconds total)