Starting phenix.real_space_refine on Thu Feb 5 13:29:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpr_61712/02_2026/9jpr_61712.cif" } resolution = 2.8 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= 0.003 sd= 0.100 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11040 2.51 5 N 2976 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s 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: 17424 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "B" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "G" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "H" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2178 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Time building chain proxies: 3.88, per 1000 atoms: 0.22 Number of scatterers: 17424 At special positions: 0 Unit cell: (139.65, 113.05, 200.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3320 8.00 N 2976 7.00 C 11040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS F 218 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS H 218 " 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: 1.57 Conformation dependent library (CDL) restraints added in 814.7 milliseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 26 sheets defined 38.5% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.961A pdb=" N THR A 40 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 41 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG A 139 " --> pdb=" O MET A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.791A pdb=" N LEU A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.771A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.960A pdb=" N THR B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 41 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG B 139 " --> pdb=" O MET B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.792A pdb=" N LEU B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 188 removed outlier: 3.771A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.961A pdb=" N THR C 40 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG C 139 " --> pdb=" O MET C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.791A pdb=" N LEU C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.771A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'D' and resid 36 through 41 removed outlier: 3.962A pdb=" N THR D 40 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 41 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.662A pdb=" N ARG D 139 " --> pdb=" O MET D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 158 removed outlier: 3.791A pdb=" N LEU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.770A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'E' and resid 36 through 41 removed outlier: 3.961A pdb=" N THR E 40 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 41 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 56 Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.664A pdb=" N ARG E 139 " --> pdb=" O MET E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 158 removed outlier: 3.791A pdb=" N LEU E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 removed outlier: 3.770A pdb=" N ASP E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 262 through 267 Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.962A pdb=" N THR F 40 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL F 41 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 87 through 90 Processing helix chain 'F' and resid 99 through 105 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG F 139 " --> pdb=" O MET F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 158 removed outlier: 3.790A pdb=" N LEU F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.770A pdb=" N ASP F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'G' and resid 36 through 41 removed outlier: 3.961A pdb=" N THR G 40 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 41 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG G 139 " --> pdb=" O MET G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 158 removed outlier: 3.791A pdb=" N LEU G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 188 removed outlier: 3.771A pdb=" N ASP G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 201 Processing helix chain 'G' and resid 262 through 267 Processing helix chain 'G' and resid 268 through 273 Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.961A pdb=" N THR H 40 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 41 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 56 Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 135 through 140 removed outlier: 3.663A pdb=" N ARG H 139 " --> pdb=" O MET H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 158 removed outlier: 3.790A pdb=" N LEU H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 188 removed outlier: 3.770A pdb=" N ASP H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 201 Processing helix chain 'H' and resid 262 through 267 Processing helix chain 'H' and resid 268 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 260 removed outlier: 3.620A pdb=" N GLN B 252 " --> pdb=" O GLN E 260 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG B 254 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN E 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 254 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 252 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AB1, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 66 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AB4, first strand: chain 'D' and resid 173 through 175 Processing sheet with id=AB5, first strand: chain 'D' and resid 252 through 260 removed outlier: 3.723A pdb=" N GLN D 252 " --> pdb=" O GLN G 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN G 260 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 254 " --> pdb=" O GLN G 258 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN G 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG G 254 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AB8, first strand: chain 'E' and resid 173 through 175 Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 66 Processing sheet with id=AC1, first strand: chain 'F' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'F' and resid 173 through 175 Processing sheet with id=AC3, first strand: chain 'G' and resid 58 through 66 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 95 Processing sheet with id=AC5, first strand: chain 'G' and resid 173 through 175 Processing sheet with id=AC6, first strand: chain 'H' and resid 58 through 66 Processing sheet with id=AC7, first strand: chain 'H' and resid 92 through 95 Processing sheet with id=AC8, first strand: chain 'H' and resid 173 through 175 648 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5816 1.34 - 1.46: 3811 1.46 - 1.58: 7997 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 17736 Sorted by residual: bond pdb=" CG PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 1.503 1.487 0.016 3.40e-02 8.65e+02 2.31e-01 bond pdb=" CG PRO H 24 " pdb=" CD PRO H 24 " ideal model delta sigma weight residual 1.503 1.487 0.016 3.40e-02 8.65e+02 2.30e-01 bond pdb=" C VAL E 145 " pdb=" O VAL E 145 " ideal model delta sigma weight residual 1.237 1.232 0.005 9.80e-03 1.04e+04 2.16e-01 bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.487 0.016 3.40e-02 8.65e+02 2.15e-01 bond pdb=" CG PRO B 24 " pdb=" CD PRO B 24 " ideal model delta sigma weight residual 1.503 1.488 0.015 3.40e-02 8.65e+02 2.06e-01 ... (remaining 17731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 23075 0.92 - 1.84: 705 1.84 - 2.75: 178 2.75 - 3.67: 42 3.67 - 4.59: 16 Bond angle restraints: 24016 Sorted by residual: angle pdb=" N LEU F 284 " pdb=" CA LEU F 284 " pdb=" C LEU F 284 " ideal model delta sigma weight residual 108.46 111.35 -2.89 1.51e+00 4.39e-01 3.66e+00 angle pdb=" N LEU A 284 " pdb=" CA LEU A 284 " pdb=" C LEU A 284 " ideal model delta sigma weight residual 108.46 111.35 -2.89 1.51e+00 4.39e-01 3.66e+00 angle pdb=" N LEU H 284 " pdb=" CA LEU H 284 " pdb=" C LEU H 284 " ideal model delta sigma weight residual 108.46 111.33 -2.87 1.51e+00 4.39e-01 3.61e+00 angle pdb=" N LEU E 284 " pdb=" CA LEU E 284 " pdb=" C LEU E 284 " ideal model delta sigma weight residual 108.46 111.33 -2.87 1.51e+00 4.39e-01 3.61e+00 angle pdb=" N LEU G 284 " pdb=" CA LEU G 284 " pdb=" C LEU G 284 " ideal model delta sigma weight residual 108.46 111.32 -2.86 1.51e+00 4.39e-01 3.60e+00 ... (remaining 24011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 9599 14.15 - 28.29: 929 28.29 - 42.44: 184 42.44 - 56.58: 80 56.58 - 70.73: 44 Dihedral angle restraints: 10836 sinusoidal: 4452 harmonic: 6384 Sorted by residual: dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS H 218 " pdb=" CB CYS H 218 " ideal model delta sinusoidal sigma weight residual -86.00 -17.00 -69.00 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -17.16 -68.84 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS E 218 " pdb=" SG CYS E 218 " pdb=" SG CYS F 218 " pdb=" CB CYS F 218 " ideal model delta sinusoidal sigma weight residual -86.00 -17.17 -68.83 1 1.00e+01 1.00e-02 6.13e+01 ... (remaining 10833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1536 0.029 - 0.058: 860 0.058 - 0.088: 178 0.088 - 0.117: 97 0.117 - 0.146: 25 Chirality restraints: 2696 Sorted by residual: chirality pdb=" CA ILE G 288 " pdb=" N ILE G 288 " pdb=" C ILE G 288 " pdb=" CB ILE G 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE F 288 " pdb=" N ILE F 288 " pdb=" C ILE F 288 " pdb=" CB ILE F 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE E 288 " pdb=" N ILE E 288 " pdb=" C ILE E 288 " pdb=" CB ILE E 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2693 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 23 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO D 24 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 24 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 24 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 23 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 24 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 23 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO H 24 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 24 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 24 " -0.021 5.00e-02 4.00e+02 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2974 2.77 - 3.30: 16151 3.30 - 3.83: 28148 3.83 - 4.37: 34127 4.37 - 4.90: 59538 Nonbonded interactions: 140938 Sorted by model distance: nonbonded pdb=" OD2 ASP E 43 " pdb=" OH TYR F 273 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP G 43 " pdb=" OH TYR H 273 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP C 43 " pdb=" OH TYR D 273 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP A 43 " pdb=" OH TYR B 273 " model vdw 2.258 3.040 nonbonded pdb=" OG SER G 36 " pdb=" OD1 ASP G 38 " model vdw 2.258 3.040 ... (remaining 140933 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.840 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 17740 Z= 0.077 Angle : 0.434 4.590 24024 Z= 0.235 Chirality : 0.039 0.146 2696 Planarity : 0.004 0.038 3144 Dihedral : 12.699 70.730 6696 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.15 (0.18), residues: 2128 helix: -0.00 (0.20), residues: 704 sheet: 0.28 (0.30), residues: 232 loop : -0.13 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 254 TYR 0.005 0.001 TYR B 149 PHE 0.010 0.001 PHE E 27 TRP 0.005 0.001 TRP A 45 HIS 0.001 0.001 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00154 (17736) covalent geometry : angle 0.43245 (24016) SS BOND : bond 0.00463 ( 4) SS BOND : angle 2.19808 ( 8) hydrogen bonds : bond 0.11577 ( 648) hydrogen bonds : angle 5.66147 ( 1653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.710 Fit side-chains REVERT: A 83 ASP cc_start: 0.7282 (m-30) cc_final: 0.7055 (m-30) REVERT: A 134 LEU cc_start: 0.7969 (mt) cc_final: 0.7687 (mt) REVERT: A 137 TYR cc_start: 0.7821 (m-80) cc_final: 0.7554 (m-80) REVERT: B 136 MET cc_start: 0.6965 (mpp) cc_final: 0.6554 (ppp) REVERT: C 136 MET cc_start: 0.7475 (mpp) cc_final: 0.7164 (mpt) REVERT: D 136 MET cc_start: 0.7124 (mpp) cc_final: 0.6758 (ppp) REVERT: D 139 ARG cc_start: 0.6693 (mtm110) cc_final: 0.5940 (tpp-160) REVERT: E 139 ARG cc_start: 0.7083 (mtm110) cc_final: 0.5734 (tpt170) REVERT: F 135 ARG cc_start: 0.6897 (mmt90) cc_final: 0.6626 (mmt90) REVERT: F 136 MET cc_start: 0.7209 (mpp) cc_final: 0.6534 (ptt) REVERT: F 248 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6826 (tm-30) REVERT: G 37 SER cc_start: 0.8744 (p) cc_final: 0.8508 (m) REVERT: H 139 ARG cc_start: 0.6869 (mtm110) cc_final: 0.5416 (mtp180) REVERT: H 183 ASP cc_start: 0.5381 (m-30) cc_final: 0.5114 (p0) outliers start: 0 outliers final: 3 residues processed: 445 average time/residue: 0.8019 time to fit residues: 388.9173 Evaluate side-chains 223 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain C residue 255 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 247 ASN A 252 GLN B 98 ASN B 247 ASN ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN D 247 ASN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN F 247 ASN G 98 ASN G 247 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN H 268 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111725 restraints weight = 20578.508| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.98 r_work: 0.3076 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17740 Z= 0.147 Angle : 0.526 8.453 24024 Z= 0.271 Chirality : 0.043 0.155 2696 Planarity : 0.004 0.044 3144 Dihedral : 3.905 30.769 2398 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.30 % Allowed : 11.08 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2128 helix: -0.30 (0.19), residues: 744 sheet: 0.16 (0.30), residues: 248 loop : -0.12 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 222 TYR 0.012 0.001 TYR B 273 PHE 0.013 0.002 PHE F 27 TRP 0.008 0.002 TRP H 45 HIS 0.003 0.002 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00349 (17736) covalent geometry : angle 0.52308 (24016) SS BOND : bond 0.00545 ( 4) SS BOND : angle 2.90547 ( 8) hydrogen bonds : bond 0.02960 ( 648) hydrogen bonds : angle 5.18385 ( 1653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.674 Fit side-chains REVERT: A 134 LEU cc_start: 0.8207 (mt) cc_final: 0.7802 (mt) REVERT: A 137 TYR cc_start: 0.7968 (m-80) cc_final: 0.7584 (m-80) REVERT: B 136 MET cc_start: 0.7212 (mpp) cc_final: 0.6217 (ppp) REVERT: B 211 GLU cc_start: 0.8403 (pm20) cc_final: 0.8009 (pm20) REVERT: B 229 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (mt) REVERT: B 239 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8068 (mm110) REVERT: C 136 MET cc_start: 0.7745 (mpp) cc_final: 0.7293 (mpt) REVERT: C 257 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 268 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7651 (tp-100) REVERT: C 286 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8136 (ptmm) REVERT: D 136 MET cc_start: 0.7108 (mpp) cc_final: 0.6474 (ppp) REVERT: D 139 ARG cc_start: 0.6913 (mtm110) cc_final: 0.5729 (tpp-160) REVERT: E 87 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: E 136 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5387 (ppp) REVERT: E 139 ARG cc_start: 0.7132 (mtm110) cc_final: 0.5472 (tpt170) REVERT: E 143 GLU cc_start: 0.6939 (pm20) cc_final: 0.6635 (pm20) REVERT: F 41 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8714 (t) REVERT: F 135 ARG cc_start: 0.7083 (mmt90) cc_final: 0.6727 (mmt90) REVERT: F 136 MET cc_start: 0.7437 (mpp) cc_final: 0.6225 (ptt) REVERT: F 139 ARG cc_start: 0.7209 (ptm160) cc_final: 0.6620 (ptt-90) REVERT: F 248 GLU cc_start: 0.7881 (mm-30) cc_final: 0.6951 (tm-30) REVERT: G 136 MET cc_start: 0.7783 (mpt) cc_final: 0.6284 (ppp) REVERT: H 43 ASP cc_start: 0.8808 (p0) cc_final: 0.8532 (p0) REVERT: H 139 ARG cc_start: 0.6877 (mtm110) cc_final: 0.5319 (mtp-110) REVERT: H 248 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8138 (mm-30) outliers start: 65 outliers final: 23 residues processed: 283 average time/residue: 0.7082 time to fit residues: 220.0077 Evaluate side-chains 243 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN D 128 ASN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111374 restraints weight = 20890.517| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.98 r_work: 0.3064 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17740 Z= 0.121 Angle : 0.480 6.484 24024 Z= 0.247 Chirality : 0.042 0.153 2696 Planarity : 0.004 0.041 3144 Dihedral : 3.679 18.668 2394 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.95 % Allowed : 14.02 % Favored : 83.03 % 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: -0.32 (0.18), residues: 2128 helix: -0.29 (0.19), residues: 744 sheet: 0.12 (0.29), residues: 248 loop : -0.09 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 154 TYR 0.008 0.001 TYR F 74 PHE 0.011 0.001 PHE F 27 TRP 0.008 0.002 TRP H 45 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00283 (17736) covalent geometry : angle 0.47840 (24016) SS BOND : bond 0.00453 ( 4) SS BOND : angle 2.40083 ( 8) hydrogen bonds : bond 0.02605 ( 648) hydrogen bonds : angle 4.98284 ( 1653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.685 Fit side-chains REVERT: A 135 ARG cc_start: 0.5954 (mmt90) cc_final: 0.5336 (pmt170) REVERT: A 137 TYR cc_start: 0.8045 (m-80) cc_final: 0.7701 (m-80) REVERT: A 172 GLU cc_start: 0.6893 (mp0) cc_final: 0.5812 (tt0) REVERT: A 268 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 14 ARG cc_start: 0.8467 (tpt170) cc_final: 0.8241 (tpt170) REVERT: B 136 MET cc_start: 0.7208 (mpp) cc_final: 0.6175 (ppp) REVERT: B 229 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8435 (mt) REVERT: C 136 MET cc_start: 0.7797 (mpp) cc_final: 0.7321 (mpm) REVERT: C 143 GLU cc_start: 0.7143 (pm20) cc_final: 0.6892 (pm20) REVERT: C 268 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7692 (tp-100) REVERT: D 132 GLN cc_start: 0.7852 (mm110) cc_final: 0.7629 (mm-40) REVERT: D 136 MET cc_start: 0.7026 (mpp) cc_final: 0.6322 (ppp) REVERT: E 127 GLN cc_start: 0.8277 (mt0) cc_final: 0.8073 (mt0) REVERT: E 136 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5429 (ppp) REVERT: E 139 ARG cc_start: 0.7055 (mtm110) cc_final: 0.5508 (tpt170) REVERT: E 143 GLU cc_start: 0.7066 (pm20) cc_final: 0.6674 (pm20) REVERT: E 222 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7912 (mmp80) REVERT: F 135 ARG cc_start: 0.7083 (mmt90) cc_final: 0.6733 (mmt90) REVERT: F 136 MET cc_start: 0.7471 (mpp) cc_final: 0.6474 (ptt) REVERT: F 248 GLU cc_start: 0.7898 (mm-30) cc_final: 0.6893 (tm-30) REVERT: F 268 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7730 (mm-40) REVERT: G 136 MET cc_start: 0.7797 (mpt) cc_final: 0.6304 (ppp) REVERT: H 130 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7673 (tt) REVERT: H 233 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: H 248 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 58 outliers final: 25 residues processed: 256 average time/residue: 0.7608 time to fit residues: 213.1283 Evaluate side-chains 239 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 56 optimal weight: 0.0010 chunk 98 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN C 128 ASN E 127 GLN E 252 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113462 restraints weight = 20949.894| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.96 r_work: 0.3105 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17740 Z= 0.084 Angle : 0.431 5.412 24024 Z= 0.222 Chirality : 0.040 0.141 2696 Planarity : 0.003 0.043 3144 Dihedral : 3.479 19.543 2394 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.24 % Allowed : 16.21 % Favored : 81.55 % 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: -0.27 (0.18), residues: 2128 helix: -0.13 (0.19), residues: 744 sheet: 0.19 (0.30), residues: 232 loop : -0.16 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 154 TYR 0.008 0.001 TYR E 149 PHE 0.009 0.001 PHE B 27 TRP 0.006 0.001 TRP C 45 HIS 0.002 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00191 (17736) covalent geometry : angle 0.43004 (24016) SS BOND : bond 0.00505 ( 4) SS BOND : angle 1.79435 ( 8) hydrogen bonds : bond 0.02201 ( 648) hydrogen bonds : angle 4.73044 ( 1653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.762 Fit side-chains REVERT: A 105 ASN cc_start: 0.8623 (m110) cc_final: 0.8115 (m-40) REVERT: A 135 ARG cc_start: 0.5901 (mmt90) cc_final: 0.5332 (pmt170) REVERT: A 137 TYR cc_start: 0.7987 (m-80) cc_final: 0.7716 (m-80) REVERT: B 135 ARG cc_start: 0.7039 (mmt90) cc_final: 0.6671 (mmt90) REVERT: B 136 MET cc_start: 0.7238 (mpp) cc_final: 0.6221 (ppp) REVERT: B 229 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8391 (mt) REVERT: C 136 MET cc_start: 0.7790 (mpp) cc_final: 0.7322 (mpm) REVERT: C 268 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7700 (tp-100) REVERT: C 286 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8075 (ptmm) REVERT: D 132 GLN cc_start: 0.7814 (mm110) cc_final: 0.7613 (mm110) REVERT: D 136 MET cc_start: 0.6967 (mpp) cc_final: 0.6371 (ppp) REVERT: D 139 ARG cc_start: 0.6712 (ptt180) cc_final: 0.5348 (mmm160) REVERT: D 268 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: D 286 LYS cc_start: 0.8795 (mtpm) cc_final: 0.8312 (ttmm) REVERT: E 87 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: E 139 ARG cc_start: 0.6947 (mtm110) cc_final: 0.5299 (tpt170) REVERT: F 135 ARG cc_start: 0.7106 (mmt90) cc_final: 0.6804 (mmt90) REVERT: F 136 MET cc_start: 0.7430 (mpp) cc_final: 0.6183 (ptt) REVERT: F 139 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6776 (ptt-90) REVERT: F 248 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6873 (tm-30) REVERT: F 268 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7704 (mm-40) REVERT: G 136 MET cc_start: 0.7829 (mpt) cc_final: 0.6270 (ppp) REVERT: G 154 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7041 (ptp90) REVERT: H 130 ILE cc_start: 0.8126 (tp) cc_final: 0.7718 (tt) REVERT: H 136 MET cc_start: 0.7216 (mpt) cc_final: 0.5985 (ptt) REVERT: H 229 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (mt) REVERT: H 233 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8058 (mtm180) REVERT: H 248 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8085 (mm-30) outliers start: 44 outliers final: 22 residues processed: 253 average time/residue: 0.8008 time to fit residues: 221.6014 Evaluate side-chains 234 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 211 optimal weight: 0.0470 chunk 189 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111409 restraints weight = 20881.057| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.97 r_work: 0.3064 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17740 Z= 0.122 Angle : 0.473 6.509 24024 Z= 0.243 Chirality : 0.042 0.148 2696 Planarity : 0.004 0.048 3144 Dihedral : 3.681 21.262 2394 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.95 % Allowed : 16.51 % Favored : 80.54 % 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: -0.32 (0.18), residues: 2128 helix: -0.21 (0.19), residues: 744 sheet: 0.15 (0.30), residues: 232 loop : -0.16 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 154 TYR 0.008 0.001 TYR B 100 PHE 0.010 0.001 PHE F 27 TRP 0.006 0.001 TRP H 45 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00288 (17736) covalent geometry : angle 0.47120 (24016) SS BOND : bond 0.00453 ( 4) SS BOND : angle 2.05634 ( 8) hydrogen bonds : bond 0.02535 ( 648) hydrogen bonds : angle 4.94533 ( 1653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.680 Fit side-chains REVERT: A 105 ASN cc_start: 0.8579 (m110) cc_final: 0.8065 (m-40) REVERT: A 134 LEU cc_start: 0.8275 (mp) cc_final: 0.8040 (mp) REVERT: A 137 TYR cc_start: 0.8024 (m-80) cc_final: 0.7771 (m-80) REVERT: B 136 MET cc_start: 0.7191 (mpp) cc_final: 0.6107 (ppp) REVERT: B 143 GLU cc_start: 0.6907 (pm20) cc_final: 0.6483 (pp20) REVERT: B 229 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8415 (mt) REVERT: C 136 MET cc_start: 0.7890 (mpp) cc_final: 0.7347 (mpm) REVERT: C 268 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7722 (tp-100) REVERT: D 132 GLN cc_start: 0.7764 (mm110) cc_final: 0.7485 (mm110) REVERT: D 136 MET cc_start: 0.7004 (mpp) cc_final: 0.6324 (ppp) REVERT: D 139 ARG cc_start: 0.6735 (ptt180) cc_final: 0.5315 (mmm160) REVERT: E 87 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: E 136 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.5602 (ppp) REVERT: E 139 ARG cc_start: 0.6990 (mtm110) cc_final: 0.5245 (tpt170) REVERT: E 182 ASP cc_start: 0.5411 (t0) cc_final: 0.4960 (t0) REVERT: E 222 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7989 (mmp80) REVERT: F 135 ARG cc_start: 0.7065 (mmt90) cc_final: 0.6737 (mmt90) REVERT: F 136 MET cc_start: 0.7416 (mpp) cc_final: 0.6461 (ptt) REVERT: F 248 GLU cc_start: 0.7913 (mm-30) cc_final: 0.6857 (tm-30) REVERT: F 268 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: G 270 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8704 (mt) REVERT: H 130 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7680 (tt) REVERT: H 136 MET cc_start: 0.7209 (mpt) cc_final: 0.5941 (ptt) REVERT: H 229 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8580 (mt) REVERT: H 233 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8121 (mtm180) REVERT: H 248 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8044 (mm-30) REVERT: H 254 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.5702 (ppt170) REVERT: H 257 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8251 (tt) outliers start: 58 outliers final: 28 residues processed: 262 average time/residue: 0.7825 time to fit residues: 224.7751 Evaluate side-chains 251 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 152 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.144362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111320 restraints weight = 20862.923| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.94 r_work: 0.3060 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17740 Z= 0.113 Angle : 0.465 8.324 24024 Z= 0.239 Chirality : 0.041 0.148 2696 Planarity : 0.004 0.050 3144 Dihedral : 3.662 19.660 2394 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.05 % Allowed : 16.57 % Favored : 80.39 % 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: -0.30 (0.18), residues: 2128 helix: -0.20 (0.19), residues: 744 sheet: 0.18 (0.30), residues: 232 loop : -0.15 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 154 TYR 0.008 0.001 TYR F 74 PHE 0.009 0.001 PHE G 186 TRP 0.006 0.001 TRP H 45 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00265 (17736) covalent geometry : angle 0.46407 (24016) SS BOND : bond 0.00420 ( 4) SS BOND : angle 2.00400 ( 8) hydrogen bonds : bond 0.02438 ( 648) hydrogen bonds : angle 4.89190 ( 1653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8615 (m110) cc_final: 0.8096 (m-40) REVERT: A 137 TYR cc_start: 0.8074 (m-80) cc_final: 0.7867 (m-80) REVERT: A 268 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: B 136 MET cc_start: 0.7277 (mpp) cc_final: 0.6173 (ppp) REVERT: B 229 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 136 MET cc_start: 0.7972 (mpp) cc_final: 0.6235 (ptt) REVERT: C 268 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7734 (tp-100) REVERT: C 286 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8109 (ptmm) REVERT: D 132 GLN cc_start: 0.7789 (mm110) cc_final: 0.7495 (mm-40) REVERT: D 136 MET cc_start: 0.7071 (mpp) cc_final: 0.6404 (ppp) REVERT: D 139 ARG cc_start: 0.6807 (ptt180) cc_final: 0.5383 (mmm160) REVERT: D 211 GLU cc_start: 0.8533 (pm20) cc_final: 0.8025 (pm20) REVERT: E 87 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: E 136 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5668 (ppp) REVERT: E 139 ARG cc_start: 0.6969 (mtm110) cc_final: 0.5345 (tpt170) REVERT: E 143 GLU cc_start: 0.6924 (pm20) cc_final: 0.6559 (mp0) REVERT: E 182 ASP cc_start: 0.5538 (t0) cc_final: 0.5149 (t0) REVERT: E 222 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8009 (mmp80) REVERT: F 135 ARG cc_start: 0.7039 (mmt90) cc_final: 0.6579 (mmt90) REVERT: F 136 MET cc_start: 0.7386 (mpp) cc_final: 0.6131 (ptt) REVERT: F 139 ARG cc_start: 0.7190 (ptm160) cc_final: 0.6674 (ptt-90) REVERT: F 248 GLU cc_start: 0.7932 (mm-30) cc_final: 0.6880 (tm-30) REVERT: F 257 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7884 (tt) REVERT: F 268 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: G 129 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7680 (mt-10) REVERT: G 270 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8725 (mt) REVERT: H 130 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7705 (tt) REVERT: H 136 MET cc_start: 0.7236 (mpt) cc_final: 0.5981 (ptt) REVERT: H 229 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8573 (mt) REVERT: H 233 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8169 (mtm180) REVERT: H 248 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8039 (mm-30) REVERT: H 254 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.5910 (ppt170) REVERT: H 257 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8300 (tt) outliers start: 60 outliers final: 29 residues processed: 270 average time/residue: 0.7787 time to fit residues: 230.8263 Evaluate side-chains 266 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 39 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 143 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 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 = 0.3678 r_free = 0.3678 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111562 restraints weight = 20824.452| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.96 r_work: 0.3069 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17740 Z= 0.104 Angle : 0.457 6.999 24024 Z= 0.234 Chirality : 0.041 0.147 2696 Planarity : 0.003 0.053 3144 Dihedral : 3.619 18.363 2394 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.05 % Allowed : 16.97 % Favored : 79.98 % 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: -0.26 (0.18), residues: 2128 helix: -0.14 (0.19), residues: 744 sheet: 0.20 (0.30), residues: 232 loop : -0.14 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 154 TYR 0.007 0.001 TYR B 100 PHE 0.009 0.001 PHE G 186 TRP 0.006 0.001 TRP H 45 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00244 (17736) covalent geometry : angle 0.45582 (24016) SS BOND : bond 0.00393 ( 4) SS BOND : angle 1.88100 ( 8) hydrogen bonds : bond 0.02387 ( 648) hydrogen bonds : angle 4.86323 ( 1653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8633 (m110) cc_final: 0.8133 (m-40) REVERT: A 134 LEU cc_start: 0.8311 (mp) cc_final: 0.8102 (mt) REVERT: A 172 GLU cc_start: 0.6836 (mp0) cc_final: 0.6513 (mp0) REVERT: B 136 MET cc_start: 0.7357 (mpp) cc_final: 0.6246 (ppp) REVERT: B 143 GLU cc_start: 0.7052 (pm20) cc_final: 0.6648 (pp20) REVERT: B 229 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8430 (mt) REVERT: C 136 MET cc_start: 0.7968 (mpp) cc_final: 0.6207 (ptt) REVERT: C 246 VAL cc_start: 0.8102 (p) cc_final: 0.7794 (t) REVERT: C 268 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7774 (tp-100) REVERT: D 132 GLN cc_start: 0.7820 (mm110) cc_final: 0.7515 (mm-40) REVERT: D 136 MET cc_start: 0.7086 (mpp) cc_final: 0.6425 (ppp) REVERT: D 139 ARG cc_start: 0.6812 (ptt180) cc_final: 0.5390 (mmm160) REVERT: D 211 GLU cc_start: 0.8534 (pm20) cc_final: 0.8306 (pm20) REVERT: D 286 LYS cc_start: 0.8843 (mtpm) cc_final: 0.8363 (ttmm) REVERT: E 87 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: E 136 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.5729 (ppp) REVERT: E 139 ARG cc_start: 0.6989 (mtm110) cc_final: 0.5347 (tpt170) REVERT: E 143 GLU cc_start: 0.6866 (pm20) cc_final: 0.6549 (mp0) REVERT: E 182 ASP cc_start: 0.5562 (t0) cc_final: 0.5257 (t0) REVERT: E 222 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8061 (mmp80) REVERT: F 135 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6688 (mmt90) REVERT: F 136 MET cc_start: 0.7419 (mpp) cc_final: 0.6430 (ptt) REVERT: F 248 GLU cc_start: 0.7921 (mm-30) cc_final: 0.6957 (tm-30) REVERT: F 257 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7945 (tt) REVERT: F 268 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7893 (mm-40) REVERT: G 129 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7691 (mt-10) REVERT: G 270 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8735 (mt) REVERT: H 130 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7745 (tt) REVERT: H 132 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7842 (pp30) REVERT: H 136 MET cc_start: 0.7314 (mpt) cc_final: 0.6096 (ptt) REVERT: H 222 ARG cc_start: 0.8029 (tpm-80) cc_final: 0.7824 (mmt180) REVERT: H 229 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8591 (mt) REVERT: H 233 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8184 (mtm180) REVERT: H 257 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8394 (tt) outliers start: 60 outliers final: 33 residues processed: 272 average time/residue: 0.7677 time to fit residues: 229.4259 Evaluate side-chains 267 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 197 optimal weight: 0.1980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110483 restraints weight = 20926.353| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.95 r_work: 0.3045 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17740 Z= 0.126 Angle : 0.488 6.684 24024 Z= 0.248 Chirality : 0.042 0.150 2696 Planarity : 0.004 0.056 3144 Dihedral : 3.750 21.009 2394 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.95 % Allowed : 17.17 % Favored : 79.88 % 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: -0.26 (0.18), residues: 2128 helix: -0.19 (0.19), residues: 744 sheet: 0.09 (0.29), residues: 248 loop : -0.07 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 154 TYR 0.009 0.001 TYR B 100 PHE 0.010 0.001 PHE G 186 TRP 0.005 0.001 TRP H 45 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00297 (17736) covalent geometry : angle 0.48611 (24016) SS BOND : bond 0.00445 ( 4) SS BOND : angle 2.10699 ( 8) hydrogen bonds : bond 0.02549 ( 648) hydrogen bonds : angle 4.98918 ( 1653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6542 (p0) cc_final: 0.5867 (t0) REVERT: A 105 ASN cc_start: 0.8586 (m110) cc_final: 0.8081 (m-40) REVERT: A 135 ARG cc_start: 0.6009 (mmt90) cc_final: 0.5363 (pmt170) REVERT: A 268 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: A 290 SER cc_start: 0.8209 (p) cc_final: 0.7967 (m) REVERT: B 136 MET cc_start: 0.7385 (mpp) cc_final: 0.6241 (ppp) REVERT: B 229 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8463 (mt) REVERT: C 136 MET cc_start: 0.7935 (mpp) cc_final: 0.6215 (ptt) REVERT: C 143 GLU cc_start: 0.7122 (pm20) cc_final: 0.6666 (pm20) REVERT: C 246 VAL cc_start: 0.7982 (p) cc_final: 0.7699 (t) REVERT: C 268 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7754 (tp-100) REVERT: C 286 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8120 (ptmm) REVERT: D 132 GLN cc_start: 0.7811 (mm110) cc_final: 0.7492 (mm-40) REVERT: D 136 MET cc_start: 0.7058 (mpp) cc_final: 0.6378 (ppp) REVERT: D 139 ARG cc_start: 0.6846 (ptt180) cc_final: 0.5381 (mmm160) REVERT: D 211 GLU cc_start: 0.8583 (pm20) cc_final: 0.8343 (pm20) REVERT: D 268 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: D 286 LYS cc_start: 0.8832 (mtpm) cc_final: 0.8315 (ttmm) REVERT: E 87 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: E 136 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5729 (ppp) REVERT: E 139 ARG cc_start: 0.6980 (mtm110) cc_final: 0.5230 (tpt170) REVERT: E 143 GLU cc_start: 0.7006 (pm20) cc_final: 0.6618 (mp0) REVERT: E 222 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8057 (mmp80) REVERT: F 135 ARG cc_start: 0.7172 (mmt90) cc_final: 0.6749 (mmt90) REVERT: F 136 MET cc_start: 0.7237 (mpp) cc_final: 0.6252 (ptt) REVERT: F 248 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6913 (tm-30) REVERT: F 257 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7944 (tt) REVERT: F 268 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7856 (mm-40) REVERT: G 129 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7767 (mt-10) REVERT: G 270 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8737 (mt) REVERT: H 130 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7704 (tt) REVERT: H 132 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7819 (pp30) REVERT: H 136 MET cc_start: 0.7293 (mpt) cc_final: 0.6024 (ptt) REVERT: H 233 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8177 (mtm180) REVERT: H 254 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5821 (ppt170) REVERT: H 257 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 58 outliers final: 35 residues processed: 261 average time/residue: 0.7782 time to fit residues: 222.8484 Evaluate side-chains 269 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 0.0970 chunk 154 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 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 = 0.3653 r_free = 0.3653 target = 0.142331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109382 restraints weight = 20821.085| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.92 r_work: 0.3033 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17740 Z= 0.157 Angle : 0.524 7.624 24024 Z= 0.267 Chirality : 0.043 0.157 2696 Planarity : 0.004 0.056 3144 Dihedral : 3.939 19.664 2394 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.15 % Allowed : 17.23 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2128 helix: -0.30 (0.19), residues: 744 sheet: 0.00 (0.29), residues: 248 loop : -0.11 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 154 TYR 0.010 0.001 TYR B 100 PHE 0.012 0.002 PHE G 140 TRP 0.006 0.002 TRP H 45 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00374 (17736) covalent geometry : angle 0.52212 (24016) SS BOND : bond 0.00483 ( 4) SS BOND : angle 2.44651 ( 8) hydrogen bonds : bond 0.02810 ( 648) hydrogen bonds : angle 5.16775 ( 1653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6408 (p0) cc_final: 0.5787 (t0) REVERT: A 132 GLN cc_start: 0.7423 (mm110) cc_final: 0.6737 (pt0) REVERT: A 135 ARG cc_start: 0.6082 (mmt90) cc_final: 0.5456 (pmt170) REVERT: A 268 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: B 136 MET cc_start: 0.7367 (mpp) cc_final: 0.6227 (ppp) REVERT: B 229 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (mt) REVERT: B 268 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: C 136 MET cc_start: 0.7896 (mpp) cc_final: 0.6188 (ptt) REVERT: C 143 GLU cc_start: 0.7213 (pm20) cc_final: 0.6856 (pm20) REVERT: C 268 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7796 (tp-100) REVERT: C 286 LYS cc_start: 0.8968 (ptpp) cc_final: 0.8204 (ptmm) REVERT: D 132 GLN cc_start: 0.7843 (mm110) cc_final: 0.7549 (mm-40) REVERT: D 136 MET cc_start: 0.7120 (mpp) cc_final: 0.6420 (ppp) REVERT: D 139 ARG cc_start: 0.6882 (ptt180) cc_final: 0.5393 (mmm160) REVERT: D 211 GLU cc_start: 0.8582 (pm20) cc_final: 0.8353 (pm20) REVERT: D 268 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: E 87 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: E 136 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.5749 (ppp) REVERT: E 139 ARG cc_start: 0.6970 (mtm110) cc_final: 0.5172 (tpt170) REVERT: E 143 GLU cc_start: 0.6956 (pm20) cc_final: 0.6613 (mp0) REVERT: E 222 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8070 (mmp80) REVERT: F 135 ARG cc_start: 0.7207 (mmt90) cc_final: 0.6789 (mmt90) REVERT: F 136 MET cc_start: 0.7236 (mpp) cc_final: 0.6282 (ptt) REVERT: F 248 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6900 (tm-30) REVERT: F 257 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7990 (tt) REVERT: F 268 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7802 (mm-40) REVERT: G 270 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8773 (mt) REVERT: H 130 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7739 (tt) REVERT: H 233 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8219 (mtm180) REVERT: H 249 ASN cc_start: 0.8649 (m-40) cc_final: 0.8353 (m-40) REVERT: H 254 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5954 (ppt170) REVERT: H 257 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 62 outliers final: 37 residues processed: 267 average time/residue: 0.7713 time to fit residues: 225.7498 Evaluate side-chains 271 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 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 = 0.3662 r_free = 0.3662 target = 0.143081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110376 restraints weight = 20623.067| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.89 r_work: 0.3052 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17740 Z= 0.123 Angle : 0.498 7.687 24024 Z= 0.253 Chirality : 0.042 0.150 2696 Planarity : 0.004 0.062 3144 Dihedral : 3.819 20.798 2394 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.74 % Allowed : 17.68 % Favored : 79.57 % 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: -0.31 (0.18), residues: 2128 helix: -0.21 (0.19), residues: 744 sheet: -0.01 (0.29), residues: 248 loop : -0.10 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 154 TYR 0.008 0.001 TYR B 100 PHE 0.011 0.001 PHE G 186 TRP 0.006 0.001 TRP H 45 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00292 (17736) covalent geometry : angle 0.49651 (24016) SS BOND : bond 0.00423 ( 4) SS BOND : angle 2.21613 ( 8) hydrogen bonds : bond 0.02541 ( 648) hydrogen bonds : angle 5.01476 ( 1653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6398 (p0) cc_final: 0.5863 (t0) REVERT: A 135 ARG cc_start: 0.6116 (mmt90) cc_final: 0.5538 (pmt170) REVERT: A 268 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: B 136 MET cc_start: 0.7348 (mpp) cc_final: 0.6193 (ppp) REVERT: B 229 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (mt) REVERT: B 268 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: C 136 MET cc_start: 0.7925 (mpp) cc_final: 0.6136 (ptt) REVERT: C 143 GLU cc_start: 0.7217 (pm20) cc_final: 0.6877 (pm20) REVERT: C 268 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7781 (tp-100) REVERT: C 286 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8159 (ptmm) REVERT: D 128 ASN cc_start: 0.7633 (m-40) cc_final: 0.7403 (m110) REVERT: D 132 GLN cc_start: 0.7862 (mm110) cc_final: 0.7583 (mm-40) REVERT: D 136 MET cc_start: 0.7093 (mpp) cc_final: 0.6423 (ppp) REVERT: D 139 ARG cc_start: 0.6787 (ptt180) cc_final: 0.5355 (mmm160) REVERT: D 268 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: D 286 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8280 (ttmm) REVERT: E 87 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: E 136 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.5741 (ppp) REVERT: E 139 ARG cc_start: 0.6941 (mtm110) cc_final: 0.5123 (tpt170) REVERT: E 222 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8054 (mmp80) REVERT: F 135 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6814 (mmt90) REVERT: F 136 MET cc_start: 0.7210 (mpp) cc_final: 0.6384 (ptt) REVERT: F 248 GLU cc_start: 0.7914 (mm-30) cc_final: 0.6918 (tm-30) REVERT: F 268 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7849 (mm-40) REVERT: G 270 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8760 (mt) REVERT: H 130 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7771 (tt) REVERT: H 233 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8187 (mtm180) REVERT: H 249 ASN cc_start: 0.8638 (m-40) cc_final: 0.8328 (m110) REVERT: H 257 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8466 (tt) outliers start: 54 outliers final: 38 residues processed: 250 average time/residue: 0.7803 time to fit residues: 213.7274 Evaluate side-chains 263 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 136 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 154 ARG Chi-restraints excluded: chain G residue 182 ASP Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 233 ARG Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 286 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 205 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113455 restraints weight = 21047.667| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.92 r_work: 0.3095 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17740 Z= 0.079 Angle : 0.442 7.325 24024 Z= 0.226 Chirality : 0.040 0.139 2696 Planarity : 0.003 0.049 3144 Dihedral : 3.442 17.313 2394 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.98 % Allowed : 18.55 % Favored : 79.47 % 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: -0.19 (0.18), residues: 2128 helix: -0.04 (0.19), residues: 752 sheet: 0.26 (0.30), residues: 232 loop : -0.14 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 154 TYR 0.007 0.001 TYR G 235 PHE 0.007 0.001 PHE B 27 TRP 0.008 0.001 TRP C 45 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00184 (17736) covalent geometry : angle 0.44089 (24016) SS BOND : bond 0.00256 ( 4) SS BOND : angle 1.47365 ( 8) hydrogen bonds : bond 0.02061 ( 648) hydrogen bonds : angle 4.67460 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7873.15 seconds wall clock time: 134 minutes 49.57 seconds (8089.57 seconds total)