Starting phenix.real_space_refine on Thu Feb 13 01:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2025/7vuz_32132.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 64 5.16 5 C 5493 2.51 5 N 1439 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1995 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1750 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.60 Number of scatterers: 8584 At special positions: 0 Unit cell: (116.833, 114.347, 100.261, 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 64 16.00 O 1588 8.00 N 1439 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.01 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.4% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 36 through 57 removed outlier: 3.521A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 95 Processing helix chain 'R' and resid 103 through 133 removed outlier: 4.282A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.946A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 3.861A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 251 removed outlier: 3.658A pdb=" N LYS R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 260 removed outlier: 3.715A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 279 Proline residue: R 276 - end of helix Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.580A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.965A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.568A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.034A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.927A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.730A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.187A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.680A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.680A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.858A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.876A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.706A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.909A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 129 through 130 removed outlier: 3.899A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.895A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET S 218 " --> pdb=" O TYR S 163 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU S 166 " --> pdb=" O GLN S 174 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1188 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: 2.58 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2523 1.34 - 1.46: 2378 1.46 - 1.59: 3780 1.59 - 1.72: 1 1.72 - 1.85: 89 Bond restraints: 8771 Sorted by residual: bond pdb=" C PRO R 238 " pdb=" N PHE R 239 " ideal model delta sigma weight residual 1.335 1.471 -0.137 1.31e-02 5.83e+03 1.09e+02 bond pdb=" C GLY R 236 " pdb=" N LEU R 237 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.626 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.25e+00 bond pdb=" CG LEU B 146 " pdb=" CD2 LEU B 146 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 8.99e+00 ... (remaining 8766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11385 3.08 - 6.15: 414 6.15 - 9.23: 64 9.23 - 12.31: 22 12.31 - 15.38: 3 Bond angle restraints: 11888 Sorted by residual: angle pdb=" N ASP R 254 " pdb=" CA ASP R 254 " pdb=" C ASP R 254 " ideal model delta sigma weight residual 111.28 120.50 -9.22 1.09e+00 8.42e-01 7.16e+01 angle pdb=" C ASN R 275 " pdb=" N PRO R 276 " pdb=" CA PRO R 276 " ideal model delta sigma weight residual 119.47 111.39 8.08 1.16e+00 7.43e-01 4.86e+01 angle pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" CD PRO R 276 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta sigma weight residual 110.16 119.85 -9.69 1.48e+00 4.57e-01 4.29e+01 angle pdb=" N PRO R 276 " pdb=" CA PRO R 276 " pdb=" C PRO R 276 " ideal model delta sigma weight residual 113.81 123.17 -9.36 1.45e+00 4.76e-01 4.17e+01 ... (remaining 11883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4518 14.51 - 29.02: 538 29.02 - 43.54: 128 43.54 - 58.05: 18 58.05 - 72.56: 10 Dihedral angle restraints: 5212 sinusoidal: 2050 harmonic: 3162 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual -180.00 -137.80 -42.20 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1212 0.122 - 0.244: 124 0.244 - 0.366: 13 0.366 - 0.488: 2 0.488 - 0.610: 3 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" C PRO R 276 " pdb=" CB PRO R 276 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL B 296 " pdb=" CA VAL B 296 " pdb=" CG1 VAL B 296 " pdb=" CG2 VAL B 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1351 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.134 5.00e-02 4.00e+02 2.01e-01 6.47e+01 pdb=" N PRO R 276 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.104 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER R 273 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER R 273 " -0.071 2.00e-02 2.50e+03 pdb=" O SER R 273 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR A 230 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " 0.002 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 88 2.61 - 3.18: 6696 3.18 - 3.75: 13745 3.75 - 4.33: 18610 4.33 - 4.90: 31109 Nonbonded interactions: 70248 Sorted by model distance: nonbonded pdb=" O CYS R 258 " pdb=" CD PRO R 262 " model vdw 2.035 3.440 nonbonded pdb=" OD1 ASN R 48 " pdb=" CG PRO R 276 " model vdw 2.170 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.294 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.295 3.040 ... (remaining 70243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.010 0.137 8771 Z= 0.654 Angle : 1.395 15.384 11888 Z= 0.754 Chirality : 0.082 0.610 1354 Planarity : 0.010 0.201 1489 Dihedral : 13.540 72.560 3162 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.39 % Allowed : 1.28 % Favored : 97.33 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.23), residues: 1081 helix: -2.11 (0.22), residues: 355 sheet: -1.33 (0.30), residues: 276 loop : -1.94 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP R 133 HIS 0.026 0.004 HIS S 220 PHE 0.035 0.004 PHE R 50 TYR 0.064 0.005 TYR A 230 ARG 0.032 0.002 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.948 Fit side-chains REVERT: R 234 LEU cc_start: 0.8434 (mt) cc_final: 0.8093 (mp) REVERT: R 252 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: A 294 ASN cc_start: 0.6673 (m110) cc_final: 0.6360 (t0) REVERT: A 318 GLU cc_start: 0.6400 (tp30) cc_final: 0.6000 (tp30) REVERT: S 206 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7145 (mmp80) outliers start: 13 outliers final: 4 residues processed: 214 average time/residue: 1.3045 time to fit residues: 296.6261 Evaluate side-chains 153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 252 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 271 ASN Chi-restraints excluded: chain R residue 276 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN R 275 ASN A 52 GLN A 331 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 259 GLN B 268 ASN S 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.197167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156617 restraints weight = 10545.151| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.94 r_work: 0.4046 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8771 Z= 0.193 Angle : 0.696 8.689 11888 Z= 0.358 Chirality : 0.046 0.346 1354 Planarity : 0.005 0.053 1489 Dihedral : 6.872 72.766 1254 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.21 % Allowed : 14.42 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.24), residues: 1081 helix: -0.17 (0.26), residues: 360 sheet: -1.10 (0.30), residues: 266 loop : -1.58 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.011 0.001 PHE S 29 TYR 0.014 0.001 TYR A 296 ARG 0.011 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.942 Fit side-chains REVERT: R 196 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8207 (ttp) REVERT: R 199 CYS cc_start: 0.7005 (p) cc_final: 0.6785 (m) REVERT: A 318 GLU cc_start: 0.6306 (tp30) cc_final: 0.5803 (tp30) REVERT: B 19 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7060 (ttp-170) REVERT: B 75 GLN cc_start: 0.7413 (tt0) cc_final: 0.7120 (tt0) REVERT: G 37 LEU cc_start: 0.7700 (mm) cc_final: 0.7496 (mm) REVERT: S 163 TYR cc_start: 0.5947 (m-80) cc_final: 0.5698 (m-80) REVERT: S 206 ARG cc_start: 0.7538 (mmt-90) cc_final: 0.7240 (tpp-160) outliers start: 30 outliers final: 7 residues processed: 196 average time/residue: 1.0671 time to fit residues: 223.8969 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 304 GLN A 331 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.196085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.155438 restraints weight = 10723.034| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.98 r_work: 0.4053 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8771 Z= 0.202 Angle : 0.662 8.663 11888 Z= 0.335 Chirality : 0.045 0.333 1354 Planarity : 0.004 0.042 1489 Dihedral : 6.226 74.583 1246 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.74 % Allowed : 17.31 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1081 helix: 0.64 (0.27), residues: 365 sheet: -0.94 (0.31), residues: 263 loop : -1.36 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.011 0.001 PHE R 35 TYR 0.024 0.001 TYR A 230 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 196 MET cc_start: 0.8430 (ttm) cc_final: 0.8201 (ttp) REVERT: R 199 CYS cc_start: 0.6945 (p) cc_final: 0.6717 (m) REVERT: A 25 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6495 (tp30) REVERT: A 33 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: A 305 CYS cc_start: 0.7930 (m) cc_final: 0.7441 (m) REVERT: B 19 ARG cc_start: 0.7398 (mtm110) cc_final: 0.7029 (ttp80) REVERT: B 219 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7659 (ttm110) REVERT: S 206 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7225 (tpp-160) outliers start: 35 outliers final: 15 residues processed: 186 average time/residue: 1.0740 time to fit residues: 214.1369 Evaluate side-chains 174 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 91 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.193036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.152399 restraints weight = 10715.076| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.94 r_work: 0.4018 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8771 Z= 0.248 Angle : 0.673 10.615 11888 Z= 0.339 Chirality : 0.046 0.338 1354 Planarity : 0.004 0.042 1489 Dihedral : 6.093 76.160 1246 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.17 % Allowed : 19.34 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1081 helix: 1.04 (0.27), residues: 362 sheet: -0.81 (0.31), residues: 265 loop : -1.21 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.008 0.001 HIS S 155 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.002 TYR S 59 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.866 Fit side-chains REVERT: R 199 CYS cc_start: 0.7005 (p) cc_final: 0.6696 (m) REVERT: R 243 TRP cc_start: 0.6548 (t-100) cc_final: 0.5834 (t-100) REVERT: A 25 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: A 33 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: A 53 MET cc_start: 0.7929 (mpt) cc_final: 0.7411 (mpt) REVERT: A 248 LYS cc_start: 0.8027 (tppt) cc_final: 0.7671 (mtpp) REVERT: A 296 TYR cc_start: 0.6925 (p90) cc_final: 0.6661 (p90) REVERT: A 297 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 305 CYS cc_start: 0.8001 (m) cc_final: 0.7501 (m) REVERT: A 318 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6036 (tp30) REVERT: B 15 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6876 (tppp) REVERT: B 19 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6991 (ttp80) REVERT: B 189 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7029 (t) REVERT: B 256 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7805 (ttp80) REVERT: B 262 MET cc_start: 0.7165 (mmt) cc_final: 0.6692 (mmm) REVERT: G 28 ILE cc_start: 0.8874 (pp) cc_final: 0.8597 (pp) REVERT: G 37 LEU cc_start: 0.7754 (mm) cc_final: 0.7537 (mm) REVERT: S 206 ARG cc_start: 0.7518 (mmt-90) cc_final: 0.7191 (tpp-160) outliers start: 39 outliers final: 18 residues processed: 180 average time/residue: 1.0989 time to fit residues: 211.8455 Evaluate side-chains 172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 49 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 340 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.201698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.162480 restraints weight = 10621.132| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.88 r_work: 0.4148 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8771 Z= 0.160 Angle : 0.636 9.386 11888 Z= 0.316 Chirality : 0.044 0.329 1354 Planarity : 0.003 0.037 1489 Dihedral : 5.879 75.927 1246 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.02 % Allowed : 19.76 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1081 helix: 1.26 (0.28), residues: 366 sheet: -0.62 (0.32), residues: 265 loop : -1.16 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.011 0.001 PHE R 183 TYR 0.011 0.001 TYR S 223 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.969 Fit side-chains REVERT: R 196 MET cc_start: 0.8440 (ttm) cc_final: 0.8238 (ttp) REVERT: R 199 CYS cc_start: 0.7025 (p) cc_final: 0.6629 (m) REVERT: R 243 TRP cc_start: 0.6735 (t-100) cc_final: 0.5951 (t-100) REVERT: A 25 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6618 (tp30) REVERT: A 53 MET cc_start: 0.7842 (mpt) cc_final: 0.7319 (mpt) REVERT: A 296 TYR cc_start: 0.6857 (p90) cc_final: 0.6520 (p90) REVERT: A 297 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 305 CYS cc_start: 0.7994 (m) cc_final: 0.7456 (m) REVERT: A 318 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6152 (tp30) REVERT: B 15 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6970 (tppp) REVERT: B 19 ARG cc_start: 0.7266 (mtm110) cc_final: 0.7007 (ttp80) REVERT: B 101 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8506 (ptp) REVERT: B 189 SER cc_start: 0.7165 (OUTLIER) cc_final: 0.6883 (t) REVERT: B 219 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7693 (ttm110) REVERT: G 37 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7561 (mm) REVERT: S 34 MET cc_start: 0.5829 (tpp) cc_final: 0.5588 (mmp) outliers start: 47 outliers final: 19 residues processed: 195 average time/residue: 1.0199 time to fit residues: 214.4165 Evaluate side-chains 172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN B 16 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.196574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.155710 restraints weight = 10631.200| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.94 r_work: 0.4073 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8771 Z= 0.232 Angle : 0.676 10.240 11888 Z= 0.340 Chirality : 0.046 0.336 1354 Planarity : 0.003 0.038 1489 Dihedral : 5.886 76.640 1245 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.49 % Allowed : 22.76 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1081 helix: 1.28 (0.27), residues: 366 sheet: -0.64 (0.32), residues: 266 loop : -1.11 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.011 0.001 PHE S 200 TYR 0.025 0.002 TYR A 230 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: R 199 CYS cc_start: 0.7052 (p) cc_final: 0.6619 (m) REVERT: R 243 TRP cc_start: 0.6696 (t-100) cc_final: 0.5931 (t-100) REVERT: A 25 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6603 (tp30) REVERT: A 33 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: A 53 MET cc_start: 0.7794 (mpt) cc_final: 0.7317 (mpt) REVERT: A 296 TYR cc_start: 0.6918 (p90) cc_final: 0.6612 (p90) REVERT: A 297 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 318 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6067 (tp30) REVERT: B 4 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4427 (tt) REVERT: B 15 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6940 (tppp) REVERT: B 17 GLN cc_start: 0.7420 (mp10) cc_final: 0.7219 (mp10) REVERT: B 19 ARG cc_start: 0.7075 (mtm110) cc_final: 0.6848 (ttp80) REVERT: B 189 SER cc_start: 0.7375 (OUTLIER) cc_final: 0.7085 (t) REVERT: B 219 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7769 (ttm110) REVERT: G 37 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7581 (mm) REVERT: S 206 ARG cc_start: 0.6878 (tpp-160) cc_final: 0.6652 (tpp-160) outliers start: 42 outliers final: 24 residues processed: 180 average time/residue: 1.0803 time to fit residues: 208.9175 Evaluate side-chains 179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4634 r_free = 0.4634 target = 0.197354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.156244 restraints weight = 10681.243| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.94 r_work: 0.4074 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8771 Z= 0.218 Angle : 0.685 10.383 11888 Z= 0.340 Chirality : 0.046 0.341 1354 Planarity : 0.003 0.038 1489 Dihedral : 5.823 76.657 1245 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.27 % Allowed : 24.15 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1081 helix: 1.30 (0.27), residues: 366 sheet: -0.63 (0.31), residues: 266 loop : -1.05 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.011 0.001 PHE R 232 TYR 0.015 0.001 TYR S 223 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 199 CYS cc_start: 0.7114 (p) cc_final: 0.6664 (m) REVERT: R 243 TRP cc_start: 0.6765 (t-100) cc_final: 0.6437 (t-100) REVERT: A 25 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: A 33 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: A 53 MET cc_start: 0.7838 (mpt) cc_final: 0.7339 (mpt) REVERT: A 296 TYR cc_start: 0.6897 (p90) cc_final: 0.6677 (p90) REVERT: A 318 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6171 (tp30) REVERT: B 15 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6986 (tppp) REVERT: B 16 ASN cc_start: 0.8743 (m-40) cc_final: 0.8348 (m110) REVERT: B 19 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6871 (ttp80) REVERT: B 189 SER cc_start: 0.7402 (OUTLIER) cc_final: 0.7117 (t) REVERT: B 215 GLU cc_start: 0.8034 (pp20) cc_final: 0.7823 (pp20) REVERT: B 219 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7822 (ttm110) REVERT: G 37 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7639 (mm) REVERT: S 206 ARG cc_start: 0.6918 (tpp-160) cc_final: 0.6699 (tpp80) REVERT: S 234 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.4511 (pm20) outliers start: 40 outliers final: 22 residues processed: 175 average time/residue: 1.0972 time to fit residues: 205.8768 Evaluate side-chains 174 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4647 r_free = 0.4647 target = 0.199200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.158261 restraints weight = 10763.959| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.95 r_work: 0.4111 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8771 Z= 0.182 Angle : 0.677 10.708 11888 Z= 0.336 Chirality : 0.045 0.351 1354 Planarity : 0.003 0.039 1489 Dihedral : 5.737 76.476 1245 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.95 % Allowed : 24.57 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1081 helix: 1.39 (0.28), residues: 366 sheet: -0.55 (0.32), residues: 264 loop : -1.01 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.012 0.001 PHE S 200 TYR 0.017 0.001 TYR S 223 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 109 MET cc_start: 0.5434 (tpt) cc_final: 0.5230 (mmt) REVERT: R 158 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7464 (tt) REVERT: R 199 CYS cc_start: 0.7027 (p) cc_final: 0.6574 (m) REVERT: R 243 TRP cc_start: 0.6618 (t-100) cc_final: 0.6315 (t-100) REVERT: A 25 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6564 (tp30) REVERT: A 53 MET cc_start: 0.7688 (mpt) cc_final: 0.7242 (mpt) REVERT: A 248 LYS cc_start: 0.8015 (tppt) cc_final: 0.7716 (mtpp) REVERT: A 318 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6058 (tp30) REVERT: B 4 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4508 (tt) REVERT: B 15 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6937 (tppp) REVERT: B 16 ASN cc_start: 0.8778 (m-40) cc_final: 0.8438 (m110) REVERT: B 19 ARG cc_start: 0.7013 (mtm110) cc_final: 0.6791 (ttp80) REVERT: B 189 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.7017 (t) REVERT: B 215 GLU cc_start: 0.8007 (pp20) cc_final: 0.7793 (pp20) REVERT: B 219 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7819 (ttm110) REVERT: G 37 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7361 (mm) REVERT: S 206 ARG cc_start: 0.6846 (tpp-160) cc_final: 0.6645 (tpp80) REVERT: S 234 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4653 (pm20) outliers start: 37 outliers final: 22 residues processed: 175 average time/residue: 1.0786 time to fit residues: 202.5530 Evaluate side-chains 180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4611 r_free = 0.4611 target = 0.195017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.153575 restraints weight = 10805.272| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.93 r_work: 0.4062 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8771 Z= 0.261 Angle : 0.720 11.641 11888 Z= 0.357 Chirality : 0.047 0.399 1354 Planarity : 0.003 0.037 1489 Dihedral : 5.820 77.023 1245 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.06 % Allowed : 25.32 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1081 helix: 1.39 (0.28), residues: 365 sheet: -0.63 (0.31), residues: 275 loop : -0.94 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 211 HIS 0.008 0.001 HIS A 213 PHE 0.013 0.001 PHE S 200 TYR 0.020 0.002 TYR S 223 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.945 Fit side-chains REVERT: R 158 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7485 (tt) REVERT: R 199 CYS cc_start: 0.7050 (p) cc_final: 0.6588 (m) REVERT: R 242 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6675 (pp30) REVERT: R 243 TRP cc_start: 0.6656 (t-100) cc_final: 0.6403 (t-100) REVERT: A 25 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: A 53 MET cc_start: 0.7806 (mpt) cc_final: 0.7309 (mpt) REVERT: A 248 LYS cc_start: 0.8022 (tppt) cc_final: 0.7722 (mtpp) REVERT: A 318 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6173 (tp30) REVERT: B 4 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4437 (tt) REVERT: B 15 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6923 (tppp) REVERT: B 16 ASN cc_start: 0.8784 (m-40) cc_final: 0.8450 (m110) REVERT: B 19 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6835 (ttp80) REVERT: B 135 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 189 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.7129 (t) REVERT: B 219 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7839 (ttm110) REVERT: G 37 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7405 (mm) REVERT: S 206 ARG cc_start: 0.6906 (tpp-160) cc_final: 0.6693 (tpp80) REVERT: S 234 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4919 (pm20) outliers start: 38 outliers final: 25 residues processed: 175 average time/residue: 1.0911 time to fit residues: 204.6093 Evaluate side-chains 180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4637 r_free = 0.4637 target = 0.197975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.156951 restraints weight = 10768.170| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.97 r_work: 0.4123 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8771 Z= 0.200 Angle : 0.691 11.326 11888 Z= 0.346 Chirality : 0.046 0.381 1354 Planarity : 0.003 0.038 1489 Dihedral : 5.773 76.833 1245 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.85 % Allowed : 26.07 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1081 helix: 1.42 (0.28), residues: 365 sheet: -0.60 (0.31), residues: 271 loop : -0.97 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 211 HIS 0.008 0.001 HIS A 213 PHE 0.012 0.001 PHE S 200 TYR 0.019 0.001 TYR S 223 ARG 0.005 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (tt) REVERT: R 199 CYS cc_start: 0.7109 (p) cc_final: 0.6631 (m) REVERT: A 25 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6663 (tp30) REVERT: A 33 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 53 MET cc_start: 0.7763 (mpt) cc_final: 0.7451 (mpt) REVERT: A 248 LYS cc_start: 0.8031 (tppt) cc_final: 0.7767 (mtpp) REVERT: A 297 GLU cc_start: 0.8062 (tp30) cc_final: 0.7760 (mm-30) REVERT: B 4 LEU cc_start: 0.4847 (OUTLIER) cc_final: 0.4509 (tt) REVERT: B 15 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6940 (tppp) REVERT: B 16 ASN cc_start: 0.8801 (m-40) cc_final: 0.8510 (m110) REVERT: B 19 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6829 (ttp80) REVERT: B 135 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 189 SER cc_start: 0.7370 (OUTLIER) cc_final: 0.7105 (t) REVERT: B 219 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7866 (ttm110) REVERT: G 37 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7471 (mm) outliers start: 36 outliers final: 23 residues processed: 173 average time/residue: 1.0985 time to fit residues: 203.9671 Evaluate side-chains 174 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 GLN A 195 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 155 HIS ** 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 = 0.4587 r_free = 0.4587 target = 0.192673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.151417 restraints weight = 10833.864| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.91 r_work: 0.4035 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8771 Z= 0.303 Angle : 0.749 11.636 11888 Z= 0.376 Chirality : 0.049 0.421 1354 Planarity : 0.004 0.045 1489 Dihedral : 5.912 77.024 1245 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.74 % Allowed : 26.07 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1081 helix: 1.36 (0.28), residues: 364 sheet: -0.77 (0.30), residues: 281 loop : -1.05 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 211 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE B 151 TYR 0.020 0.002 TYR S 223 ARG 0.004 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7312.21 seconds wall clock time: 129 minutes 28.85 seconds (7768.85 seconds total)