Starting phenix.real_space_refine on Sat Aug 8 02:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.map" model { file = "/net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vf4_43185/08_2026/8vf4_43185.cif" } resolution = 4.1 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= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 87 5.49 5 S 66 5.16 5 C 7782 2.51 5 N 2214 2.21 5 O 2628 1.98 5 H 11790 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24567 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3607 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "B" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3626 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 476 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "F" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 476 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 480 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 476 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3607 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "J" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3626 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "K" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3607 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "L" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3626 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Time building chain proxies: 4.39, per 1000 atoms: 0.18 Number of scatterers: 24567 At special positions: 0 Unit cell: (189.924, 89.964, 96.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 87 15.00 O 2628 8.00 N 2214 7.00 C 7782 6.00 H 11790 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 51 " distance=2.04 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 51 " distance=2.04 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 51 " distance=2.04 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 51 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 51 " distance=2.04 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 51 " distance=2.03 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: 2.72 Conformation dependent library (CDL) restraints added in 498.1 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 19 sheets defined 29.1% alpha, 23.9% beta 37 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 75 through 82 removed outlier: 3.772A pdb=" N ILE A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.654A pdb=" N LEU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.845A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.682A pdb=" N GLN B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'I' and resid 75 through 82 removed outlier: 4.451A pdb=" N ILE I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU I 82 " --> pdb=" O ASP I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 87 removed outlier: 3.555A pdb=" N ARG I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 Processing helix chain 'I' and resid 178 through 183 removed outlier: 3.675A pdb=" N ASP I 182 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN I 183 " --> pdb=" O PRO I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 178 through 183' Processing helix chain 'I' and resid 188 through 203 Processing helix chain 'I' and resid 213 through 226 Processing helix chain 'J' and resid 75 through 80 removed outlier: 3.712A pdb=" N ALA J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 115 through 117 No H-bonds generated for 'chain 'J' and resid 115 through 117' Processing helix chain 'J' and resid 118 through 133 removed outlier: 3.745A pdb=" N TYR J 122 " --> pdb=" O SER J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 removed outlier: 3.540A pdb=" N ASP J 182 " --> pdb=" O PHE J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 202 removed outlier: 3.843A pdb=" N VAL J 198 " --> pdb=" O MET J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 227 Processing helix chain 'K' and resid 75 through 82 removed outlier: 4.424A pdb=" N ILE K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU K 82 " --> pdb=" O ASP K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 removed outlier: 3.984A pdb=" N ARG K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 119 through 133 Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 213 through 226 Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.090A pdb=" N ARG L 86 " --> pdb=" O PRO L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 101 No H-bonds generated for 'chain 'L' and resid 99 through 101' Processing helix chain 'L' and resid 102 through 104 No H-bonds generated for 'chain 'L' and resid 102 through 104' Processing helix chain 'L' and resid 118 through 133 Processing helix chain 'L' and resid 169 through 173 removed outlier: 3.783A pdb=" N ILE L 173 " --> pdb=" O PRO L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 202 removed outlier: 3.809A pdb=" N VAL L 198 " --> pdb=" O MET L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 227 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.527A pdb=" N TYR A 21 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 108 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 153 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARG A 134 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 94 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N HIS A 139 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 92 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.696A pdb=" N GLU A 53 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 45 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 45 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 43 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.696A pdb=" N GLU A 53 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 45 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 45 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 43 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 53 " --> pdb=" O CYS B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 22 removed outlier: 4.037A pdb=" N ARG B 108 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 161 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL B 153 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ARG B 134 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 94 " --> pdb=" O ILE B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AB1, first strand: chain 'I' and resid 5 through 11 removed outlier: 4.066A pdb=" N TRP I 5 " --> pdb=" O VAL I 20 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG I 108 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET I 162 " --> pdb=" O LEU I 112 " (cutoff:3.500A) removed outlier: 13.374A pdb=" N GLU I 160 " --> pdb=" O PRO I 114 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU I 148 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 136 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL I 153 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N ARG I 134 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU I 94 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS I 139 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL I 92 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR I 141 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE I 90 " --> pdb=" O THR I 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL I 92 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 42 through 48 removed outlier: 3.590A pdb=" N GLY J 40 " --> pdb=" O HIS J 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.529A pdb=" N TYR J 21 " --> pdb=" O PHE J 111 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N MET J 162 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU J 148 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS J 139 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL J 92 " --> pdb=" O HIS J 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 63 through 65 Processing sheet with id=AB5, first strand: chain 'K' and resid 8 through 11 removed outlier: 4.468A pdb=" N MET K 162 " --> pdb=" O LEU K 112 " (cutoff:3.500A) removed outlier: 14.063A pdb=" N GLU K 160 " --> pdb=" O PRO K 114 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 136 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N VAL K 153 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ARG K 134 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU K 94 " --> pdb=" O ILE K 137 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS K 139 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL K 92 " --> pdb=" O HIS K 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 31 through 35 removed outlier: 3.829A pdb=" N ALA L 63 " --> pdb=" O HIS K 32 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.822A pdb=" N ARG K 46 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS L 45 " --> pdb=" O LYS K 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 61 through 64 Processing sheet with id=AB9, first strand: chain 'L' and resid 3 through 9 removed outlier: 8.304A pdb=" N ALA L 3 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER L 22 " --> pdb=" O ALA L 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 108 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N MET L 162 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 12.563A pdb=" N GLU L 160 " --> pdb=" O PRO L 114 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG L 159 " --> pdb=" O PHE L 156 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL L 153 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N ARG L 134 " --> pdb=" O VAL L 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 141 through 142 412 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11778 1.03 - 1.23: 91 1.23 - 1.42: 5610 1.42 - 1.62: 7403 1.62 - 1.81: 120 Bond restraints: 25002 Sorted by residual: bond pdb=" C3' DA G 12 " pdb=" C2' DA G 12 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.46e+01 bond pdb=" C3' DA D 28 " pdb=" C2' DA D 28 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DT G 5 " pdb=" C2' DT G 5 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA C 12 " pdb=" C2' DA C 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C1' DT G 3 " pdb=" N1 DT G 3 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 24997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 44434 1.84 - 3.69: 759 3.69 - 5.53: 42 5.53 - 7.37: 4 7.37 - 9.22: 1 Bond angle restraints: 45240 Sorted by residual: angle pdb=" O4' DG C 15 " pdb=" C1' DG C 15 " pdb=" N9 DG C 15 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" N3 DT G 9 " pdb=" C4 DT G 9 " pdb=" O4 DT G 9 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT G 14 " pdb=" C4 DT G 14 " pdb=" O4 DT G 14 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT G 11 " pdb=" C4 DT G 11 " pdb=" O4 DT G 11 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 45235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9283 17.99 - 35.99: 1358 35.99 - 53.98: 652 53.98 - 71.97: 173 71.97 - 89.96: 21 Dihedral angle restraints: 11487 sinusoidal: 6822 harmonic: 4665 Sorted by residual: dihedral pdb=" CB CYS I 48 " pdb=" SG CYS I 48 " pdb=" SG CYS I 51 " pdb=" CB CYS I 51 " ideal model delta sinusoidal sigma weight residual 93.00 32.17 60.83 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CA ARG B 30 " pdb=" C ARG B 30 " pdb=" N PHE B 31 " pdb=" CA PHE B 31 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ARG A 30 " pdb=" C ARG A 30 " pdb=" N PHE A 31 " pdb=" CA PHE A 31 " ideal model delta harmonic sigma weight residual 180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 11484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1455 0.038 - 0.077: 292 0.077 - 0.115: 179 0.115 - 0.153: 80 0.153 - 0.192: 19 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C3' DT C 9 " pdb=" C4' DT C 9 " pdb=" O3' DT C 9 " pdb=" C2' DT C 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" C3' DA E 7 " pdb=" C4' DA E 7 " pdb=" O3' DA E 7 " pdb=" C2' DA E 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" C3' DT C 14 " pdb=" C4' DT C 14 " pdb=" O3' DT C 14 " pdb=" C2' DT C 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 2022 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 2 " 0.242 9.50e-02 1.11e+02 8.11e-02 7.93e+00 pdb=" NE ARG B 2 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 2 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 2 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 2 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG B 2 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 2 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 2 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 2 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 31 " 0.015 2.00e-02 2.50e+03 9.27e-03 2.58e+00 pdb=" CG PHE A 31 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 31 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 31 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 31 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE A 31 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 31 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 31 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 31 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 31 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP L 102 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO L 103 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 103 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 103 " -0.021 5.00e-02 4.00e+02 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1064 2.13 - 2.75: 45023 2.75 - 3.37: 72723 3.37 - 3.98: 91802 3.98 - 4.60: 135939 Nonbonded interactions: 346551 Sorted by model distance: nonbonded pdb=" O ARG K 108 " pdb=" H THR K 166 " model vdw 1.515 2.450 nonbonded pdb="HH21 ARG B 88 " pdb=" OP1 DT C 14 " model vdw 1.517 2.450 nonbonded pdb="HH12 ARG B 147 " pdb=" OP1 DA D 22 " model vdw 1.581 2.450 nonbonded pdb=" O ARG B 86 " pdb="HH11 ARG B 86 " model vdw 1.583 2.450 nonbonded pdb=" O4' DT E 5 " pdb="HH22 ARG J 143 " model vdw 1.589 2.450 ... (remaining 346546 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) selection = chain 'I' selection = (chain 'J' and resid 1 through 226) selection = chain 'K' selection = (chain 'L' and resid 1 through 226) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 11.780 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: 0.090 Extract box with map and model: 0.490 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 27.150 Find NCS groups from input model: 0.270 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 : 0.004 0.046 13218 Z= 0.310 Angle : 0.658 9.219 18264 Z= 0.490 Chirality : 0.050 0.192 2025 Planarity : 0.004 0.108 2067 Dihedral : 22.041 89.963 5256 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.42 % Allowed : 32.33 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1347 helix: 2.14 (0.30), residues: 307 sheet: -1.08 (0.33), residues: 266 loop : -0.23 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 2 TYR 0.017 0.001 TYR J 122 PHE 0.026 0.001 PHE A 31 TRP 0.008 0.001 TRP B 5 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.31 (13212) covalent geometry : angle 0.65673 / 0.49 (18252) SS BOND : bond 0.00575 / 0.32 ( 6) SS BOND : angle 1.40573 / 0.76 ( 12) hydrogen bonds : bond 0.21359 / 14.49 ( 489) hydrogen bonds : angle 8.35180 / 6.01 ( 1292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8537 (ttm) cc_final: 0.8090 (tpp) REVERT: A 222 LEU cc_start: 0.9534 (tt) cc_final: 0.9118 (tp) REVERT: B 129 LEU cc_start: 0.7410 (tp) cc_final: 0.7193 (tp) REVERT: B 221 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9029 (tm-30) REVERT: I 24 THR cc_start: 0.8334 (p) cc_final: 0.8127 (p) REVERT: I 202 MET cc_start: 0.7322 (mmm) cc_final: 0.6773 (mmt) REVERT: J 151 LEU cc_start: 0.9151 (pp) cc_final: 0.8860 (pp) REVERT: J 163 MET cc_start: 0.6442 (ptp) cc_final: 0.5866 (ptp) REVERT: K 105 MET cc_start: 0.7514 (mtt) cc_final: 0.6469 (mmm) REVERT: K 135 MET cc_start: 0.6846 (mmp) cc_final: 0.5757 (mtt) REVERT: K 181 LEU cc_start: 0.7945 (tt) cc_final: 0.7209 (tt) REVERT: K 202 MET cc_start: 0.7735 (mmm) cc_final: 0.7343 (mmt) outliers start: 5 outliers final: 3 residues processed: 205 average time/residue: 0.2778 time to fit residues: 79.3486 Evaluate side-chains 161 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS I 33 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 GLN K 218 GLN L 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.109820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.086096 restraints weight = 136947.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.088914 restraints weight = 71543.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.090193 restraints weight = 46723.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.090227 restraints weight = 38739.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.090623 restraints weight = 38293.141| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 13218 Z= 0.220 Angle : 0.737 13.066 18264 Z= 0.424 Chirality : 0.047 0.287 2025 Planarity : 0.008 0.098 2067 Dihedral : 21.916 85.216 2526 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1347 helix: 1.26 (0.29), residues: 325 sheet: -1.73 (0.33), residues: 257 loop : -0.46 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 159 TYR 0.013 0.002 TYR K 110 PHE 0.052 0.003 PHE A 31 TRP 0.011 0.002 TRP K 5 HIS 0.015 0.002 HIS J 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (13212) covalent geometry : angle 0.73639 / 0.42 (18252) SS BOND : bond 0.00702 / 0.35 ( 6) SS BOND : angle 1.65157 / 0.91 ( 12) hydrogen bonds : bond 0.06301 / 4.38 ( 489) hydrogen bonds : angle 7.34065 / 5.19 ( 1292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7425 (mmp80) cc_final: 0.7171 (mmp80) REVERT: A 129 LEU cc_start: 0.7740 (tp) cc_final: 0.7231 (mm) REVERT: A 222 LEU cc_start: 0.9416 (tt) cc_final: 0.9018 (tp) REVERT: B 2 ARG cc_start: 0.6862 (tpt-90) cc_final: 0.6624 (tpt170) REVERT: B 129 LEU cc_start: 0.7792 (tp) cc_final: 0.7524 (mm) REVERT: I 24 THR cc_start: 0.8099 (p) cc_final: 0.7867 (p) REVERT: I 95 PHE cc_start: 0.7850 (m-10) cc_final: 0.7469 (m-10) REVERT: I 152 ARG cc_start: 0.8590 (ttt90) cc_final: 0.8317 (ttm-80) REVERT: I 202 MET cc_start: 0.7653 (mmm) cc_final: 0.7116 (mmt) REVERT: J 151 LEU cc_start: 0.8962 (pp) cc_final: 0.8631 (pp) REVERT: K 202 MET cc_start: 0.7989 (mmm) cc_final: 0.7505 (mmt) REVERT: L 71 MET cc_start: 0.6605 (mtt) cc_final: 0.5943 (pmm) REVERT: L 121 SER cc_start: 0.8654 (m) cc_final: 0.8323 (t) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.2573 time to fit residues: 76.1701 Evaluate side-chains 143 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 32 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.559 > 50:) chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 183 GLN K 144 ASN L 165 HIS L 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.109567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.084029 restraints weight = 131893.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.087549 restraints weight = 66593.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.089916 restraints weight = 43534.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.091393 restraints weight = 32967.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.092318 restraints weight = 27540.401| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13218 Z= 0.169 Angle : 0.634 7.064 18264 Z= 0.371 Chirality : 0.045 0.175 2025 Planarity : 0.006 0.055 2067 Dihedral : 21.987 86.220 2526 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1347 helix: 1.19 (0.29), residues: 327 sheet: -1.84 (0.33), residues: 257 loop : -0.51 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 43 TYR 0.010 0.001 TYR J 122 PHE 0.041 0.002 PHE K 11 TRP 0.009 0.002 TRP K 5 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (13212) covalent geometry : angle 0.63326 / 0.37 (18252) SS BOND : bond 0.01792 / 0.91 ( 6) SS BOND : angle 1.63850 / 0.83 ( 12) hydrogen bonds : bond 0.05615 / 3.96 ( 489) hydrogen bonds : angle 6.95997 / 4.93 ( 1292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7538 (tp) cc_final: 0.7237 (mm) REVERT: B 2 ARG cc_start: 0.6619 (tpt-90) cc_final: 0.6295 (tpt170) REVERT: I 24 THR cc_start: 0.8094 (p) cc_final: 0.7869 (p) REVERT: I 152 ARG cc_start: 0.8619 (ttt90) cc_final: 0.8407 (ttt90) REVERT: J 194 MET cc_start: 0.8640 (mmm) cc_final: 0.8369 (tpp) REVERT: K 90 ILE cc_start: 0.7658 (mt) cc_final: 0.7455 (mt) REVERT: K 135 MET cc_start: 0.7514 (mmp) cc_final: 0.6400 (mtt) REVERT: K 202 MET cc_start: 0.7886 (mmm) cc_final: 0.7424 (mmt) REVERT: L 121 SER cc_start: 0.8596 (m) cc_final: 0.8372 (t) REVERT: L 194 MET cc_start: 0.8558 (tpp) cc_final: 0.8294 (tpp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2536 time to fit residues: 64.2706 Evaluate side-chains 135 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 HIS L 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.109067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.083122 restraints weight = 135219.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.086624 restraints weight = 67999.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.088923 restraints weight = 44899.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090339 restraints weight = 34324.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.091279 restraints weight = 28942.609| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13218 Z= 0.166 Angle : 0.615 7.149 18264 Z= 0.361 Chirality : 0.045 0.173 2025 Planarity : 0.006 0.051 2067 Dihedral : 21.984 86.464 2526 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1347 helix: 1.19 (0.29), residues: 327 sheet: -2.04 (0.32), residues: 261 loop : -0.47 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 88 TYR 0.015 0.001 TYR K 110 PHE 0.025 0.002 PHE A 31 TRP 0.008 0.002 TRP B 169 HIS 0.017 0.002 HIS L 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (13212) covalent geometry : angle 0.61294 / 0.36 (18252) SS BOND : bond 0.01563 / 0.80 ( 6) SS BOND : angle 2.10134 / 1.10 ( 12) hydrogen bonds : bond 0.05156 / 3.63 ( 489) hydrogen bonds : angle 6.77916 / 4.81 ( 1292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7640 (tp) cc_final: 0.7330 (mm) REVERT: A 194 MET cc_start: 0.8086 (tpp) cc_final: 0.7810 (tpp) REVERT: B 2 ARG cc_start: 0.6558 (tpt-90) cc_final: 0.6182 (tpt170) REVERT: B 202 MET cc_start: 0.7144 (mmm) cc_final: 0.6740 (mmt) REVERT: I 24 THR cc_start: 0.8037 (p) cc_final: 0.7821 (p) REVERT: I 104 MET cc_start: 0.7703 (mmp) cc_final: 0.7442 (mmp) REVERT: I 135 MET cc_start: 0.7472 (mmp) cc_final: 0.7053 (tpp) REVERT: I 202 MET cc_start: 0.7738 (mmm) cc_final: 0.7031 (mmt) REVERT: J 151 LEU cc_start: 0.8912 (pp) cc_final: 0.8589 (pp) REVERT: J 194 MET cc_start: 0.8628 (mmm) cc_final: 0.8395 (tpp) REVERT: K 90 ILE cc_start: 0.7621 (mt) cc_final: 0.7402 (mt) REVERT: K 135 MET cc_start: 0.7450 (mmp) cc_final: 0.6396 (mtt) REVERT: K 151 LEU cc_start: 0.8782 (mp) cc_final: 0.8548 (mp) REVERT: K 172 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7782 (mt-10) REVERT: K 202 MET cc_start: 0.7863 (mmm) cc_final: 0.7395 (mmt) REVERT: K 218 GLN cc_start: 0.8520 (mt0) cc_final: 0.7850 (tp40) REVERT: L 71 MET cc_start: 0.6449 (mtt) cc_final: 0.5867 (pmm) REVERT: L 121 SER cc_start: 0.8600 (m) cc_final: 0.8348 (t) REVERT: L 194 MET cc_start: 0.8779 (tpp) cc_final: 0.8464 (tpp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2593 time to fit residues: 66.1861 Evaluate side-chains 133 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 HIS I 144 ASN J 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.108683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082827 restraints weight = 130475.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.086350 restraints weight = 65495.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.088577 restraints weight = 43076.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.089974 restraints weight = 33017.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.090862 restraints weight = 27842.117| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13218 Z= 0.163 Angle : 0.593 7.205 18264 Z= 0.349 Chirality : 0.044 0.171 2025 Planarity : 0.005 0.050 2067 Dihedral : 21.984 86.538 2526 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1347 helix: 1.24 (0.29), residues: 327 sheet: -2.15 (0.31), residues: 271 loop : -0.49 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 30 TYR 0.015 0.001 TYR I 211 PHE 0.025 0.002 PHE A 31 TRP 0.009 0.002 TRP B 169 HIS 0.005 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (13212) covalent geometry : angle 0.59193 / 0.35 (18252) SS BOND : bond 0.00800 / 0.41 ( 6) SS BOND : angle 1.48110 / 0.79 ( 12) hydrogen bonds : bond 0.04911 / 3.45 ( 489) hydrogen bonds : angle 6.54113 / 4.64 ( 1292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7643 (tp) cc_final: 0.7328 (mm) REVERT: A 194 MET cc_start: 0.8035 (tpp) cc_final: 0.7835 (tpp) REVERT: B 2 ARG cc_start: 0.6425 (tpt-90) cc_final: 0.6220 (tpt170) REVERT: B 122 TYR cc_start: 0.7028 (t80) cc_final: 0.6674 (t80) REVERT: B 202 MET cc_start: 0.7189 (mmm) cc_final: 0.6822 (mmt) REVERT: I 24 THR cc_start: 0.8076 (p) cc_final: 0.7875 (p) REVERT: J 151 LEU cc_start: 0.8979 (pp) cc_final: 0.8668 (pp) REVERT: J 194 MET cc_start: 0.8630 (mmm) cc_final: 0.8372 (tpp) REVERT: K 89 GLU cc_start: 0.7906 (pp20) cc_final: 0.7573 (pp20) REVERT: K 135 MET cc_start: 0.7355 (mmp) cc_final: 0.6341 (mtt) REVERT: K 151 LEU cc_start: 0.8718 (mp) cc_final: 0.8433 (mp) REVERT: L 71 MET cc_start: 0.6354 (mtt) cc_final: 0.5838 (pmm) REVERT: L 121 SER cc_start: 0.8588 (m) cc_final: 0.8367 (t) REVERT: L 178 PHE cc_start: 0.6520 (m-10) cc_final: 0.6304 (m-10) REVERT: L 194 MET cc_start: 0.8801 (tpp) cc_final: 0.8597 (tpt) outliers start: 2 outliers final: 0 residues processed: 174 average time/residue: 0.2415 time to fit residues: 60.9890 Evaluate side-chains 138 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 126 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 183 GLN K 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.109049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.082876 restraints weight = 133072.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.086406 restraints weight = 66740.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.088732 restraints weight = 43977.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.090212 restraints weight = 33517.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.091006 restraints weight = 28070.378| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13218 Z= 0.148 Angle : 0.589 7.255 18264 Z= 0.345 Chirality : 0.044 0.173 2025 Planarity : 0.005 0.062 2067 Dihedral : 21.996 86.655 2526 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.08 % Allowed : 1.34 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1347 helix: 1.33 (0.29), residues: 327 sheet: -2.10 (0.31), residues: 269 loop : -0.47 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 152 TYR 0.017 0.001 TYR K 44 PHE 0.061 0.002 PHE A 31 TRP 0.008 0.001 TRP B 169 HIS 0.013 0.001 HIS J 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (13212) covalent geometry : angle 0.58835 / 0.34 (18252) SS BOND : bond 0.01292 / 0.65 ( 6) SS BOND : angle 1.48106 / 0.76 ( 12) hydrogen bonds : bond 0.04739 / 3.33 ( 489) hydrogen bonds : angle 6.42209 / 4.54 ( 1292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7531 (tp) cc_final: 0.7286 (mm) REVERT: A 194 MET cc_start: 0.8026 (tpp) cc_final: 0.7812 (tpp) REVERT: B 2 ARG cc_start: 0.6366 (tpt-90) cc_final: 0.5984 (tpt170) REVERT: I 24 THR cc_start: 0.8066 (p) cc_final: 0.7866 (p) REVERT: J 151 LEU cc_start: 0.8967 (pp) cc_final: 0.8676 (pp) REVERT: J 194 MET cc_start: 0.8619 (mmm) cc_final: 0.8362 (tpp) REVERT: K 89 GLU cc_start: 0.7911 (pp20) cc_final: 0.7566 (pp20) REVERT: K 135 MET cc_start: 0.7486 (mmp) cc_final: 0.6436 (mtt) REVERT: K 151 LEU cc_start: 0.8720 (mp) cc_final: 0.8462 (mp) REVERT: K 202 MET cc_start: 0.7807 (mmm) cc_final: 0.7328 (mmt) REVERT: K 218 GLN cc_start: 0.8517 (mt0) cc_final: 0.7865 (tp40) REVERT: L 71 MET cc_start: 0.6392 (mtt) cc_final: 0.5855 (pmm) REVERT: L 105 MET cc_start: 0.7592 (mpp) cc_final: 0.7038 (tpp) REVERT: L 121 SER cc_start: 0.8596 (m) cc_final: 0.8358 (t) REVERT: L 178 PHE cc_start: 0.6548 (m-10) cc_final: 0.6333 (m-10) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2625 time to fit residues: 65.2970 Evaluate side-chains 138 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.107619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.080980 restraints weight = 133161.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.084551 restraints weight = 65472.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086838 restraints weight = 42881.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.088247 restraints weight = 32764.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.089109 restraints weight = 27670.063| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13218 Z= 0.193 Angle : 0.611 7.455 18264 Z= 0.355 Chirality : 0.044 0.169 2025 Planarity : 0.005 0.047 2067 Dihedral : 21.987 85.990 2526 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.23), residues: 1347 helix: 1.22 (0.29), residues: 333 sheet: -2.06 (0.30), residues: 283 loop : -0.55 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 30 TYR 0.016 0.002 TYR L 122 PHE 0.045 0.002 PHE A 31 TRP 0.011 0.002 TRP B 169 HIS 0.012 0.002 HIS J 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (13212) covalent geometry : angle 0.61002 / 0.36 (18252) SS BOND : bond 0.01343 / 0.97 ( 6) SS BOND : angle 1.21281 / 0.63 ( 12) hydrogen bonds : bond 0.04997 / 3.47 ( 489) hydrogen bonds : angle 6.33940 / 4.47 ( 1292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7651 (tp) cc_final: 0.7360 (mm) REVERT: A 191 GLU cc_start: 0.8773 (mp0) cc_final: 0.8553 (mt-10) REVERT: A 194 MET cc_start: 0.8136 (tpp) cc_final: 0.7916 (tpp) REVERT: B 2 ARG cc_start: 0.6524 (tpt-90) cc_final: 0.6110 (tpt170) REVERT: B 122 TYR cc_start: 0.7333 (t80) cc_final: 0.7057 (t80) REVERT: B 194 MET cc_start: 0.8519 (tpt) cc_final: 0.8111 (tpp) REVERT: B 202 MET cc_start: 0.7303 (mmm) cc_final: 0.6922 (mmt) REVERT: J 151 LEU cc_start: 0.9044 (pp) cc_final: 0.8711 (pp) REVERT: J 163 MET cc_start: 0.8021 (ptp) cc_final: 0.7707 (ptp) REVERT: J 194 MET cc_start: 0.8636 (mmm) cc_final: 0.8381 (tpp) REVERT: K 90 ILE cc_start: 0.7669 (mt) cc_final: 0.7444 (mt) REVERT: K 218 GLN cc_start: 0.8529 (mt0) cc_final: 0.7873 (tp40) REVERT: L 71 MET cc_start: 0.6387 (mtt) cc_final: 0.5973 (pmm) REVERT: L 105 MET cc_start: 0.7702 (mpp) cc_final: 0.7062 (tpp) REVERT: L 178 PHE cc_start: 0.6741 (m-10) cc_final: 0.6467 (m-10) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2655 time to fit residues: 65.6083 Evaluate side-chains 136 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 48 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.105493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.078835 restraints weight = 131220.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082185 restraints weight = 66793.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.084307 restraints weight = 44501.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085641 restraints weight = 34494.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.086484 restraints weight = 29269.176| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13218 Z= 0.276 Angle : 0.686 7.619 18264 Z= 0.394 Chirality : 0.045 0.169 2025 Planarity : 0.006 0.105 2067 Dihedral : 22.035 90.282 2526 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1347 helix: 0.79 (0.28), residues: 345 sheet: -2.36 (0.29), residues: 287 loop : -0.68 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.024 0.002 TYR L 122 PHE 0.034 0.003 PHE A 31 TRP 0.019 0.002 TRP A 5 HIS 0.009 0.002 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (13212) covalent geometry : angle 0.68542 / 0.39 (18252) SS BOND : bond 0.01229 / 0.63 ( 6) SS BOND : angle 1.44352 / 0.64 ( 12) hydrogen bonds : bond 0.05838 / 4.07 ( 489) hydrogen bonds : angle 6.49325 / 4.58 ( 1292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7786 (tp) cc_final: 0.7447 (mm) REVERT: A 202 MET cc_start: 0.8040 (mmm) cc_final: 0.7738 (mmt) REVERT: B 2 ARG cc_start: 0.6683 (tpt-90) cc_final: 0.6021 (tpt170) REVERT: B 194 MET cc_start: 0.8454 (tpt) cc_final: 0.8000 (tpp) REVERT: B 202 MET cc_start: 0.7443 (mmm) cc_final: 0.7153 (mmt) REVERT: I 24 THR cc_start: 0.8358 (p) cc_final: 0.8126 (p) REVERT: J 163 MET cc_start: 0.8192 (ptp) cc_final: 0.7908 (ptp) REVERT: K 89 GLU cc_start: 0.7821 (pp20) cc_final: 0.7501 (pp20) REVERT: K 218 GLN cc_start: 0.8539 (mt0) cc_final: 0.7871 (tp40) REVERT: L 71 MET cc_start: 0.6503 (mtt) cc_final: 0.6039 (pmm) REVERT: L 105 MET cc_start: 0.7703 (mpp) cc_final: 0.7150 (mpp) REVERT: L 178 PHE cc_start: 0.6790 (m-10) cc_final: 0.6510 (m-10) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2504 time to fit residues: 57.8025 Evaluate side-chains 135 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.106278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079412 restraints weight = 134337.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.082858 restraints weight = 67416.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.085085 restraints weight = 44674.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086428 restraints weight = 34375.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.087271 restraints weight = 29203.407| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13218 Z= 0.200 Angle : 0.624 7.547 18264 Z= 0.364 Chirality : 0.044 0.178 2025 Planarity : 0.006 0.057 2067 Dihedral : 22.065 91.924 2526 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1347 helix: 0.86 (0.28), residues: 333 sheet: -2.32 (0.29), residues: 293 loop : -0.61 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 210 TYR 0.014 0.002 TYR K 110 PHE 0.039 0.002 PHE A 31 TRP 0.015 0.002 TRP A 5 HIS 0.008 0.002 HIS I 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (13212) covalent geometry : angle 0.62317 / 0.36 (18252) SS BOND : bond 0.00693 / 0.37 ( 6) SS BOND : angle 1.46254 / 0.72 ( 12) hydrogen bonds : bond 0.05243 / 3.62 ( 489) hydrogen bonds : angle 6.35212 / 4.47 ( 1292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7720 (tp) cc_final: 0.7371 (mm) REVERT: A 191 GLU cc_start: 0.8733 (mp0) cc_final: 0.8507 (mt-10) REVERT: A 194 MET cc_start: 0.8160 (tpp) cc_final: 0.7951 (tpp) REVERT: A 202 MET cc_start: 0.8078 (mmm) cc_final: 0.7736 (mmt) REVERT: B 2 ARG cc_start: 0.6613 (tpt-90) cc_final: 0.6093 (tpt170) REVERT: B 194 MET cc_start: 0.8440 (tpt) cc_final: 0.7980 (tpp) REVERT: B 202 MET cc_start: 0.7485 (mmm) cc_final: 0.7235 (mmt) REVERT: B 211 TYR cc_start: 0.7469 (m-10) cc_final: 0.7220 (m-10) REVERT: I 24 THR cc_start: 0.8387 (p) cc_final: 0.8159 (p) REVERT: J 151 LEU cc_start: 0.9087 (pp) cc_final: 0.8760 (pp) REVERT: J 163 MET cc_start: 0.8139 (ptp) cc_final: 0.7879 (ptp) REVERT: K 89 GLU cc_start: 0.7873 (pp20) cc_final: 0.7546 (pp20) REVERT: K 218 GLN cc_start: 0.8548 (mt0) cc_final: 0.7906 (tp40) REVERT: L 71 MET cc_start: 0.6626 (mtt) cc_final: 0.6132 (pmm) REVERT: L 105 MET cc_start: 0.7684 (mpp) cc_final: 0.7109 (mpp) REVERT: L 178 PHE cc_start: 0.6782 (m-10) cc_final: 0.6496 (m-10) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2639 time to fit residues: 61.1683 Evaluate side-chains 139 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.107009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080246 restraints weight = 133814.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083751 restraints weight = 65943.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.086012 restraints weight = 43278.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.087406 restraints weight = 33141.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.088261 restraints weight = 28015.566| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13218 Z= 0.161 Angle : 0.610 7.662 18264 Z= 0.356 Chirality : 0.045 0.182 2025 Planarity : 0.006 0.086 2067 Dihedral : 22.079 92.141 2526 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1347 helix: 0.90 (0.28), residues: 333 sheet: -2.21 (0.30), residues: 291 loop : -0.58 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 2 TYR 0.015 0.002 TYR B 122 PHE 0.033 0.002 PHE A 31 TRP 0.013 0.002 TRP A 5 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (13212) covalent geometry : angle 0.60860 / 0.36 (18252) SS BOND : bond 0.01060 / 0.55 ( 6) SS BOND : angle 1.79244 / 0.82 ( 12) hydrogen bonds : bond 0.04903 / 3.41 ( 489) hydrogen bonds : angle 6.28980 / 4.43 ( 1292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7673 (tp) cc_final: 0.7348 (mm) REVERT: A 191 GLU cc_start: 0.8729 (mp0) cc_final: 0.8495 (mt-10) REVERT: A 194 MET cc_start: 0.8157 (tpp) cc_final: 0.7920 (tpp) REVERT: A 202 MET cc_start: 0.8050 (mmm) cc_final: 0.7750 (mmt) REVERT: B 194 MET cc_start: 0.8441 (tpt) cc_final: 0.7981 (tpp) REVERT: B 202 MET cc_start: 0.7523 (mmm) cc_final: 0.7284 (mmt) REVERT: B 211 TYR cc_start: 0.7529 (m-10) cc_final: 0.7287 (m-10) REVERT: I 24 THR cc_start: 0.8389 (p) cc_final: 0.8148 (p) REVERT: J 151 LEU cc_start: 0.9093 (pp) cc_final: 0.8769 (pp) REVERT: J 163 MET cc_start: 0.8151 (ptp) cc_final: 0.7819 (ptp) REVERT: J 172 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6962 (mt-10) REVERT: K 89 GLU cc_start: 0.7844 (pp20) cc_final: 0.7508 (pp20) REVERT: K 218 GLN cc_start: 0.8562 (mt0) cc_final: 0.7916 (tp40) REVERT: L 71 MET cc_start: 0.6419 (mtt) cc_final: 0.6059 (pmm) REVERT: L 105 MET cc_start: 0.7662 (mpp) cc_final: 0.7077 (mpp) REVERT: L 178 PHE cc_start: 0.6776 (m-10) cc_final: 0.6478 (m-10) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2631 time to fit residues: 60.8201 Evaluate side-chains 138 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 9 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.107166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080650 restraints weight = 129934.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.084125 restraints weight = 64895.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.086326 restraints weight = 42739.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.087719 restraints weight = 32781.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.088441 restraints weight = 27651.130| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13218 Z= 0.145 Angle : 0.593 7.741 18264 Z= 0.345 Chirality : 0.045 0.183 2025 Planarity : 0.005 0.051 2067 Dihedral : 22.093 91.420 2526 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1347 helix: 1.05 (0.29), residues: 333 sheet: -2.08 (0.30), residues: 287 loop : -0.50 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 2 TYR 0.030 0.002 TYR B 122 PHE 0.037 0.002 PHE A 31 TRP 0.013 0.002 TRP B 5 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (13212) covalent geometry : angle 0.59178 / 0.34 (18252) SS BOND : bond 0.00942 / 0.50 ( 6) SS BOND : angle 1.40775 / 0.69 ( 12) hydrogen bonds : bond 0.04575 / 3.18 ( 489) hydrogen bonds : angle 6.13839 / 4.33 ( 1292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.05 seconds wall clock time: 78 minutes 59.84 seconds (4739.84 seconds total)