Starting phenix.real_space_refine on Fri Feb 6 12:15:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vf4_43185/02_2026/8vf4_43185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vf4_43185/02_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_43185/02_2026/8vf4_43185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vf4_43185/02_2026/8vf4_43185.map" model { file = "/net/cci-nas-00/data/ceres_data/8vf4_43185/02_2026/8vf4_43185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vf4_43185/02_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-2.0-5952/lib/python3.9/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: 4.57, per 1000 atoms: 0.19 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: 2.26 Conformation dependent library (CDL) restraints added in 697.5 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: 4.53 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: 5.64 Time building geometry restraints manager: 3.12 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=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N MET L 1 " pdb=" CA MET L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 ... (remaining 24997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 44593 1.84 - 3.69: 604 3.69 - 5.53: 38 5.53 - 7.37: 4 7.37 - 9.22: 1 Bond angle restraints: 45240 Sorted by residual: angle pdb=" CG MET K 104 " pdb=" SD MET K 104 " pdb=" CE MET K 104 " ideal model delta sigma weight residual 100.90 107.98 -7.08 2.20e+00 2.07e-01 1.04e+01 angle pdb=" CG ARG B 2 " pdb=" CD ARG B 2 " pdb=" NE ARG B 2 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.95e+00 angle pdb=" CB MET K 104 " pdb=" CG MET K 104 " pdb=" SD MET K 104 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" CB ARG B 2 " pdb=" CG ARG B 2 " pdb=" CD ARG B 2 " ideal model delta sigma weight residual 111.30 104.83 6.47 2.30e+00 1.89e-01 7.91e+00 angle pdb=" C3' DT F 25 " pdb=" C2' DT F 25 " pdb=" C1' DT F 25 " ideal model delta sigma weight residual 101.60 105.47 -3.87 1.50e+00 4.44e-01 6.64e+00 ... (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 - 0.035: 1385 0.035 - 0.070: 392 0.070 - 0.104: 180 0.104 - 0.139: 62 0.139 - 0.174: 6 Chirality restraints: 2025 Sorted by residual: chirality pdb=" CA MET B 1 " pdb=" N MET B 1 " pdb=" C MET B 1 " pdb=" CB MET B 1 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA MET I 162 " pdb=" N MET I 162 " pdb=" C MET I 162 " pdb=" CB MET I 162 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA ILE B 187 " pdb=" N ILE B 187 " pdb=" C ILE B 187 " pdb=" CB ILE B 187 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-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: 8.750 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: 0.140 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.880 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 : 0.003 0.041 13218 Z= 0.141 Angle : 0.588 9.219 18264 Z= 0.329 Chirality : 0.043 0.174 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 covalent geometry : bond 0.00310 (13212) covalent geometry : angle 0.58741 (18252) SS BOND : bond 0.00575 ( 6) SS BOND : angle 1.40573 ( 12) hydrogen bonds : bond 0.21359 ( 489) hydrogen bonds : angle 8.35180 ( 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 : 0.647 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 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: 0.8128 (p) REVERT: I 202 MET cc_start: 0.7322 (mmm) cc_final: 0.6774 (mmt) REVERT: J 151 LEU cc_start: 0.9151 (pp) cc_final: 0.8859 (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: 0.3071 time to fit residues: 85.4158 Evaluate side-chains 160 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 144 ASN K 218 GLN L 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.109354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.083371 restraints weight = 136061.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087008 restraints weight = 66907.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.089354 restraints weight = 43573.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.090799 restraints weight = 33055.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.091758 restraints weight = 27706.275| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13218 Z= 0.195 Angle : 0.660 5.018 18264 Z= 0.376 Chirality : 0.046 0.168 2025 Planarity : 0.007 0.079 2067 Dihedral : 21.803 86.997 2526 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.97 % 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: -0.53 (0.23), residues: 1347 helix: 1.23 (0.28), residues: 327 sheet: -1.76 (0.32), residues: 256 loop : -0.48 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 134 TYR 0.016 0.002 TYR K 110 PHE 0.058 0.002 PHE A 31 TRP 0.019 0.002 TRP I 5 HIS 0.015 0.002 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00434 (13212) covalent geometry : angle 0.65942 (18252) SS BOND : bond 0.00962 ( 6) SS BOND : angle 1.45804 ( 12) hydrogen bonds : bond 0.05635 ( 489) hydrogen bonds : angle 7.01591 ( 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 210 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.668 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 30 ARG cc_start: 0.7493 (mmp80) cc_final: 0.7285 (mmp80) REVERT: A 129 LEU cc_start: 0.7689 (tp) cc_final: 0.7186 (mm) REVERT: B 129 LEU cc_start: 0.7780 (tp) cc_final: 0.7550 (mm) REVERT: I 24 THR cc_start: 0.8097 (p) cc_final: 0.7892 (p) REVERT: I 95 PHE cc_start: 0.7701 (m-10) cc_final: 0.7319 (m-10) REVERT: I 152 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8350 (ttm-80) REVERT: J 151 LEU cc_start: 0.8984 (pp) cc_final: 0.8528 (pp) REVERT: J 194 MET cc_start: 0.8636 (mmm) cc_final: 0.8387 (tpp) REVERT: K 135 MET cc_start: 0.7659 (mmp) cc_final: 0.6488 (mtt) REVERT: K 202 MET cc_start: 0.7898 (mmm) cc_final: 0.7407 (mmt) REVERT: L 71 MET cc_start: 0.6440 (mtt) cc_final: 0.5856 (pmm) REVERT: L 121 SER cc_start: 0.8652 (m) cc_final: 0.8341 (t) outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 0.3143 time to fit residues: 88.6638 Evaluate side-chains 142 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 1.9990 chunk 103 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS J 183 GLN L 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.108786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083317 restraints weight = 129685.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.086906 restraints weight = 63614.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.089201 restraints weight = 41132.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.090632 restraints weight = 31152.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.091526 restraints weight = 26020.122| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13218 Z= 0.159 Angle : 0.600 5.062 18264 Z= 0.343 Chirality : 0.044 0.163 2025 Planarity : 0.005 0.053 2067 Dihedral : 21.733 87.091 2526 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 1.18 (0.28), residues: 327 sheet: -2.01 (0.32), residues: 265 loop : -0.41 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 210 TYR 0.010 0.001 TYR I 21 PHE 0.028 0.002 PHE A 31 TRP 0.008 0.002 TRP I 5 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00355 (13212) covalent geometry : angle 0.59922 (18252) SS BOND : bond 0.00522 ( 6) SS BOND : angle 1.27176 ( 12) hydrogen bonds : bond 0.04734 ( 489) hydrogen bonds : angle 6.59714 ( 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 181 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.598 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: 0.7605 (tp) cc_final: 0.7302 (mm) REVERT: A 194 MET cc_start: 0.8106 (tpp) cc_final: 0.7904 (tpp) REVERT: B 122 TYR cc_start: 0.6974 (t80) cc_final: 0.6731 (t80) REVERT: B 202 MET cc_start: 0.7224 (mmm) cc_final: 0.6807 (mmt) REVERT: I 24 THR cc_start: 0.8002 (p) cc_final: 0.7782 (p) REVERT: I 135 MET cc_start: 0.7470 (mmp) cc_final: 0.7089 (tpp) REVERT: J 151 LEU cc_start: 0.9075 (pp) cc_final: 0.8732 (pp) REVERT: J 194 MET cc_start: 0.8667 (mmm) cc_final: 0.8416 (tpp) REVERT: K 135 MET cc_start: 0.7473 (mmp) cc_final: 0.6335 (mtt) REVERT: K 202 MET cc_start: 0.7901 (mmm) cc_final: 0.7437 (mmt) REVERT: K 218 GLN cc_start: 0.8503 (mt0) cc_final: 0.7844 (tp40) REVERT: L 71 MET cc_start: 0.6406 (mtt) cc_final: 0.5821 (pmm) REVERT: L 121 SER cc_start: 0.8616 (m) cc_final: 0.8388 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2917 time to fit residues: 72.6918 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 : 0.615 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 HIS ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.107953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.081597 restraints weight = 133613.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.085166 restraints weight = 65559.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.087399 restraints weight = 42959.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.088798 restraints weight = 33016.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.089661 restraints weight = 27912.505| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13218 Z= 0.170 Angle : 0.591 4.933 18264 Z= 0.338 Chirality : 0.044 0.159 2025 Planarity : 0.005 0.049 2067 Dihedral : 21.638 87.625 2526 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % 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: -0.61 (0.23), residues: 1347 helix: 1.21 (0.29), residues: 327 sheet: -2.12 (0.32), residues: 263 loop : -0.40 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 210 TYR 0.011 0.001 TYR K 44 PHE 0.026 0.002 PHE A 31 TRP 0.010 0.002 TRP I 5 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00376 (13212) covalent geometry : angle 0.59061 (18252) SS BOND : bond 0.00951 ( 6) SS BOND : angle 1.23030 ( 12) hydrogen bonds : bond 0.04432 ( 489) hydrogen bonds : angle 6.25370 ( 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: 1 poor density : 178 time to evaluate : 0.689 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: 0.7657 (tp) cc_final: 0.7335 (mm) REVERT: A 194 MET cc_start: 0.8142 (tpp) cc_final: 0.7924 (tpp) REVERT: B 202 MET cc_start: 0.7380 (mmm) cc_final: 0.6983 (mmt) REVERT: J 151 LEU cc_start: 0.9062 (pp) cc_final: 0.8693 (pp) REVERT: J 194 MET cc_start: 0.8675 (mmm) cc_final: 0.8423 (tpp) REVERT: K 89 GLU cc_start: 0.7923 (pp20) cc_final: 0.7553 (pp20) REVERT: K 135 MET cc_start: 0.7450 (mmp) cc_final: 0.6413 (mtt) REVERT: K 151 LEU cc_start: 0.8617 (mp) cc_final: 0.8364 (mp) REVERT: K 218 GLN cc_start: 0.8577 (mt0) cc_final: 0.7912 (tp40) REVERT: L 71 MET cc_start: 0.6334 (mtt) cc_final: 0.5890 (pmm) REVERT: L 121 SER cc_start: 0.8622 (m) cc_final: 0.8396 (t) REVERT: L 122 TYR cc_start: 0.8426 (t80) cc_final: 0.7887 (t80) REVERT: L 178 PHE cc_start: 0.6540 (m-10) cc_final: 0.6286 (m-10) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2697 time to fit residues: 65.7654 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 : 0.605 ------------------------------------------------------------------------------- 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: 0.9990 chunk 137 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.107523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.081159 restraints weight = 129033.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.084573 restraints weight = 64708.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.086776 restraints weight = 42896.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.088141 restraints weight = 32990.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.088989 restraints weight = 27910.512| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13218 Z= 0.172 Angle : 0.587 5.191 18264 Z= 0.335 Chirality : 0.044 0.158 2025 Planarity : 0.005 0.045 2067 Dihedral : 21.590 88.307 2526 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1347 helix: 1.17 (0.29), residues: 333 sheet: -2.12 (0.32), residues: 267 loop : -0.44 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.036 0.002 TYR A 21 PHE 0.022 0.002 PHE A 31 TRP 0.009 0.001 TRP B 169 HIS 0.009 0.001 HIS J 139 Details of bonding type rmsd covalent geometry : bond 0.00379 (13212) covalent geometry : angle 0.58602 (18252) SS BOND : bond 0.00692 ( 6) SS BOND : angle 1.16242 ( 12) hydrogen bonds : bond 0.04369 ( 489) hydrogen bonds : angle 6.12353 ( 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 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.667 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: 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: 0.7309 (mm) REVERT: A 194 MET cc_start: 0.8111 (tpp) cc_final: 0.7889 (tpp) REVERT: A 202 MET cc_start: 0.8017 (mmm) cc_final: 0.7694 (mmt) REVERT: B 122 TYR cc_start: 0.7227 (t80) cc_final: 0.6833 (t80) REVERT: B 154 LYS cc_start: 0.8355 (tmtt) cc_final: 0.7979 (tttp) REVERT: B 202 MET cc_start: 0.7400 (mmm) cc_final: 0.7112 (mmt) REVERT: I 111 PHE cc_start: 0.7463 (m-10) cc_final: 0.7170 (m-10) REVERT: J 104 MET cc_start: 0.9001 (mmm) cc_final: 0.8719 (mmm) REVERT: J 194 MET cc_start: 0.8681 (mmm) cc_final: 0.8426 (tpp) REVERT: K 110 TYR cc_start: 0.8065 (m-80) cc_final: 0.7848 (m-80) REVERT: K 218 GLN cc_start: 0.8534 (mt0) cc_final: 0.7936 (tp40) REVERT: L 71 MET cc_start: 0.6326 (mtt) cc_final: 0.5942 (pmm) REVERT: L 105 MET cc_start: 0.7539 (mpp) cc_final: 0.6994 (tpp) REVERT: L 121 SER cc_start: 0.8600 (m) cc_final: 0.8398 (t) REVERT: L 178 PHE cc_start: 0.6586 (m-10) cc_final: 0.6304 (m-10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2633 time to fit residues: 62.4023 Evaluate side-chains 141 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.106894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.080480 restraints weight = 129386.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.083962 restraints weight = 64985.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.086170 restraints weight = 42766.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.087522 restraints weight = 32782.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.088331 restraints weight = 27793.382| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13218 Z= 0.176 Angle : 0.583 4.749 18264 Z= 0.333 Chirality : 0.044 0.152 2025 Planarity : 0.005 0.045 2067 Dihedral : 21.566 89.628 2526 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.46 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: -0.69 (0.23), residues: 1347 helix: 1.13 (0.29), residues: 333 sheet: -2.04 (0.31), residues: 283 loop : -0.44 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 30 TYR 0.016 0.002 TYR B 211 PHE 0.055 0.002 PHE A 31 TRP 0.009 0.001 TRP A 5 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00389 (13212) covalent geometry : angle 0.58286 (18252) SS BOND : bond 0.00837 ( 6) SS BOND : angle 1.04145 ( 12) hydrogen bonds : bond 0.04330 ( 489) hydrogen bonds : angle 6.03705 ( 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 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.623 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: symmetry clash REVERT: A 129 LEU cc_start: 0.7729 (tp) cc_final: 0.7355 (mm) REVERT: A 154 LYS cc_start: 0.8108 (tttt) cc_final: 0.7824 (tttm) REVERT: A 191 GLU cc_start: 0.8700 (mp0) cc_final: 0.8453 (mt-10) REVERT: A 194 MET cc_start: 0.8096 (tpp) cc_final: 0.7881 (tpp) REVERT: A 202 MET cc_start: 0.7990 (mmm) cc_final: 0.7676 (mmt) REVERT: B 202 MET cc_start: 0.7387 (mmm) cc_final: 0.7164 (mmt) REVERT: J 151 LEU cc_start: 0.9144 (pp) cc_final: 0.8797 (pp) REVERT: J 194 MET cc_start: 0.8675 (mmm) cc_final: 0.8412 (tpp) REVERT: K 89 GLU cc_start: 0.7814 (pp20) cc_final: 0.7475 (pp20) REVERT: K 218 GLN cc_start: 0.8547 (mt0) cc_final: 0.7935 (tp40) REVERT: L 71 MET cc_start: 0.6326 (mtt) cc_final: 0.5981 (pmm) REVERT: L 105 MET cc_start: 0.7585 (mpp) cc_final: 0.6885 (tpp) REVERT: L 122 TYR cc_start: 0.8443 (t80) cc_final: 0.8189 (t80) REVERT: L 178 PHE cc_start: 0.6594 (m-10) cc_final: 0.6333 (m-10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2623 time to fit residues: 62.3796 Evaluate side-chains 140 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079901 restraints weight = 134770.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083329 restraints weight = 67701.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.085499 restraints weight = 44833.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.086815 restraints weight = 34633.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.087659 restraints weight = 29460.510| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4433 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= 0.195 Angle : 0.599 5.533 18264 Z= 0.342 Chirality : 0.044 0.153 2025 Planarity : 0.005 0.046 2067 Dihedral : 21.561 91.838 2526 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % 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 : 0.00 % 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: -0.79 (0.23), residues: 1347 helix: 1.05 (0.28), residues: 333 sheet: -2.14 (0.30), residues: 287 loop : -0.48 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 30 TYR 0.024 0.002 TYR B 122 PHE 0.028 0.002 PHE A 31 TRP 0.011 0.002 TRP B 169 HIS 0.006 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00427 (13212) covalent geometry : angle 0.59799 (18252) SS BOND : bond 0.00572 ( 6) SS BOND : angle 1.40248 ( 12) hydrogen bonds : bond 0.04521 ( 489) hydrogen bonds : angle 6.04317 ( 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 163 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.601 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: 0.7737 (tp) cc_final: 0.7357 (mm) REVERT: A 191 GLU cc_start: 0.8726 (mp0) cc_final: 0.8483 (mt-10) REVERT: A 194 MET cc_start: 0.8116 (tpp) cc_final: 0.7866 (tpp) REVERT: A 202 MET cc_start: 0.7993 (mmm) cc_final: 0.7711 (mmt) REVERT: K 89 GLU cc_start: 0.7817 (pp20) cc_final: 0.7474 (pp20) REVERT: K 135 MET cc_start: 0.7406 (mmp) cc_final: 0.6391 (mtt) REVERT: L 71 MET cc_start: 0.6422 (mtt) cc_final: 0.6076 (pmm) REVERT: L 105 MET cc_start: 0.7693 (mpp) cc_final: 0.7015 (mpp) REVERT: L 178 PHE cc_start: 0.6736 (m-10) cc_final: 0.6438 (m-10) REVERT: L 194 MET cc_start: 0.8809 (tpp) cc_final: 0.8355 (tpt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2594 time to fit residues: 58.8375 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 : 0.577 ------------------------------------------------------------------------------- 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: 4.9990 chunk 116 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.105228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078490 restraints weight = 134060.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081769 restraints weight = 68369.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083885 restraints weight = 45863.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085135 restraints weight = 35638.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.086058 restraints weight = 30532.021| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13218 Z= 0.229 Angle : 0.623 9.607 18264 Z= 0.354 Chirality : 0.045 0.151 2025 Planarity : 0.006 0.060 2067 Dihedral : 21.631 96.851 2526 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -0.95 (0.23), residues: 1347 helix: 0.85 (0.28), residues: 333 sheet: -2.23 (0.29), residues: 291 loop : -0.53 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 30 TYR 0.021 0.002 TYR B 122 PHE 0.033 0.002 PHE A 31 TRP 0.014 0.002 TRP B 169 HIS 0.008 0.002 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00501 (13212) covalent geometry : angle 0.62209 (18252) SS BOND : bond 0.00591 ( 6) SS BOND : angle 1.70961 ( 12) hydrogen bonds : bond 0.04897 ( 489) hydrogen bonds : angle 6.06221 ( 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 159 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.533 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: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7864 (t80) cc_final: 0.7455 (t80) REVERT: A 129 LEU cc_start: 0.7836 (tp) cc_final: 0.7370 (mm) REVERT: A 194 MET cc_start: 0.8175 (tpp) cc_final: 0.7875 (tpp) REVERT: A 202 MET cc_start: 0.8047 (mmm) cc_final: 0.7803 (mmt) REVERT: K 89 GLU cc_start: 0.7831 (pp20) cc_final: 0.7478 (pp20) REVERT: K 135 MET cc_start: 0.7406 (mmp) cc_final: 0.6367 (mtt) REVERT: K 202 MET cc_start: 0.7919 (mmm) cc_final: 0.7506 (mmt) REVERT: K 218 GLN cc_start: 0.8546 (mt0) cc_final: 0.7950 (tp40) REVERT: L 71 MET cc_start: 0.6541 (mtt) cc_final: 0.6062 (pmm) REVERT: L 163 MET cc_start: 0.8270 (ptt) cc_final: 0.7862 (ptp) REVERT: L 178 PHE cc_start: 0.6789 (m-10) cc_final: 0.6438 (m-10) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2811 time to fit residues: 61.0073 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 : 0.512 ------------------------------------------------------------------------------- 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: 0.6980 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.105459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078730 restraints weight = 131340.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082155 restraints weight = 65652.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.084335 restraints weight = 43276.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.085670 restraints weight = 33257.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086568 restraints weight = 28232.491| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13218 Z= 0.191 Angle : 0.602 6.751 18264 Z= 0.342 Chirality : 0.044 0.147 2025 Planarity : 0.006 0.074 2067 Dihedral : 21.647 100.313 2526 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.84 (0.23), residues: 1347 helix: 0.98 (0.28), residues: 333 sheet: -2.14 (0.30), residues: 283 loop : -0.53 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 46 TYR 0.020 0.002 TYR L 122 PHE 0.027 0.002 PHE A 31 TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00421 (13212) covalent geometry : angle 0.60094 (18252) SS BOND : bond 0.00476 ( 6) SS BOND : angle 1.43448 ( 12) hydrogen bonds : bond 0.04515 ( 489) hydrogen bonds : angle 5.95661 ( 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 161 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.417 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 122 TYR cc_start: 0.7851 (t80) cc_final: 0.7507 (t80) REVERT: A 129 LEU cc_start: 0.7789 (tp) cc_final: 0.7331 (mm) REVERT: A 191 GLU cc_start: 0.8723 (mp0) cc_final: 0.8466 (mt-10) REVERT: A 194 MET cc_start: 0.8202 (tpp) cc_final: 0.7908 (tpp) REVERT: A 202 MET cc_start: 0.8047 (mmm) cc_final: 0.7821 (mmt) REVERT: J 151 LEU cc_start: 0.9168 (pp) cc_final: 0.8877 (pp) REVERT: J 163 MET cc_start: 0.7792 (ptp) cc_final: 0.7577 (ptp) REVERT: K 89 GLU cc_start: 0.7784 (pp20) cc_final: 0.7431 (pp20) REVERT: K 135 MET cc_start: 0.7422 (mmp) cc_final: 0.6384 (mtt) REVERT: K 202 MET cc_start: 0.7899 (mmm) cc_final: 0.7509 (mmt) REVERT: K 218 GLN cc_start: 0.8519 (mt0) cc_final: 0.7928 (tp40) REVERT: L 71 MET cc_start: 0.6539 (mtt) cc_final: 0.6101 (pmm) REVERT: L 122 TYR cc_start: 0.8499 (t80) cc_final: 0.8271 (t80) REVERT: L 163 MET cc_start: 0.8249 (ptt) cc_final: 0.7861 (ptp) REVERT: L 178 PHE cc_start: 0.6824 (m-10) cc_final: 0.6512 (m-10) REVERT: L 194 MET cc_start: 0.8842 (tpp) cc_final: 0.8148 (tpt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2958 time to fit residues: 64.3282 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 : 0.538 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.0270 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.106143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079242 restraints weight = 134205.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082682 restraints weight = 66613.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.084885 restraints weight = 43997.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.086263 restraints weight = 33840.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.087115 restraints weight = 28666.429| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13218 Z= 0.164 Angle : 0.582 6.869 18264 Z= 0.330 Chirality : 0.044 0.146 2025 Planarity : 0.005 0.049 2067 Dihedral : 21.648 103.821 2526 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.72 (0.23), residues: 1347 helix: 1.13 (0.29), residues: 333 sheet: -2.14 (0.29), residues: 291 loop : -0.41 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 152 TYR 0.017 0.002 TYR L 122 PHE 0.024 0.002 PHE A 31 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00364 (13212) covalent geometry : angle 0.58158 (18252) SS BOND : bond 0.00463 ( 6) SS BOND : angle 1.21447 ( 12) hydrogen bonds : bond 0.04131 ( 489) hydrogen bonds : angle 5.82984 ( 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 162 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.636 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 122 TYR cc_start: 0.7836 (t80) cc_final: 0.7541 (t80) REVERT: A 129 LEU cc_start: 0.7779 (tp) cc_final: 0.7342 (mm) REVERT: A 191 GLU cc_start: 0.8723 (mp0) cc_final: 0.8449 (mt-10) REVERT: A 194 MET cc_start: 0.8194 (tpp) cc_final: 0.7921 (tpp) REVERT: A 202 MET cc_start: 0.8003 (mmm) cc_final: 0.7770 (mmt) REVERT: J 151 LEU cc_start: 0.9137 (pp) cc_final: 0.8881 (pp) REVERT: J 163 MET cc_start: 0.7832 (ptp) cc_final: 0.7564 (ptp) REVERT: K 89 GLU cc_start: 0.7810 (pp20) cc_final: 0.7429 (pp20) REVERT: K 105 MET cc_start: 0.8071 (mtt) cc_final: 0.7443 (mtt) REVERT: K 135 MET cc_start: 0.7592 (mmp) cc_final: 0.6634 (mtt) REVERT: K 202 MET cc_start: 0.7860 (mmm) cc_final: 0.7497 (mmt) REVERT: K 218 GLN cc_start: 0.8536 (mt0) cc_final: 0.7924 (tp40) REVERT: L 71 MET cc_start: 0.6558 (mtt) cc_final: 0.6115 (pmm) REVERT: L 122 TYR cc_start: 0.8523 (t80) cc_final: 0.8311 (t80) REVERT: L 178 PHE cc_start: 0.6792 (m-10) cc_final: 0.6514 (m-10) REVERT: L 194 MET cc_start: 0.8833 (tpp) cc_final: 0.8214 (tpt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2868 time to fit residues: 63.7635 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 : 0.468 ------------------------------------------------------------------------------- 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: 0.0980 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4136 r_free = 0.4136 target = 0.106510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079595 restraints weight = 134597.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083131 restraints weight = 66074.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085393 restraints weight = 43540.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.086798 restraints weight = 33466.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.087660 restraints weight = 28268.862| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4978 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= 0.146 Angle : 0.578 6.963 18264 Z= 0.326 Chirality : 0.044 0.144 2025 Planarity : 0.005 0.045 2067 Dihedral : 21.626 104.273 2526 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -0.63 (0.23), residues: 1347 helix: 1.21 (0.29), residues: 333 sheet: -2.11 (0.29), residues: 293 loop : -0.34 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.017 0.001 TYR L 122 PHE 0.023 0.001 PHE A 31 TRP 0.030 0.002 TRP A 5 HIS 0.006 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00326 (13212) covalent geometry : angle 0.57745 (18252) SS BOND : bond 0.00570 ( 6) SS BOND : angle 0.99356 ( 12) hydrogen bonds : bond 0.04013 ( 489) hydrogen bonds : angle 5.75536 ( 1292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4556.13 seconds wall clock time: 78 minutes 18.03 seconds (4698.03 seconds total)