Starting phenix.real_space_refine on Wed Sep 17 14:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991.map" model { file = "/net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k26_61991/09_2025/9k26_61991_neut_trim.cif" } resolution = 3.0 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= -0.001 sd= 0.012 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 57 5.16 5 C 5721 2.51 5 N 1554 2.21 5 O 1635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2406 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 147 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1630 Classifications: {'peptide': 204} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 8967 At special positions: 0 Unit cell: (91.3, 120.35, 127.82, 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 57 16.00 O 1635 8.00 N 1554 7.00 C 5721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 340.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 59 through 88 removed outlier: 3.720A pdb=" N ILE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 121 Proline residue: A 115 - end of helix removed outlier: 3.753A pdb=" N ALA A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 165 Proline residue: A 142 - end of helix Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.709A pdb=" N SER A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 218 through 234 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.684A pdb=" N ASN A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 302 removed outlier: 3.720A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Proline residue: A 293 - end of helix removed outlier: 3.801A pdb=" N LEU A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.093A pdb=" N ILE A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.557A pdb=" N VAL A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Proline residue: A 332 - end of helix Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.645A pdb=" N ARG A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 23 removed outlier: 3.586A pdb=" N TYR F 20 " --> pdb=" O PRO F 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.814A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.377A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 4.164A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.520A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.636A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 351 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 4.057A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.538A 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 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.705A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.678A pdb=" N LEU A 203 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 208 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.560A pdb=" N ASP C 200 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.617A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.877A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.671A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.854A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.197A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AB3, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.961A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 157 through 159 401 hydrogen bonds defined for protein. 1107 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: 1.24 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2375 1.33 - 1.45: 1723 1.45 - 1.57: 4984 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9160 Sorted by residual: bond pdb=" N ILE B 338 " pdb=" CA ILE B 338 " ideal model delta sigma weight residual 1.460 1.492 -0.031 1.10e-02 8.26e+03 8.15e+00 bond pdb=" N ILE S 189 " pdb=" CA ILE S 189 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.17e-02 7.31e+03 7.59e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" CA GLU A 213 " pdb=" C GLU A 213 " ideal model delta sigma weight residual 1.530 1.500 0.030 1.14e-02 7.69e+03 6.97e+00 bond pdb=" N SER S 146 " pdb=" CA SER S 146 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.25e-02 6.40e+03 6.35e+00 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12154 2.20 - 4.40: 250 4.40 - 6.60: 23 6.60 - 8.80: 5 8.80 - 11.00: 2 Bond angle restraints: 12434 Sorted by residual: angle pdb=" N PHE A 214 " pdb=" CA PHE A 214 " pdb=" C PHE A 214 " ideal model delta sigma weight residual 110.30 99.30 11.00 1.50e+00 4.44e-01 5.37e+01 angle pdb=" C PHE A 214 " pdb=" CA PHE A 214 " pdb=" CB PHE A 214 " ideal model delta sigma weight residual 110.06 118.00 -7.94 1.39e+00 5.18e-01 3.26e+01 angle pdb=" N VAL S 149 " pdb=" CA VAL S 149 " pdb=" C VAL S 149 " ideal model delta sigma weight residual 108.45 115.20 -6.75 1.48e+00 4.57e-01 2.08e+01 angle pdb=" N GLN A 218 " pdb=" CA GLN A 218 " pdb=" C GLN A 218 " ideal model delta sigma weight residual 111.52 106.42 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" N CYS A 329 " pdb=" CA CYS A 329 " pdb=" C CYS A 329 " ideal model delta sigma weight residual 113.41 117.70 -4.29 1.22e+00 6.72e-01 1.24e+01 ... (remaining 12429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 5034 21.29 - 42.58: 339 42.58 - 63.86: 29 63.86 - 85.15: 9 85.15 - 106.44: 1 Dihedral angle restraints: 5412 sinusoidal: 2088 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ALA S 143 " pdb=" C ALA S 143 " pdb=" N THR S 144 " pdb=" CA THR S 144 " ideal model delta harmonic sigma weight residual 180.00 73.56 106.44 0 5.00e+00 4.00e-02 4.53e+02 dihedral pdb=" CA GLN S 142 " pdb=" C GLN S 142 " pdb=" N ALA S 143 " pdb=" CA ALA S 143 " ideal model delta harmonic sigma weight residual -180.00 -117.91 -62.09 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA THR S 144 " pdb=" C THR S 144 " pdb=" N SER S 145 " pdb=" CA SER S 145 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1081 0.049 - 0.097: 260 0.097 - 0.146: 64 0.146 - 0.195: 13 0.195 - 0.244: 3 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA ALA A 328 " pdb=" N ALA A 328 " pdb=" C ALA A 328 " pdb=" CB ALA A 328 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 1418 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER S 146 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C SER S 146 " 0.039 2.00e-02 2.50e+03 pdb=" O SER S 146 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL S 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.015 2.00e-02 2.50e+03 1.18e-02 3.49e+00 pdb=" CG TRP B 332 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 166 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LEU S 166 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU S 166 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS S 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 84 2.58 - 3.16: 7544 3.16 - 3.74: 13941 3.74 - 4.32: 18261 4.32 - 4.90: 31444 Nonbonded interactions: 71274 Sorted by model distance: nonbonded pdb=" NE2 HIS A 321 " pdb=" O PHE F 31 " model vdw 1.994 3.120 nonbonded pdb=" OE1 GLN A 141 " pdb=" N NH2 F 33 " model vdw 2.053 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.181 3.040 nonbonded pdb=" OE2 GLU C 318 " pdb=" OH TYR C 320 " model vdw 2.202 3.040 nonbonded pdb=" O LEU A 229 " pdb=" OG1 THR A 233 " model vdw 2.206 3.040 ... (remaining 71269 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: 2.030 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.800 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 9164 Z= 0.264 Angle : 0.714 10.997 12440 Z= 0.424 Chirality : 0.046 0.244 1421 Planarity : 0.004 0.045 1571 Dihedral : 13.766 106.442 3259 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 0.72 % Allowed : 1.03 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.26), residues: 1127 helix: 1.54 (0.27), residues: 382 sheet: -1.48 (0.31), residues: 290 loop : -2.09 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 160 TYR 0.019 0.001 TYR C 296 PHE 0.021 0.001 PHE S 212 TRP 0.032 0.001 TRP B 332 HIS 0.009 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9160) covalent geometry : angle 0.71412 (12434) SS BOND : bond 0.00388 ( 3) SS BOND : angle 1.10385 ( 6) hydrogen bonds : bond 0.15059 ( 401) hydrogen bonds : angle 5.67881 ( 1107) Misc. bond : bond 0.14042 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 335 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8145 (mm) cc_final: 0.7503 (tt) REVERT: A 113 CYS cc_start: 0.8362 (m) cc_final: 0.7797 (m) REVERT: A 192 LEU cc_start: 0.8178 (mt) cc_final: 0.7951 (mm) REVERT: A 209 ARG cc_start: 0.6503 (mmt90) cc_final: 0.6273 (mmm-85) REVERT: A 320 CYS cc_start: 0.7764 (m) cc_final: 0.7506 (m) REVERT: A 322 TRP cc_start: 0.8997 (t60) cc_final: 0.8651 (t60) REVERT: C 197 LYS cc_start: 0.6058 (mtpt) cc_final: 0.5719 (ttpp) REVERT: C 285 ILE cc_start: 0.6911 (mt) cc_final: 0.6657 (mp) REVERT: B 10 GLU cc_start: 0.8392 (pp20) cc_final: 0.8151 (pp20) REVERT: B 292 PHE cc_start: 0.8557 (m-10) cc_final: 0.8349 (m-80) outliers start: 7 outliers final: 6 residues processed: 338 average time/residue: 0.4457 time to fit residues: 162.4929 Evaluate side-chains 205 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.0770 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 317 GLN C 241 ASN C 255 ASN B 142 HIS B 266 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.129815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100079 restraints weight = 17869.269| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.13 r_work: 0.3347 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9164 Z= 0.207 Angle : 0.838 12.409 12440 Z= 0.433 Chirality : 0.048 0.190 1421 Planarity : 0.007 0.084 1571 Dihedral : 7.058 136.831 1262 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.52 % Favored : 91.39 % Rotamer: Outliers : 6.00 % Allowed : 18.10 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.24), residues: 1127 helix: 0.95 (0.25), residues: 390 sheet: -1.53 (0.32), residues: 258 loop : -2.24 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.031 0.003 TYR S 59 PHE 0.022 0.002 PHE B 335 TRP 0.038 0.003 TRP S 111 HIS 0.010 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9160) covalent geometry : angle 0.83683 (12434) SS BOND : bond 0.00652 ( 3) SS BOND : angle 2.17177 ( 6) hydrogen bonds : bond 0.04662 ( 401) hydrogen bonds : angle 4.53738 ( 1107) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8156 (mm) cc_final: 0.7617 (tt) REVERT: A 160 TYR cc_start: 0.6744 (t80) cc_final: 0.6538 (t80) REVERT: A 209 ARG cc_start: 0.6660 (mmt90) cc_final: 0.6253 (mmm-85) REVERT: A 214 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: A 219 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8878 (tm-30) REVERT: A 221 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: A 231 LEU cc_start: 0.8691 (mm) cc_final: 0.8332 (tm) REVERT: A 320 CYS cc_start: 0.7370 (m) cc_final: 0.7089 (m) REVERT: F 19 TRP cc_start: 0.8709 (p-90) cc_final: 0.8321 (p-90) REVERT: C 216 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8507 (tp30) REVERT: C 309 ASP cc_start: 0.9240 (t0) cc_final: 0.8416 (m-30) REVERT: B 10 GLU cc_start: 0.8325 (pp20) cc_final: 0.8023 (pp20) REVERT: B 42 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7906 (ttt-90) REVERT: B 44 GLN cc_start: 0.8281 (pm20) cc_final: 0.8071 (pm20) REVERT: B 217 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7513 (pmt) REVERT: B 226 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8830 (mt-10) REVERT: B 280 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8682 (tttm) REVERT: B 292 PHE cc_start: 0.9043 (m-10) cc_final: 0.8513 (m-80) REVERT: B 332 TRP cc_start: 0.8527 (m-10) cc_final: 0.8287 (m-10) REVERT: G 9 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7839 (tt) REVERT: G 21 MET cc_start: 0.8803 (ttp) cc_final: 0.8424 (ttt) REVERT: G 22 GLU cc_start: 0.7428 (tt0) cc_final: 0.7054 (tt0) REVERT: G 25 ILE cc_start: 0.7822 (pt) cc_final: 0.7501 (pp) REVERT: G 26 ASP cc_start: 0.8701 (p0) cc_final: 0.8451 (p0) REVERT: S 59 TYR cc_start: 0.7685 (m-10) cc_final: 0.7450 (m-10) REVERT: S 95 TYR cc_start: 0.8172 (m-80) cc_final: 0.7607 (m-10) REVERT: S 105 SER cc_start: 0.8962 (t) cc_final: 0.8476 (p) REVERT: S 142 GLN cc_start: 0.4919 (mt0) cc_final: 0.4337 (pp30) outliers start: 58 outliers final: 12 residues processed: 295 average time/residue: 0.4609 time to fit residues: 146.7313 Evaluate side-chains 214 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** S 142 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 = 0.3633 r_free = 0.3633 target = 0.109969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078992 restraints weight = 18228.270| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.05 r_work: 0.2984 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9164 Z= 0.236 Angle : 0.783 10.930 12440 Z= 0.405 Chirality : 0.047 0.191 1421 Planarity : 0.005 0.047 1571 Dihedral : 5.521 38.773 1254 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 7.34 % Allowed : 22.44 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.25), residues: 1127 helix: 1.21 (0.26), residues: 382 sheet: -1.60 (0.32), residues: 268 loop : -2.09 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 23 TYR 0.018 0.002 TYR A 311 PHE 0.014 0.002 PHE S 110 TRP 0.020 0.002 TRP A 227 HIS 0.007 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9160) covalent geometry : angle 0.78311 (12434) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.21871 ( 6) hydrogen bonds : bond 0.04942 ( 401) hydrogen bonds : angle 4.52382 ( 1107) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8306 (mm) cc_final: 0.7603 (tt) REVERT: A 129 PHE cc_start: 0.8246 (m-80) cc_final: 0.7895 (m-80) REVERT: A 160 TYR cc_start: 0.7186 (t80) cc_final: 0.6983 (t80) REVERT: A 209 ARG cc_start: 0.6646 (mmt90) cc_final: 0.6318 (mmm-85) REVERT: A 221 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: A 231 LEU cc_start: 0.8784 (mm) cc_final: 0.8343 (tm) REVERT: A 270 ARG cc_start: 0.8070 (mmp-170) cc_final: 0.7425 (tpt170) REVERT: A 303 LEU cc_start: 0.7929 (pt) cc_final: 0.7478 (tm) REVERT: A 317 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: C 23 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7279 (mp) REVERT: C 32 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7414 (tmm-80) REVERT: C 276 GLU cc_start: 0.8961 (tp30) cc_final: 0.8536 (pm20) REVERT: C 290 TYR cc_start: 0.7005 (t80) cc_final: 0.6376 (t80) REVERT: C 306 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8676 (tp40) REVERT: C 309 ASP cc_start: 0.9364 (t0) cc_final: 0.8880 (m-30) REVERT: C 318 GLU cc_start: 0.7441 (pt0) cc_final: 0.6853 (pm20) REVERT: B 127 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8552 (mtmm) REVERT: B 130 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 142 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8104 (m-70) REVERT: B 217 MET cc_start: 0.7488 (ptt) cc_final: 0.7008 (pmt) REVERT: B 226 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8672 (mt-10) REVERT: B 280 LYS cc_start: 0.8931 (tttp) cc_final: 0.8554 (tttm) REVERT: B 292 PHE cc_start: 0.8976 (m-10) cc_final: 0.8439 (m-10) REVERT: G 9 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7792 (tt) REVERT: G 21 MET cc_start: 0.8956 (ttp) cc_final: 0.8465 (ttt) REVERT: G 22 GLU cc_start: 0.7417 (tt0) cc_final: 0.7040 (tt0) REVERT: G 25 ILE cc_start: 0.8198 (pt) cc_final: 0.7836 (pp) REVERT: G 26 ASP cc_start: 0.9120 (p0) cc_final: 0.8879 (p0) REVERT: G 47 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8597 (tm-30) REVERT: G 48 ASP cc_start: 0.8166 (t0) cc_final: 0.7612 (t0) REVERT: S 59 TYR cc_start: 0.8139 (m-10) cc_final: 0.7643 (m-10) REVERT: S 67 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6806 (ttp-110) REVERT: S 82 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7816 (mm-40) REVERT: S 222 GLU cc_start: 0.7974 (mp0) cc_final: 0.7668 (mp0) REVERT: S 223 ASP cc_start: 0.8190 (m-30) cc_final: 0.7737 (m-30) outliers start: 71 outliers final: 29 residues processed: 268 average time/residue: 0.5957 time to fit residues: 169.8017 Evaluate side-chains 215 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN C 213 HIS B 259 GLN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.109239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078913 restraints weight = 18156.484| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.97 r_work: 0.2970 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.9000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9164 Z= 0.162 Angle : 0.728 13.877 12440 Z= 0.367 Chirality : 0.045 0.219 1421 Planarity : 0.005 0.061 1571 Dihedral : 5.078 36.969 1254 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.41 % Allowed : 24.92 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.25), residues: 1127 helix: 1.37 (0.27), residues: 383 sheet: -1.51 (0.32), residues: 265 loop : -2.03 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 30 TYR 0.021 0.001 TYR C 296 PHE 0.012 0.002 PHE S 212 TRP 0.023 0.002 TRP F 19 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9160) covalent geometry : angle 0.72739 (12434) SS BOND : bond 0.00297 ( 3) SS BOND : angle 1.19824 ( 6) hydrogen bonds : bond 0.04195 ( 401) hydrogen bonds : angle 4.33602 ( 1107) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.364 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8404 (mm) cc_final: 0.7577 (tt) REVERT: A 129 PHE cc_start: 0.8209 (m-80) cc_final: 0.7854 (m-80) REVERT: A 209 ARG cc_start: 0.6640 (mmt90) cc_final: 0.6175 (mmm-85) REVERT: A 221 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: A 231 LEU cc_start: 0.8774 (mm) cc_final: 0.8381 (tm) REVERT: A 270 ARG cc_start: 0.8131 (mmp-170) cc_final: 0.7351 (tpt170) REVERT: A 302 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7650 (t0) REVERT: A 317 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 325 MET cc_start: 0.8731 (tpp) cc_final: 0.8196 (tpp) REVERT: F 16 ASN cc_start: 0.8819 (t0) cc_final: 0.7764 (m-40) REVERT: F 19 TRP cc_start: 0.8323 (p-90) cc_final: 0.7850 (p-90) REVERT: C 23 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7331 (mp) REVERT: C 32 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7403 (tmm-80) REVERT: C 276 GLU cc_start: 0.8987 (tp30) cc_final: 0.8706 (pt0) REVERT: C 290 TYR cc_start: 0.7118 (t80) cc_final: 0.6700 (t80) REVERT: C 306 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8693 (tp40) REVERT: C 309 ASP cc_start: 0.9382 (t0) cc_final: 0.9006 (m-30) REVERT: C 318 GLU cc_start: 0.7452 (pt0) cc_final: 0.6832 (pm20) REVERT: B 42 ARG cc_start: 0.8281 (ttt180) cc_final: 0.8046 (tmt170) REVERT: B 59 TYR cc_start: 0.8200 (m-80) cc_final: 0.7996 (m-80) REVERT: B 127 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8474 (mtmm) REVERT: B 130 GLU cc_start: 0.8706 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 217 MET cc_start: 0.7718 (ptt) cc_final: 0.7353 (pmt) REVERT: B 226 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 280 LYS cc_start: 0.8966 (tttp) cc_final: 0.8581 (ttmm) REVERT: B 292 PHE cc_start: 0.8955 (m-10) cc_final: 0.8456 (m-10) REVERT: G 9 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7927 (tt) REVERT: G 21 MET cc_start: 0.9015 (ttp) cc_final: 0.8506 (ttt) REVERT: G 22 GLU cc_start: 0.7422 (tt0) cc_final: 0.6970 (tt0) REVERT: G 30 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8258 (p) REVERT: G 46 LYS cc_start: 0.9387 (ptpp) cc_final: 0.9171 (pptt) REVERT: G 48 ASP cc_start: 0.8223 (t0) cc_final: 0.7786 (t0) REVERT: S 59 TYR cc_start: 0.7848 (m-10) cc_final: 0.7458 (m-10) REVERT: S 65 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7616 (ttpt) REVERT: S 82 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8136 (mm-40) REVERT: S 93 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6322 (tpt) REVERT: S 220 GLU cc_start: 0.8720 (pp20) cc_final: 0.8435 (pp20) REVERT: S 223 ASP cc_start: 0.8373 (m-30) cc_final: 0.7719 (m-30) REVERT: S 246 GLU cc_start: 0.8692 (tp30) cc_final: 0.6744 (pm20) outliers start: 62 outliers final: 25 residues processed: 239 average time/residue: 0.5528 time to fit residues: 140.9857 Evaluate side-chains 209 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076842 restraints weight = 18386.823| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.95 r_work: 0.2936 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.9535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9164 Z= 0.178 Angle : 0.733 12.215 12440 Z= 0.372 Chirality : 0.045 0.217 1421 Planarity : 0.004 0.046 1571 Dihedral : 4.959 36.976 1251 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.62 % Allowed : 26.27 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.25), residues: 1127 helix: 1.48 (0.27), residues: 382 sheet: -1.42 (0.32), residues: 267 loop : -2.01 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 160 TYR 0.020 0.001 TYR A 311 PHE 0.012 0.002 PHE S 212 TRP 0.019 0.002 TRP A 227 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9160) covalent geometry : angle 0.73258 (12434) SS BOND : bond 0.00243 ( 3) SS BOND : angle 1.21043 ( 6) hydrogen bonds : bond 0.04115 ( 401) hydrogen bonds : angle 4.29727 ( 1107) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 0.357 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8424 (mm) cc_final: 0.7728 (tt) REVERT: A 129 PHE cc_start: 0.8238 (m-80) cc_final: 0.7869 (m-80) REVERT: A 209 ARG cc_start: 0.6606 (mmt90) cc_final: 0.6135 (mmm-85) REVERT: A 218 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 231 LEU cc_start: 0.8828 (mm) cc_final: 0.8438 (tm) REVERT: A 267 ASP cc_start: 0.8282 (p0) cc_final: 0.8058 (p0) REVERT: A 268 TRP cc_start: 0.8540 (m100) cc_final: 0.7343 (m-90) REVERT: A 270 ARG cc_start: 0.8113 (mmp-170) cc_final: 0.7322 (tpt170) REVERT: A 302 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7700 (t0) REVERT: A 325 MET cc_start: 0.8771 (tpp) cc_final: 0.8131 (mpp) REVERT: F 16 ASN cc_start: 0.8828 (t0) cc_final: 0.8252 (t0) REVERT: C 23 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7249 (mp) REVERT: C 32 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7560 (tmm-80) REVERT: C 276 GLU cc_start: 0.9063 (tp30) cc_final: 0.8775 (pt0) REVERT: C 290 TYR cc_start: 0.7208 (t80) cc_final: 0.6877 (t80) REVERT: C 306 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8744 (tp40) REVERT: C 309 ASP cc_start: 0.9370 (t0) cc_final: 0.9011 (m-30) REVERT: C 313 ARG cc_start: 0.8112 (mpp80) cc_final: 0.7878 (mpp80) REVERT: C 318 GLU cc_start: 0.7594 (pt0) cc_final: 0.7096 (pm20) REVERT: B 9 GLN cc_start: 0.9070 (tp40) cc_final: 0.8811 (tp40) REVERT: B 19 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8170 (tmm-80) REVERT: B 42 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7920 (tmt170) REVERT: B 59 TYR cc_start: 0.8449 (m-80) cc_final: 0.8138 (m-80) REVERT: B 127 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8517 (mtmm) REVERT: B 130 GLU cc_start: 0.8776 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 142 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8245 (m-70) REVERT: B 217 MET cc_start: 0.7780 (ptt) cc_final: 0.7352 (pmt) REVERT: B 226 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8746 (mt-10) REVERT: B 259 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: B 280 LYS cc_start: 0.8942 (tttp) cc_final: 0.8600 (ttmm) REVERT: B 292 PHE cc_start: 0.8969 (m-10) cc_final: 0.8466 (m-10) REVERT: B 332 TRP cc_start: 0.8498 (m-10) cc_final: 0.7622 (m-10) REVERT: G 9 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8001 (tt) REVERT: G 22 GLU cc_start: 0.7479 (tt0) cc_final: 0.7131 (tt0) REVERT: G 48 ASP cc_start: 0.8420 (t0) cc_final: 0.7759 (t0) REVERT: S 46 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: S 59 TYR cc_start: 0.7953 (m-10) cc_final: 0.7692 (m-10) REVERT: S 62 ASP cc_start: 0.8715 (m-30) cc_final: 0.8455 (p0) REVERT: S 82 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8252 (mm-40) REVERT: S 220 GLU cc_start: 0.8924 (pp20) cc_final: 0.8702 (pp20) REVERT: S 223 ASP cc_start: 0.8589 (m-30) cc_final: 0.7925 (m-30) REVERT: S 246 GLU cc_start: 0.8713 (tp30) cc_final: 0.6917 (pm20) REVERT: S 247 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7163 (tp) outliers start: 64 outliers final: 35 residues processed: 234 average time/residue: 0.5639 time to fit residues: 140.5237 Evaluate side-chains 218 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 40 optimal weight: 0.0010 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 254 ASN A 317 GLN C 256 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.108233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078711 restraints weight = 17923.741| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.81 r_work: 0.2984 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.9696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9164 Z= 0.139 Angle : 0.732 12.471 12440 Z= 0.367 Chirality : 0.044 0.243 1421 Planarity : 0.004 0.048 1571 Dihedral : 4.777 36.614 1251 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.79 % Allowed : 28.54 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.25), residues: 1127 helix: 1.43 (0.27), residues: 388 sheet: -1.39 (0.32), residues: 264 loop : -2.02 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 208 TYR 0.022 0.001 TYR C 296 PHE 0.012 0.001 PHE S 212 TRP 0.031 0.002 TRP F 19 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9160) covalent geometry : angle 0.73134 (12434) SS BOND : bond 0.00314 ( 3) SS BOND : angle 1.03931 ( 6) hydrogen bonds : bond 0.03802 ( 401) hydrogen bonds : angle 4.24946 ( 1107) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.371 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8502 (mm) cc_final: 0.7824 (tt) REVERT: A 129 PHE cc_start: 0.8262 (m-80) cc_final: 0.7867 (m-80) REVERT: A 209 ARG cc_start: 0.6596 (mmt90) cc_final: 0.6146 (mmm-85) REVERT: A 221 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: A 231 LEU cc_start: 0.8783 (mm) cc_final: 0.8427 (tm) REVERT: A 268 TRP cc_start: 0.8534 (m100) cc_final: 0.7374 (m-90) REVERT: A 302 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 325 MET cc_start: 0.8694 (tpp) cc_final: 0.8115 (mpp) REVERT: F 16 ASN cc_start: 0.8913 (t0) cc_final: 0.7963 (m-40) REVERT: C 23 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7238 (mp) REVERT: C 32 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7153 (tmm-80) REVERT: C 205 ARG cc_start: 0.8904 (tpm170) cc_final: 0.8702 (tpm170) REVERT: C 247 MET cc_start: 0.9025 (ttm) cc_final: 0.8790 (mtp) REVERT: C 276 GLU cc_start: 0.9094 (tp30) cc_final: 0.8807 (pt0) REVERT: C 290 TYR cc_start: 0.7284 (t80) cc_final: 0.7015 (t80) REVERT: C 306 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8808 (tp40) REVERT: C 309 ASP cc_start: 0.9379 (t0) cc_final: 0.9022 (m-30) REVERT: C 313 ARG cc_start: 0.8115 (mpp80) cc_final: 0.7859 (mpp80) REVERT: C 318 GLU cc_start: 0.7619 (pt0) cc_final: 0.7146 (pm20) REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.8093 (m-80) REVERT: B 127 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8523 (mtmm) REVERT: B 130 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7982 (mm-30) REVERT: B 163 ASP cc_start: 0.8520 (t0) cc_final: 0.8125 (t0) REVERT: B 217 MET cc_start: 0.7973 (ptt) cc_final: 0.7582 (pmt) REVERT: B 280 LYS cc_start: 0.8928 (tttp) cc_final: 0.8564 (ttmm) REVERT: B 292 PHE cc_start: 0.8920 (m-10) cc_final: 0.8430 (m-10) REVERT: G 9 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8211 (tt) REVERT: G 22 GLU cc_start: 0.7578 (tt0) cc_final: 0.7152 (tm-30) REVERT: G 47 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8569 (tm-30) REVERT: G 48 ASP cc_start: 0.8371 (t0) cc_final: 0.7820 (t0) REVERT: S 46 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7763 (pp20) REVERT: S 59 TYR cc_start: 0.7885 (m-10) cc_final: 0.7650 (m-10) REVERT: S 62 ASP cc_start: 0.8677 (m-30) cc_final: 0.8424 (p0) REVERT: S 82 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8344 (mm-40) REVERT: S 212 PHE cc_start: 0.8142 (m-10) cc_final: 0.7780 (m-10) REVERT: S 223 ASP cc_start: 0.8561 (m-30) cc_final: 0.8019 (m-30) REVERT: S 246 GLU cc_start: 0.8793 (tp30) cc_final: 0.7027 (pm20) REVERT: S 247 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7128 (tp) outliers start: 56 outliers final: 30 residues processed: 241 average time/residue: 0.5263 time to fit residues: 135.8997 Evaluate side-chains 222 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077473 restraints weight = 18335.924| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.92 r_work: 0.2956 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.9931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9164 Z= 0.159 Angle : 0.768 14.178 12440 Z= 0.382 Chirality : 0.045 0.248 1421 Planarity : 0.004 0.050 1571 Dihedral : 4.766 36.629 1251 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.10 % Allowed : 30.71 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1127 helix: 1.49 (0.27), residues: 388 sheet: -1.39 (0.32), residues: 259 loop : -1.91 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 208 TYR 0.019 0.001 TYR A 311 PHE 0.015 0.001 PHE S 212 TRP 0.026 0.002 TRP A 227 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9160) covalent geometry : angle 0.76726 (12434) SS BOND : bond 0.00478 ( 3) SS BOND : angle 1.16440 ( 6) hydrogen bonds : bond 0.03825 ( 401) hydrogen bonds : angle 4.23117 ( 1107) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8574 (mm) cc_final: 0.7942 (tt) REVERT: A 129 PHE cc_start: 0.8295 (m-80) cc_final: 0.7958 (m-80) REVERT: A 209 ARG cc_start: 0.6607 (mmt90) cc_final: 0.6167 (mmm-85) REVERT: A 221 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: A 231 LEU cc_start: 0.8726 (mm) cc_final: 0.8348 (tm) REVERT: A 268 TRP cc_start: 0.8598 (m100) cc_final: 0.7427 (m-90) REVERT: F 16 ASN cc_start: 0.8799 (t0) cc_final: 0.8351 (t0) REVERT: F 19 TRP cc_start: 0.8948 (t60) cc_final: 0.8601 (p-90) REVERT: F 30 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8034 (tpp80) REVERT: F 31 PHE cc_start: 0.8039 (m-10) cc_final: 0.7739 (m-80) REVERT: C 23 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7238 (mp) REVERT: C 32 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7344 (tmm-80) REVERT: C 247 MET cc_start: 0.9009 (ttm) cc_final: 0.8803 (mtp) REVERT: C 252 SER cc_start: 0.8928 (m) cc_final: 0.8544 (p) REVERT: C 302 TYR cc_start: 0.8903 (t80) cc_final: 0.8561 (t80) REVERT: C 306 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8762 (tp40) REVERT: C 309 ASP cc_start: 0.9361 (t0) cc_final: 0.9008 (m-30) REVERT: C 313 ARG cc_start: 0.8150 (mpp80) cc_final: 0.7734 (mpp80) REVERT: C 318 GLU cc_start: 0.7633 (pt0) cc_final: 0.7016 (pm20) REVERT: C 325 CYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6840 (t) REVERT: B 44 GLN cc_start: 0.8384 (pm20) cc_final: 0.8141 (pm20) REVERT: B 59 TYR cc_start: 0.8444 (m-80) cc_final: 0.8138 (m-80) REVERT: B 127 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8550 (mtmm) REVERT: B 130 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 163 ASP cc_start: 0.8569 (t0) cc_final: 0.8172 (t0) REVERT: B 217 MET cc_start: 0.7999 (ptt) cc_final: 0.7563 (pmt) REVERT: B 255 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7191 (mp) REVERT: B 280 LYS cc_start: 0.8936 (tttp) cc_final: 0.8537 (ttmm) REVERT: B 292 PHE cc_start: 0.8934 (m-10) cc_final: 0.8446 (m-10) REVERT: B 332 TRP cc_start: 0.8426 (m-10) cc_final: 0.8080 (m-10) REVERT: G 9 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8182 (tt) REVERT: G 22 GLU cc_start: 0.7589 (tt0) cc_final: 0.7170 (tm-30) REVERT: G 27 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7727 (mtt-85) REVERT: G 46 LYS cc_start: 0.9556 (ptmm) cc_final: 0.9314 (pptt) REVERT: G 48 ASP cc_start: 0.8457 (t0) cc_final: 0.7953 (t0) REVERT: S 46 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7762 (pp20) REVERT: S 59 TYR cc_start: 0.7893 (m-10) cc_final: 0.7683 (m-10) REVERT: S 82 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8330 (mm-40) REVERT: S 192 MET cc_start: 0.8826 (ttt) cc_final: 0.8469 (ptm) REVERT: S 222 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7785 (tm-30) REVERT: S 223 ASP cc_start: 0.8663 (m-30) cc_final: 0.7963 (m-30) REVERT: S 246 GLU cc_start: 0.8772 (tp30) cc_final: 0.7124 (pm20) REVERT: S 247 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7035 (tt) outliers start: 59 outliers final: 34 residues processed: 237 average time/residue: 0.5135 time to fit residues: 130.1286 Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077346 restraints weight = 18257.091| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.88 r_work: 0.2948 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 1.0168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9164 Z= 0.165 Angle : 0.802 13.531 12440 Z= 0.399 Chirality : 0.045 0.260 1421 Planarity : 0.004 0.053 1571 Dihedral : 4.790 36.607 1251 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 6.10 % Allowed : 32.16 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1127 helix: 1.41 (0.27), residues: 388 sheet: -1.41 (0.32), residues: 259 loop : -1.85 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 160 TYR 0.023 0.001 TYR C 296 PHE 0.011 0.001 PHE F 31 TRP 0.032 0.002 TRP A 227 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9160) covalent geometry : angle 0.80160 (12434) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.14570 ( 6) hydrogen bonds : bond 0.03873 ( 401) hydrogen bonds : angle 4.28022 ( 1107) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.390 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8588 (mm) cc_final: 0.7995 (tt) REVERT: A 63 ILE cc_start: 0.8003 (mm) cc_final: 0.7770 (mm) REVERT: A 129 PHE cc_start: 0.8301 (m-80) cc_final: 0.7918 (m-80) REVERT: A 209 ARG cc_start: 0.6634 (mmt90) cc_final: 0.6205 (mmm-85) REVERT: A 221 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: A 231 LEU cc_start: 0.8738 (mm) cc_final: 0.8351 (tm) REVERT: A 268 TRP cc_start: 0.8623 (m100) cc_final: 0.7453 (m-90) REVERT: F 16 ASN cc_start: 0.8834 (t0) cc_final: 0.8428 (t0) REVERT: F 19 TRP cc_start: 0.8924 (t60) cc_final: 0.8625 (p-90) REVERT: C 23 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7240 (mp) REVERT: C 32 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7522 (tmm-80) REVERT: C 242 ARG cc_start: 0.8405 (mpt180) cc_final: 0.8190 (mpt-90) REVERT: C 252 SER cc_start: 0.8882 (m) cc_final: 0.8514 (p) REVERT: C 287 TYR cc_start: 0.7662 (m-10) cc_final: 0.7458 (m-10) REVERT: C 302 TYR cc_start: 0.8865 (t80) cc_final: 0.8543 (t80) REVERT: C 306 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8781 (tp40) REVERT: C 309 ASP cc_start: 0.9334 (t0) cc_final: 0.8994 (m-30) REVERT: C 313 ARG cc_start: 0.8188 (mpp80) cc_final: 0.7772 (mpp80) REVERT: C 318 GLU cc_start: 0.7697 (pt0) cc_final: 0.7012 (pm20) REVERT: C 325 CYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6977 (t) REVERT: C 341 ASP cc_start: 0.7880 (t0) cc_final: 0.7666 (t0) REVERT: B 19 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8185 (tmm-80) REVERT: B 42 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7876 (tmt170) REVERT: B 44 GLN cc_start: 0.8394 (pm20) cc_final: 0.8035 (pm20) REVERT: B 59 TYR cc_start: 0.8422 (m-80) cc_final: 0.8110 (m-80) REVERT: B 127 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8560 (mtmm) REVERT: B 130 GLU cc_start: 0.8770 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 217 MET cc_start: 0.7999 (ptt) cc_final: 0.7556 (pmt) REVERT: B 255 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7159 (mp) REVERT: B 280 LYS cc_start: 0.8917 (tttp) cc_final: 0.8571 (ttmm) REVERT: B 292 PHE cc_start: 0.8923 (m-10) cc_final: 0.8436 (m-10) REVERT: B 332 TRP cc_start: 0.8466 (m-10) cc_final: 0.7610 (m-10) REVERT: G 9 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (tt) REVERT: G 22 GLU cc_start: 0.7555 (tt0) cc_final: 0.7168 (tm-30) REVERT: G 46 LYS cc_start: 0.9557 (ptmm) cc_final: 0.9307 (pptt) REVERT: S 46 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7757 (pp20) REVERT: S 82 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8335 (mm-40) REVERT: S 192 MET cc_start: 0.8851 (ttt) cc_final: 0.8560 (ptm) REVERT: S 220 GLU cc_start: 0.8996 (pp20) cc_final: 0.8400 (pp20) REVERT: S 222 GLU cc_start: 0.8673 (mm-30) cc_final: 0.7981 (tm-30) REVERT: S 223 ASP cc_start: 0.8785 (m-30) cc_final: 0.7820 (m-30) REVERT: S 246 GLU cc_start: 0.8744 (tp30) cc_final: 0.7182 (pm20) REVERT: S 247 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7118 (tt) outliers start: 59 outliers final: 36 residues processed: 232 average time/residue: 0.5248 time to fit residues: 130.5560 Evaluate side-chains 218 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.105946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076303 restraints weight = 18137.151| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.82 r_work: 0.2944 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 1.0340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9164 Z= 0.166 Angle : 0.822 15.446 12440 Z= 0.408 Chirality : 0.045 0.272 1421 Planarity : 0.004 0.047 1571 Dihedral : 4.780 36.531 1251 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.38 % Allowed : 33.20 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1127 helix: 1.39 (0.27), residues: 394 sheet: -1.38 (0.32), residues: 265 loop : -1.79 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 160 TYR 0.023 0.001 TYR A 311 PHE 0.010 0.001 PHE A 313 TRP 0.024 0.001 TRP A 127 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9160) covalent geometry : angle 0.82167 (12434) SS BOND : bond 0.00399 ( 3) SS BOND : angle 0.88077 ( 6) hydrogen bonds : bond 0.03943 ( 401) hydrogen bonds : angle 4.28498 ( 1107) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.360 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8640 (mm) cc_final: 0.8039 (tt) REVERT: A 63 ILE cc_start: 0.7972 (mm) cc_final: 0.7741 (mm) REVERT: A 129 PHE cc_start: 0.8346 (m-80) cc_final: 0.8095 (m-80) REVERT: A 209 ARG cc_start: 0.6632 (mmt90) cc_final: 0.6218 (mmm-85) REVERT: A 221 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: A 231 LEU cc_start: 0.8724 (mm) cc_final: 0.8337 (tm) REVERT: A 268 TRP cc_start: 0.8642 (m100) cc_final: 0.7453 (m-90) REVERT: F 16 ASN cc_start: 0.8815 (t0) cc_final: 0.8558 (t0) REVERT: F 19 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8660 (p-90) REVERT: F 23 ARG cc_start: 0.6474 (ptt90) cc_final: 0.6176 (ptt90) REVERT: F 31 PHE cc_start: 0.8423 (m-80) cc_final: 0.8156 (m-10) REVERT: C 23 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (mp) REVERT: C 32 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7487 (tmm-80) REVERT: C 242 ARG cc_start: 0.8411 (mpt180) cc_final: 0.8187 (mpt-90) REVERT: C 252 SER cc_start: 0.8874 (m) cc_final: 0.8503 (p) REVERT: C 287 TYR cc_start: 0.7817 (m-10) cc_final: 0.7603 (m-10) REVERT: C 302 TYR cc_start: 0.8907 (t80) cc_final: 0.8564 (t80) REVERT: C 304 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 306 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8787 (tp40) REVERT: C 309 ASP cc_start: 0.9330 (t0) cc_final: 0.9008 (m-30) REVERT: C 318 GLU cc_start: 0.7715 (pt0) cc_final: 0.7036 (pm20) REVERT: C 325 CYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6999 (t) REVERT: C 341 ASP cc_start: 0.7892 (t0) cc_final: 0.7674 (t0) REVERT: B 19 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8418 (tmm-80) REVERT: B 44 GLN cc_start: 0.8390 (pm20) cc_final: 0.8140 (pm20) REVERT: B 127 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8571 (mtmm) REVERT: B 130 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 217 MET cc_start: 0.8038 (ptt) cc_final: 0.7607 (pmt) REVERT: B 280 LYS cc_start: 0.8913 (tttp) cc_final: 0.8561 (ttmm) REVERT: B 292 PHE cc_start: 0.8945 (m-10) cc_final: 0.8460 (m-10) REVERT: B 332 TRP cc_start: 0.8482 (m-10) cc_final: 0.7651 (m-10) REVERT: G 9 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8110 (tt) REVERT: G 22 GLU cc_start: 0.7628 (tt0) cc_final: 0.7278 (tm-30) REVERT: G 46 LYS cc_start: 0.9556 (ptmm) cc_final: 0.9303 (pptt) REVERT: S 46 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7716 (pp20) REVERT: S 82 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8317 (mm-40) REVERT: S 192 MET cc_start: 0.8932 (ttt) cc_final: 0.8585 (ptm) REVERT: S 220 GLU cc_start: 0.9129 (pp20) cc_final: 0.8662 (pp20) REVERT: S 222 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8046 (tm-30) REVERT: S 223 ASP cc_start: 0.8828 (m-30) cc_final: 0.7857 (m-30) REVERT: S 246 GLU cc_start: 0.8750 (tp30) cc_final: 0.7295 (pm20) REVERT: S 247 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7075 (tt) outliers start: 52 outliers final: 35 residues processed: 225 average time/residue: 0.4976 time to fit residues: 120.1197 Evaluate side-chains 212 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain F residue 19 TRP Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 317 GLN C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077750 restraints weight = 18134.626| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.81 r_work: 0.2968 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 1.0476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9164 Z= 0.154 Angle : 0.849 15.854 12440 Z= 0.418 Chirality : 0.045 0.275 1421 Planarity : 0.004 0.054 1571 Dihedral : 4.719 36.229 1251 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.58 % Allowed : 33.61 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.25), residues: 1127 helix: 1.39 (0.27), residues: 392 sheet: -1.28 (0.32), residues: 263 loop : -1.83 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 160 TYR 0.026 0.001 TYR C 290 PHE 0.009 0.001 PHE A 313 TRP 0.026 0.002 TRP A 127 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9160) covalent geometry : angle 0.84903 (12434) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.07593 ( 6) hydrogen bonds : bond 0.03865 ( 401) hydrogen bonds : angle 4.26045 ( 1107) Misc. bond : bond 0.00019 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.358 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8628 (mm) cc_final: 0.7882 (tt) REVERT: A 63 ILE cc_start: 0.7973 (mm) cc_final: 0.7654 (mm) REVERT: A 129 PHE cc_start: 0.8273 (m-80) cc_final: 0.7995 (m-80) REVERT: A 209 ARG cc_start: 0.6639 (mmt90) cc_final: 0.6290 (mmm-85) REVERT: A 221 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: A 231 LEU cc_start: 0.8671 (mm) cc_final: 0.8294 (tm) REVERT: A 268 TRP cc_start: 0.8620 (m100) cc_final: 0.7420 (m-90) REVERT: C 23 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7212 (mp) REVERT: C 32 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7491 (tmm-80) REVERT: C 242 ARG cc_start: 0.8384 (mpt180) cc_final: 0.8168 (mpt-90) REVERT: C 252 SER cc_start: 0.8863 (m) cc_final: 0.8520 (p) REVERT: C 287 TYR cc_start: 0.7714 (m-10) cc_final: 0.7500 (m-10) REVERT: C 302 TYR cc_start: 0.8882 (t80) cc_final: 0.8500 (t80) REVERT: C 304 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 306 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8785 (tp40) REVERT: C 308 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: C 309 ASP cc_start: 0.9294 (t0) cc_final: 0.8981 (m-30) REVERT: C 318 GLU cc_start: 0.7704 (pt0) cc_final: 0.7024 (pm20) REVERT: C 325 CYS cc_start: 0.7276 (OUTLIER) cc_final: 0.7075 (t) REVERT: C 341 ASP cc_start: 0.7866 (t0) cc_final: 0.7650 (t0) REVERT: B 19 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8444 (tmm-80) REVERT: B 44 GLN cc_start: 0.8374 (pm20) cc_final: 0.8122 (pm20) REVERT: B 58 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 59 TYR cc_start: 0.8303 (m-80) cc_final: 0.8086 (m-80) REVERT: B 127 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8536 (mtmm) REVERT: B 130 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7992 (mm-30) REVERT: B 163 ASP cc_start: 0.8580 (t0) cc_final: 0.8159 (t0) REVERT: B 280 LYS cc_start: 0.8890 (tttp) cc_final: 0.8520 (ttmm) REVERT: B 292 PHE cc_start: 0.8914 (m-10) cc_final: 0.8427 (m-10) REVERT: B 332 TRP cc_start: 0.8421 (m-10) cc_final: 0.7547 (m-10) REVERT: G 9 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8133 (tt) REVERT: G 22 GLU cc_start: 0.7611 (tt0) cc_final: 0.7272 (tm-30) REVERT: G 27 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7808 (mtm-85) REVERT: G 46 LYS cc_start: 0.9552 (ptmm) cc_final: 0.9293 (pptt) REVERT: S 39 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: S 46 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: S 59 TYR cc_start: 0.8087 (m-10) cc_final: 0.7875 (m-10) REVERT: S 82 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8310 (mm-40) REVERT: S 220 GLU cc_start: 0.9161 (pp20) cc_final: 0.8749 (pp20) REVERT: S 222 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8175 (tm-30) REVERT: S 223 ASP cc_start: 0.8825 (m-30) cc_final: 0.7833 (m-30) REVERT: S 246 GLU cc_start: 0.8745 (tp30) cc_final: 0.7441 (pm20) outliers start: 54 outliers final: 35 residues processed: 231 average time/residue: 0.5047 time to fit residues: 125.4586 Evaluate side-chains 219 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.077546 restraints weight = 17861.362| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.80 r_work: 0.2964 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 1.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9164 Z= 0.158 Angle : 0.861 15.420 12440 Z= 0.424 Chirality : 0.045 0.272 1421 Planarity : 0.004 0.061 1571 Dihedral : 4.707 36.109 1251 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.76 % Allowed : 34.23 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.25), residues: 1127 helix: 1.44 (0.27), residues: 392 sheet: -1.20 (0.32), residues: 266 loop : -1.88 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 160 TYR 0.026 0.001 TYR A 311 PHE 0.013 0.001 PHE A 214 TRP 0.027 0.002 TRP A 127 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9160) covalent geometry : angle 0.86060 (12434) SS BOND : bond 0.00356 ( 3) SS BOND : angle 1.13809 ( 6) hydrogen bonds : bond 0.03841 ( 401) hydrogen bonds : angle 4.22079 ( 1107) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.81 seconds wall clock time: 60 minutes 35.03 seconds (3635.03 seconds total)