Starting phenix.real_space_refine on Thu Mar 13 15:58:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k26_61991/03_2025/9k26_61991_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k26_61991/03_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_61991/03_2025/9k26_61991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k26_61991/03_2025/9k26_61991.map" model { file = "/net/cci-nas-00/data/ceres_data/9k26_61991/03_2025/9k26_61991_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k26_61991/03_2025/9k26_61991_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ASP:plan': 3} 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: 8.15, per 1000 atoms: 0.91 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.21 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: 2.63 Time building geometry restraints manager: 2.93 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: 88.580 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.680 ------------------------------------------------------------------------------- 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 0.043 9160 Z= 0.238 Angle : 0.714 10.997 12434 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 : 11.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (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 TRP 0.032 0.001 TRP B 332 HIS 0.009 0.001 HIS A 321 PHE 0.021 0.001 PHE S 212 TYR 0.019 0.001 TYR C 296 ARG 0.009 0.001 ARG S 160 *********************** 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 : 1.335 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: 1.0711 time to fit residues: 394.6971 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 : 0.926 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 241 ASN B 119 ASN B 142 HIS B 266 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.122499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092303 restraints weight = 17796.636| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.08 r_work: 0.3222 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9160 Z= 0.371 Angle : 0.861 10.397 12434 Z= 0.449 Chirality : 0.048 0.185 1421 Planarity : 0.007 0.071 1571 Dihedral : 7.141 131.224 1262 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.61 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 : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1127 helix: 0.84 (0.25), residues: 391 sheet: -1.64 (0.31), residues: 264 loop : -2.30 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP S 111 HIS 0.013 0.002 HIS S 35 PHE 0.026 0.002 PHE C 191 TYR 0.029 0.003 TYR S 59 ARG 0.013 0.001 ARG S 67 *********************** 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 316 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8217 (mm) cc_final: 0.7659 (tt) REVERT: A 209 ARG cc_start: 0.6688 (mmt90) cc_final: 0.6358 (mmm-85) REVERT: A 219 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8910 (tm-30) REVERT: A 221 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 231 LEU cc_start: 0.8800 (mm) cc_final: 0.8405 (tm) REVERT: A 270 ARG cc_start: 0.8192 (mmp-170) cc_final: 0.7531 (tpt170) REVERT: A 320 CYS cc_start: 0.7480 (m) cc_final: 0.7164 (m) REVERT: A 325 MET cc_start: 0.8839 (tpp) cc_final: 0.8638 (tpp) REVERT: F 19 TRP cc_start: 0.8697 (p-90) cc_final: 0.8433 (p-90) REVERT: F 30 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7482 (mtt180) REVERT: C 222 ILE cc_start: 0.8017 (mt) cc_final: 0.7761 (mp) REVERT: C 254 CYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 309 ASP cc_start: 0.9281 (t0) cc_final: 0.8441 (m-30) REVERT: B 10 GLU cc_start: 0.8323 (pp20) cc_final: 0.8019 (pp20) REVERT: B 12 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8720 (pp20) REVERT: B 42 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8101 (ttt-90) REVERT: B 217 MET cc_start: 0.7924 (ptt) cc_final: 0.7564 (pmt) REVERT: B 226 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8778 (mt-10) REVERT: B 280 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8716 (ttmm) REVERT: B 292 PHE cc_start: 0.9042 (m-10) cc_final: 0.8467 (m-10) REVERT: B 301 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8458 (mmmm) REVERT: G 9 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7820 (tt) REVERT: G 22 GLU cc_start: 0.7498 (tt0) cc_final: 0.7088 (tt0) REVERT: G 48 ASP cc_start: 0.8327 (t70) cc_final: 0.8024 (t0) REVERT: S 38 ARG cc_start: 0.7472 (ptt180) cc_final: 0.6850 (ptp90) REVERT: S 67 ARG cc_start: 0.5609 (ttp80) cc_final: 0.5228 (ttp-110) REVERT: S 100 ILE cc_start: 0.8491 (tt) cc_final: 0.8198 (tt) REVERT: S 105 SER cc_start: 0.9240 (t) cc_final: 0.8929 (p) outliers start: 58 outliers final: 15 residues processed: 297 average time/residue: 1.0846 time to fit residues: 347.9042 Evaluate side-chains 220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain C residue 254 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 C 256 ASN B 75 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084251 restraints weight = 18094.409| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.98 r_work: 0.3092 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9160 Z= 0.250 Angle : 0.730 11.396 12434 Z= 0.371 Chirality : 0.044 0.170 1421 Planarity : 0.005 0.038 1571 Dihedral : 6.734 149.087 1257 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.00 % Allowed : 24.10 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1127 helix: 1.24 (0.26), residues: 389 sheet: -1.43 (0.32), residues: 253 loop : -2.14 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 332 HIS 0.005 0.001 HIS B 183 PHE 0.021 0.002 PHE F 31 TYR 0.021 0.002 TYR A 311 ARG 0.007 0.001 ARG G 13 *********************** 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 284 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.991 Fit side-chains 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: symmetry clash REVERT: A 62 LEU cc_start: 0.8357 (mm) cc_final: 0.7649 (tt) REVERT: A 129 PHE cc_start: 0.8018 (m-80) cc_final: 0.7806 (m-80) REVERT: A 209 ARG cc_start: 0.6611 (mmt90) cc_final: 0.6236 (mmm-85) REVERT: A 214 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: A 221 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: A 231 LEU cc_start: 0.8763 (mm) cc_final: 0.8373 (tm) REVERT: A 270 ARG cc_start: 0.8147 (mmp-170) cc_final: 0.7411 (tpt170) REVERT: A 303 LEU cc_start: 0.8085 (pt) cc_final: 0.7702 (tm) REVERT: F 16 ASN cc_start: 0.8815 (t0) cc_final: 0.8533 (t0) REVERT: C 23 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7218 (mp) REVERT: C 32 ARG cc_start: 0.7170 (tmm-80) cc_final: 0.6933 (tmm-80) REVERT: C 276 GLU cc_start: 0.8960 (tp30) cc_final: 0.8457 (pm20) REVERT: C 296 TYR cc_start: 0.7340 (t80) cc_final: 0.6958 (t80) REVERT: C 306 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8694 (tp40) REVERT: C 309 ASP cc_start: 0.9316 (t0) cc_final: 0.8770 (m-30) REVERT: C 318 GLU cc_start: 0.7049 (pt0) cc_final: 0.6459 (pm20) REVERT: B 19 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8384 (tmm-80) REVERT: B 42 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8023 (tmt170) REVERT: B 127 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8376 (mtmm) REVERT: B 142 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.8075 (m-70) REVERT: B 163 ASP cc_start: 0.8490 (t0) cc_final: 0.8185 (t0) REVERT: B 217 MET cc_start: 0.7775 (ptt) cc_final: 0.7395 (pmt) REVERT: B 226 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8697 (mt-10) REVERT: B 280 LYS cc_start: 0.9034 (tttp) cc_final: 0.8781 (ttmm) REVERT: B 292 PHE cc_start: 0.8956 (m-10) cc_final: 0.8436 (m-10) REVERT: B 327 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7443 (m) REVERT: B 332 TRP cc_start: 0.8145 (m-10) cc_final: 0.7368 (m-10) REVERT: G 9 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7769 (tt) REVERT: G 21 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8401 (ttt) REVERT: G 22 GLU cc_start: 0.7288 (tt0) cc_final: 0.6704 (tm-30) REVERT: G 25 ILE cc_start: 0.7690 (pt) cc_final: 0.7336 (pp) REVERT: G 26 ASP cc_start: 0.8859 (p0) cc_final: 0.8621 (p0) REVERT: G 47 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8515 (tm-30) REVERT: G 48 ASP cc_start: 0.8366 (t70) cc_final: 0.7913 (t0) REVERT: S 87 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7889 (mtm110) REVERT: S 93 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6378 (tpt) outliers start: 58 outliers final: 22 residues processed: 263 average time/residue: 1.0511 time to fit residues: 296.4808 Evaluate side-chains 221 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 214 PHE 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 C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 354 PHE 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 210 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR 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 21 MET Chi-restraints excluded: chain G residue 36 ASP 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 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 144 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 265 GLN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 HIS C 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.111064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080332 restraints weight = 18130.861| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 4.00 r_work: 0.3001 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9160 Z= 0.258 Angle : 0.717 11.515 12434 Z= 0.366 Chirality : 0.044 0.180 1421 Planarity : 0.004 0.034 1571 Dihedral : 6.591 147.889 1257 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.51 % Allowed : 26.06 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1127 helix: 1.40 (0.27), residues: 388 sheet: -1.38 (0.32), residues: 257 loop : -2.13 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 19 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE S 108 TYR 0.021 0.002 TYR S 59 ARG 0.009 0.001 ARG G 13 *********************** 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 269 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.940 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: symmetry clash REVERT: A 62 LEU cc_start: 0.8349 (mm) cc_final: 0.7662 (tt) REVERT: A 209 ARG cc_start: 0.6573 (mmt90) cc_final: 0.6156 (mmm-85) REVERT: A 214 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6253 (m-10) REVERT: A 221 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: A 231 LEU cc_start: 0.8777 (mm) cc_final: 0.8370 (tm) REVERT: A 268 TRP cc_start: 0.8538 (m100) cc_final: 0.7327 (m-90) REVERT: A 270 ARG cc_start: 0.8110 (mmp-170) cc_final: 0.7337 (tpt170) REVERT: A 302 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7573 (t0) REVERT: A 317 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: A 325 MET cc_start: 0.8648 (tpp) cc_final: 0.8046 (mpp) REVERT: F 16 ASN cc_start: 0.8761 (t0) cc_final: 0.8479 (t0) REVERT: F 19 TRP cc_start: 0.8223 (p-90) cc_final: 0.7841 (p-90) REVERT: C 23 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7318 (mp) REVERT: C 32 ARG cc_start: 0.7397 (tmm-80) cc_final: 0.6915 (tmm-80) REVERT: C 276 GLU cc_start: 0.8991 (tp30) cc_final: 0.8588 (pt0) REVERT: C 290 TYR cc_start: 0.7092 (t80) cc_final: 0.6513 (t80) REVERT: C 296 TYR cc_start: 0.7515 (t80) cc_final: 0.7029 (t80) REVERT: C 306 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8757 (tp40) REVERT: C 309 ASP cc_start: 0.9365 (t0) cc_final: 0.8928 (m-30) REVERT: C 318 GLU cc_start: 0.7317 (pt0) cc_final: 0.6728 (pm20) REVERT: B 127 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8446 (mtmm) REVERT: B 163 ASP cc_start: 0.8457 (t0) cc_final: 0.8126 (t0) REVERT: B 217 MET cc_start: 0.7795 (ptt) cc_final: 0.7334 (pmt) REVERT: B 226 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8662 (mt-10) REVERT: B 280 LYS cc_start: 0.9041 (tttp) cc_final: 0.8695 (ttmm) REVERT: B 292 PHE cc_start: 0.8931 (m-10) cc_final: 0.8410 (m-10) REVERT: G 9 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7891 (tt) REVERT: G 22 GLU cc_start: 0.7259 (tt0) cc_final: 0.6839 (tm-30) REVERT: G 28 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.6555 (pp) REVERT: G 36 ASP cc_start: 0.8497 (t0) cc_final: 0.8252 (t0) REVERT: S 82 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8130 (mm-40) REVERT: S 93 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6455 (tpt) REVERT: S 183 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8226 (mt0) REVERT: S 220 GLU cc_start: 0.8559 (pp20) cc_final: 0.8226 (pp20) REVERT: S 223 ASP cc_start: 0.8156 (m-30) cc_final: 0.7544 (m-30) REVERT: S 246 GLU cc_start: 0.8724 (tp30) cc_final: 0.6792 (pm20) outliers start: 63 outliers final: 28 residues processed: 246 average time/residue: 1.0720 time to fit residues: 283.2434 Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 257 VAL 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 317 GLN Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE 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 188 MET 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 28 ILE Chi-restraints excluded: chain G residue 38 MET 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 84 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 224 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 3 optimal weight: 0.0170 chunk 43 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- 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 340 ASN S 39 GLN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077382 restraints weight = 18076.514| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.90 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: 0.7405 moved from start: 0.9463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9160 Z= 0.262 Angle : 0.732 12.633 12434 Z= 0.373 Chirality : 0.045 0.176 1421 Planarity : 0.004 0.054 1571 Dihedral : 6.540 148.643 1254 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 6.72 % Allowed : 26.89 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1127 helix: 1.46 (0.27), residues: 388 sheet: -1.45 (0.31), residues: 266 loop : -2.01 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 227 HIS 0.004 0.001 HIS C 188 PHE 0.014 0.001 PHE S 108 TYR 0.022 0.002 TYR A 311 ARG 0.012 0.001 ARG C 208 *********************** 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 273 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 1.019 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: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8468 (mm) cc_final: 0.7819 (tt) REVERT: A 129 PHE cc_start: 0.8160 (m-80) cc_final: 0.7824 (m-80) REVERT: A 209 ARG cc_start: 0.6587 (mmt90) cc_final: 0.6180 (mmm-85) REVERT: A 214 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.6511 (m-10) REVERT: A 218 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7916 (mm-40) REVERT: A 221 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 231 LEU cc_start: 0.8819 (mm) cc_final: 0.8426 (tm) REVERT: A 267 ASP cc_start: 0.8307 (p0) cc_final: 0.8106 (p0) REVERT: A 268 TRP cc_start: 0.8562 (m100) cc_final: 0.7366 (m-90) REVERT: A 270 ARG cc_start: 0.8112 (mmp-170) cc_final: 0.7308 (tpt170) REVERT: A 302 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7779 (t0) REVERT: A 317 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: F 31 PHE cc_start: 0.8274 (m-10) cc_final: 0.7997 (m-80) REVERT: C 23 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7324 (mp) REVERT: C 32 ARG cc_start: 0.7567 (tmm-80) cc_final: 0.7204 (tmm-80) REVERT: C 276 GLU cc_start: 0.9022 (tp30) cc_final: 0.8672 (pt0) REVERT: C 287 TYR cc_start: 0.7569 (m-10) cc_final: 0.7356 (m-10) REVERT: C 290 TYR cc_start: 0.7256 (t80) cc_final: 0.6930 (t80) REVERT: C 306 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8767 (tp40) REVERT: C 309 ASP cc_start: 0.9371 (t0) cc_final: 0.9014 (m-30) REVERT: C 313 ARG cc_start: 0.8045 (mpp80) cc_final: 0.7700 (mpp80) REVERT: C 318 GLU cc_start: 0.7508 (pt0) cc_final: 0.6934 (pm20) REVERT: B 42 ARG cc_start: 0.8273 (ttt180) cc_final: 0.7885 (tmt170) REVERT: B 127 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8511 (mtmm) REVERT: B 217 MET cc_start: 0.7825 (ptt) cc_final: 0.7390 (pmt) REVERT: B 226 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8751 (mt-10) REVERT: B 280 LYS cc_start: 0.9027 (tttp) cc_final: 0.8626 (tttt) REVERT: B 292 PHE cc_start: 0.8932 (m-10) cc_final: 0.8430 (m-10) REVERT: B 332 TRP cc_start: 0.8474 (m-10) cc_final: 0.7741 (m-10) REVERT: G 9 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7941 (tt) REVERT: G 22 GLU cc_start: 0.7352 (tt0) cc_final: 0.7002 (tm-30) REVERT: G 47 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8539 (tm-30) REVERT: G 48 ASP cc_start: 0.8281 (t0) cc_final: 0.7927 (t0) REVERT: S 59 TYR cc_start: 0.8023 (m-10) cc_final: 0.7614 (m-10) REVERT: S 82 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8294 (mm-40) REVERT: S 93 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6556 (tpt) REVERT: S 223 ASP cc_start: 0.8629 (m-30) cc_final: 0.7887 (m-30) REVERT: S 246 GLU cc_start: 0.8793 (tp30) cc_final: 0.7077 (pp20) outliers start: 65 outliers final: 31 residues processed: 253 average time/residue: 1.2033 time to fit residues: 325.3191 Evaluate side-chains 220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 214 PHE 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 284 VAL 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 A residue 317 GLN Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 263 SER 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 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 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 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN C 256 ASN B 142 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077839 restraints weight = 17803.216| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.77 r_work: 0.2980 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.9790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9160 Z= 0.221 Angle : 0.748 11.844 12434 Z= 0.374 Chirality : 0.045 0.245 1421 Planarity : 0.004 0.046 1571 Dihedral : 6.476 153.688 1254 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.38 % Allowed : 30.71 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1127 helix: 1.51 (0.27), residues: 389 sheet: -1.33 (0.32), residues: 264 loop : -1.95 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 19 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE S 212 TYR 0.017 0.001 TYR S 59 ARG 0.010 0.001 ARG F 30 *********************** 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 249 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.439 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: symmetry clash REVERT: A 62 LEU cc_start: 0.8510 (mm) cc_final: 0.7875 (tt) REVERT: A 129 PHE cc_start: 0.8174 (m-80) cc_final: 0.7809 (m-80) REVERT: A 209 ARG cc_start: 0.6518 (mmt90) cc_final: 0.6105 (mmm-85) REVERT: A 218 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7988 (mm-40) REVERT: A 221 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: A 231 LEU cc_start: 0.8740 (mm) cc_final: 0.8376 (tm) REVERT: A 267 ASP cc_start: 0.8305 (p0) cc_final: 0.8098 (p0) REVERT: A 268 TRP cc_start: 0.8572 (m100) cc_final: 0.7397 (m-90) REVERT: A 302 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7517 (t0) REVERT: A 317 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: F 16 ASN cc_start: 0.8910 (t0) cc_final: 0.7862 (m-40) REVERT: F 31 PHE cc_start: 0.8107 (m-10) cc_final: 0.7791 (m-80) REVERT: C 23 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7234 (mp) REVERT: C 32 ARG cc_start: 0.7558 (tmm-80) cc_final: 0.7246 (tmm-80) REVERT: C 247 MET cc_start: 0.9054 (ttm) cc_final: 0.8757 (mtp) REVERT: C 252 SER cc_start: 0.8925 (m) cc_final: 0.8545 (p) REVERT: C 290 TYR cc_start: 0.7308 (t80) cc_final: 0.7091 (t80) REVERT: C 306 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8818 (tp40) REVERT: C 309 ASP cc_start: 0.9364 (t0) cc_final: 0.8984 (m-30) REVERT: C 313 ARG cc_start: 0.8146 (mpp80) cc_final: 0.7749 (mpp80) REVERT: C 318 GLU cc_start: 0.7609 (pt0) cc_final: 0.7012 (pm20) REVERT: C 325 CYS cc_start: 0.7408 (p) cc_final: 0.6937 (t) REVERT: B 19 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8414 (tmm-80) REVERT: B 42 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7772 (tmt170) REVERT: B 75 GLN cc_start: 0.9013 (mm110) cc_final: 0.8185 (mp10) REVERT: B 127 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8477 (mtmm) REVERT: B 163 ASP cc_start: 0.8538 (t0) cc_final: 0.8129 (t0) REVERT: B 217 MET cc_start: 0.8027 (ptt) cc_final: 0.7602 (pmt) REVERT: B 260 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7996 (tp30) REVERT: B 280 LYS cc_start: 0.8976 (tttp) cc_final: 0.8579 (ttmm) REVERT: B 292 PHE cc_start: 0.8924 (m-10) cc_final: 0.8437 (m-10) REVERT: B 332 TRP cc_start: 0.8487 (m-10) cc_final: 0.7700 (m-10) REVERT: G 9 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8206 (tt) REVERT: G 22 GLU cc_start: 0.7477 (tt0) cc_final: 0.7151 (tm-30) REVERT: G 48 ASP cc_start: 0.8390 (t0) cc_final: 0.8054 (t0) REVERT: S 59 TYR cc_start: 0.7925 (m-10) cc_final: 0.7632 (m-10) REVERT: S 82 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8309 (mm-40) REVERT: S 87 ARG cc_start: 0.8434 (mtm180) cc_final: 0.7893 (mtt90) REVERT: S 93 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6690 (tpt) REVERT: S 140 MET cc_start: 0.8248 (mmm) cc_final: 0.7179 (mmm) REVERT: S 160 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8419 (ptp-110) REVERT: S 220 GLU cc_start: 0.8824 (pp20) cc_final: 0.8505 (pp20) REVERT: S 223 ASP cc_start: 0.8648 (m-30) cc_final: 0.7926 (m-30) REVERT: S 246 GLU cc_start: 0.8790 (tp30) cc_final: 0.7115 (pm20) outliers start: 52 outliers final: 28 residues processed: 234 average time/residue: 1.1509 time to fit residues: 288.4335 Evaluate side-chains 218 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 LEU 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 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 354 PHE 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 259 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU 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 63 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.0970 chunk 101 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN F 16 ASN C 256 ASN B 142 HIS B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078814 restraints weight = 18003.040| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.84 r_work: 0.2993 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.9896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9160 Z= 0.207 Angle : 0.759 11.971 12434 Z= 0.377 Chirality : 0.044 0.249 1421 Planarity : 0.004 0.052 1571 Dihedral : 6.361 151.662 1254 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.17 % Allowed : 30.82 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.25), residues: 1127 helix: 1.54 (0.27), residues: 389 sheet: -1.19 (0.33), residues: 248 loop : -1.93 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 227 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE S 108 TYR 0.035 0.001 TYR A 160 ARG 0.012 0.001 ARG C 208 *********************** 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 250 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.959 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: symmetry clash REVERT: A 62 LEU cc_start: 0.8534 (mm) cc_final: 0.7934 (tt) REVERT: A 63 ILE cc_start: 0.7961 (mm) cc_final: 0.7728 (mm) REVERT: A 209 ARG cc_start: 0.6541 (mmt90) cc_final: 0.6145 (mmm-85) REVERT: A 218 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 221 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 231 LEU cc_start: 0.8688 (mm) cc_final: 0.8323 (tm) REVERT: A 267 ASP cc_start: 0.8324 (p0) cc_final: 0.8102 (p0) REVERT: A 268 TRP cc_start: 0.8583 (m100) cc_final: 0.7431 (m-90) REVERT: A 315 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8574 (mm) REVERT: F 16 ASN cc_start: 0.8824 (t0) cc_final: 0.8301 (t0) REVERT: F 19 TRP cc_start: 0.8858 (t60) cc_final: 0.8632 (p-90) REVERT: F 31 PHE cc_start: 0.7998 (m-10) cc_final: 0.7725 (m-10) REVERT: C 23 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7234 (mp) REVERT: C 32 ARG cc_start: 0.7533 (tmm-80) cc_final: 0.7230 (tmm-80) REVERT: C 216 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8877 (tp30) REVERT: C 247 MET cc_start: 0.9001 (ttm) cc_final: 0.8771 (mtp) REVERT: C 252 SER cc_start: 0.8924 (m) cc_final: 0.8531 (p) REVERT: C 302 TYR cc_start: 0.8921 (t80) cc_final: 0.8610 (t80) REVERT: C 306 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8785 (tp40) REVERT: C 309 ASP cc_start: 0.9347 (t0) cc_final: 0.8983 (m-30) REVERT: C 313 ARG cc_start: 0.8137 (mpp80) cc_final: 0.7744 (mpp80) REVERT: C 318 GLU cc_start: 0.7619 (pt0) cc_final: 0.7063 (pm20) REVERT: C 325 CYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6911 (t) REVERT: B 75 GLN cc_start: 0.8987 (mm110) cc_final: 0.8242 (mp10) REVERT: B 127 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8509 (mtmm) REVERT: B 163 ASP cc_start: 0.8537 (t0) cc_final: 0.8119 (t0) REVERT: B 217 MET cc_start: 0.8038 (ptt) cc_final: 0.7626 (pmt) REVERT: B 260 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7928 (tp30) REVERT: B 280 LYS cc_start: 0.8951 (tttp) cc_final: 0.8530 (ttmm) REVERT: B 292 PHE cc_start: 0.8904 (m-10) cc_final: 0.8447 (m-10) REVERT: B 332 TRP cc_start: 0.8437 (m-10) cc_final: 0.7609 (m-10) REVERT: G 9 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8134 (tt) REVERT: G 22 GLU cc_start: 0.7446 (tt0) cc_final: 0.7201 (tm-30) REVERT: G 27 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7644 (mtt-85) REVERT: G 47 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 48 ASP cc_start: 0.8345 (t0) cc_final: 0.7853 (t0) REVERT: S 59 TYR cc_start: 0.7954 (m-10) cc_final: 0.7720 (m-10) REVERT: S 82 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8295 (mm-40) REVERT: S 183 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8494 (mt0) REVERT: S 220 GLU cc_start: 0.8838 (pp20) cc_final: 0.8610 (pp20) REVERT: S 223 ASP cc_start: 0.8677 (m-30) cc_final: 0.7980 (m-30) REVERT: S 246 GLU cc_start: 0.8800 (tp30) cc_final: 0.7174 (pm20) outliers start: 50 outliers final: 30 residues processed: 237 average time/residue: 1.0739 time to fit residues: 273.0345 Evaluate side-chains 221 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 167 LEU 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 306 HIS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 CYS 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 216 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER 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 12 GLU 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 263 THR 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 63 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 110 ASN B 142 HIS B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.072885 restraints weight = 18462.997| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.82 r_work: 0.2884 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 1.0352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9160 Z= 0.369 Angle : 0.841 12.225 12434 Z= 0.423 Chirality : 0.047 0.259 1421 Planarity : 0.004 0.058 1571 Dihedral : 5.000 37.101 1251 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.89 % Allowed : 31.23 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1127 helix: 1.42 (0.27), residues: 390 sheet: -1.50 (0.32), residues: 259 loop : -1.91 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 227 HIS 0.006 0.001 HIS B 142 PHE 0.012 0.002 PHE A 313 TYR 0.025 0.002 TYR C 290 ARG 0.013 0.001 ARG C 208 *********************** 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 243 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.859 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8594 (mm) cc_final: 0.8004 (tt) REVERT: A 63 ILE cc_start: 0.8004 (mm) cc_final: 0.7780 (mm) REVERT: A 209 ARG cc_start: 0.6668 (mmt90) cc_final: 0.6259 (mmm-85) REVERT: A 221 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 231 LEU cc_start: 0.8792 (mm) cc_final: 0.8370 (tm) REVERT: A 302 ASP cc_start: 0.7757 (t0) cc_final: 0.7434 (t0) REVERT: A 317 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: F 19 TRP cc_start: 0.8921 (t60) cc_final: 0.8614 (p-90) REVERT: C 23 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 32 ARG cc_start: 0.8083 (tmm-80) cc_final: 0.7867 (tmm-80) REVERT: C 247 MET cc_start: 0.9049 (ttm) cc_final: 0.8820 (mtp) REVERT: C 252 SER cc_start: 0.8872 (m) cc_final: 0.8531 (p) REVERT: C 287 TYR cc_start: 0.8000 (m-10) cc_final: 0.7773 (m-10) REVERT: C 302 TYR cc_start: 0.8904 (t80) cc_final: 0.8629 (t80) REVERT: C 306 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8720 (tp40) REVERT: C 309 ASP cc_start: 0.9323 (t0) cc_final: 0.9002 (m-30) REVERT: C 318 GLU cc_start: 0.7711 (pt0) cc_final: 0.7005 (pm20) REVERT: C 325 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7145 (t) REVERT: C 341 ASP cc_start: 0.7892 (t0) cc_final: 0.7660 (t0) REVERT: B 19 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8448 (tmm-80) REVERT: B 42 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7925 (ttt-90) REVERT: B 58 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (pp) REVERT: B 127 LYS cc_start: 0.8884 (mtmm) cc_final: 0.8573 (mtmm) REVERT: B 217 MET cc_start: 0.7912 (ptt) cc_final: 0.7464 (pmt) REVERT: B 259 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6249 (mp10) REVERT: B 280 LYS cc_start: 0.8957 (tttp) cc_final: 0.8687 (ttmm) REVERT: B 292 PHE cc_start: 0.8825 (m-10) cc_final: 0.8287 (m-10) REVERT: G 9 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8253 (tt) REVERT: G 22 GLU cc_start: 0.7549 (tt0) cc_final: 0.7280 (tm-30) REVERT: G 46 LYS cc_start: 0.9574 (ptmm) cc_final: 0.9351 (pptt) REVERT: G 48 ASP cc_start: 0.8597 (t0) cc_final: 0.8259 (t0) REVERT: S 82 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8337 (mm-40) REVERT: S 223 ASP cc_start: 0.8772 (m-30) cc_final: 0.8207 (m-30) REVERT: S 246 GLU cc_start: 0.8737 (tp30) cc_final: 0.7272 (pm20) outliers start: 57 outliers final: 32 residues processed: 227 average time/residue: 1.0843 time to fit residues: 263.6517 Evaluate side-chains 211 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 167 LEU 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 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 315 LEU Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER 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 58 ILE 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 263 THR 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 S residue 2 VAL Chi-restraints excluded: chain S residue 63 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076099 restraints weight = 18337.944| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.87 r_work: 0.2915 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 1.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9160 Z= 0.253 Angle : 0.844 14.361 12434 Z= 0.419 Chirality : 0.045 0.264 1421 Planarity : 0.004 0.060 1571 Dihedral : 4.854 36.959 1251 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.55 % Allowed : 33.20 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1127 helix: 1.44 (0.27), residues: 390 sheet: -1.38 (0.32), residues: 260 loop : -1.93 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 227 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE S 108 TYR 0.025 0.001 TYR C 296 ARG 0.014 0.001 ARG C 208 *********************** 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 220 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.934 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: 0.8602 (mm) cc_final: 0.7999 (tt) REVERT: A 63 ILE cc_start: 0.7946 (mm) cc_final: 0.7725 (mm) REVERT: A 209 ARG cc_start: 0.6625 (mmt90) cc_final: 0.6221 (mmm-85) REVERT: A 221 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: A 231 LEU cc_start: 0.8739 (mm) cc_final: 0.8364 (tm) REVERT: A 302 ASP cc_start: 0.7861 (t0) cc_final: 0.7520 (t0) REVERT: A 317 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: F 16 ASN cc_start: 0.8759 (t0) cc_final: 0.8547 (t0) REVERT: C 23 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7209 (mp) REVERT: C 32 ARG cc_start: 0.7540 (tmm-80) cc_final: 0.7269 (tmm-80) REVERT: C 242 ARG cc_start: 0.8439 (mpt180) cc_final: 0.8043 (mpt-90) REVERT: C 252 SER cc_start: 0.8839 (m) cc_final: 0.8496 (p) REVERT: C 287 TYR cc_start: 0.7957 (m-10) cc_final: 0.7731 (m-10) REVERT: C 302 TYR cc_start: 0.8899 (t80) cc_final: 0.8599 (t80) REVERT: C 304 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8126 (tm-30) REVERT: C 306 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8757 (tp40) REVERT: C 309 ASP cc_start: 0.9279 (t0) cc_final: 0.8974 (m-30) REVERT: C 318 GLU cc_start: 0.7694 (pt0) cc_final: 0.7007 (pm20) REVERT: C 325 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7133 (t) REVERT: C 341 ASP cc_start: 0.7855 (t0) cc_final: 0.7631 (t0) REVERT: B 42 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7921 (tmt170) REVERT: B 127 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8544 (mtmm) REVERT: B 217 MET cc_start: 0.8014 (ptt) cc_final: 0.7578 (pmt) REVERT: B 280 LYS cc_start: 0.8973 (tttp) cc_final: 0.8532 (ttmm) REVERT: B 292 PHE cc_start: 0.8786 (m-10) cc_final: 0.8283 (m-10) REVERT: G 9 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8145 (tt) REVERT: G 22 GLU cc_start: 0.7494 (tt0) cc_final: 0.7252 (tm-30) REVERT: G 27 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7652 (mtt-85) REVERT: G 46 LYS cc_start: 0.9586 (ptmm) cc_final: 0.9325 (pptt) REVERT: G 48 ASP cc_start: 0.8573 (t0) cc_final: 0.8144 (t0) REVERT: S 82 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8243 (mm-40) REVERT: S 140 MET cc_start: 0.8343 (mmm) cc_final: 0.7911 (tpt) REVERT: S 183 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8681 (mt0) REVERT: S 208 SER cc_start: 0.8927 (p) cc_final: 0.8632 (t) REVERT: S 220 GLU cc_start: 0.9057 (pp20) cc_final: 0.8554 (pp20) REVERT: S 222 GLU cc_start: 0.8292 (tp30) cc_final: 0.8026 (tm-30) REVERT: S 223 ASP cc_start: 0.8646 (m-30) cc_final: 0.8133 (m-30) REVERT: S 246 GLU cc_start: 0.8723 (tp30) cc_final: 0.7393 (pm20) outliers start: 44 outliers final: 29 residues processed: 212 average time/residue: 1.0403 time to fit residues: 237.1063 Evaluate side-chains 206 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 LEU 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 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 315 LEU 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 227 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE 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 263 THR 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 S residue 2 VAL Chi-restraints excluded: chain S residue 63 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 80 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 255 ASN C 256 ASN B 142 HIS B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076700 restraints weight = 18137.715| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.81 r_work: 0.2945 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 1.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9160 Z= 0.241 Angle : 0.854 16.019 12434 Z= 0.422 Chirality : 0.045 0.247 1421 Planarity : 0.004 0.062 1571 Dihedral : 4.790 36.698 1251 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.83 % Allowed : 34.13 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1127 helix: 1.42 (0.27), residues: 389 sheet: -1.41 (0.32), residues: 264 loop : -1.94 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 127 HIS 0.004 0.001 HIS B 54 PHE 0.010 0.001 PHE S 108 TYR 0.010 0.001 TYR S 59 ARG 0.014 0.001 ARG C 208 ********************** 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 219 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.052 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: 0.8664 (mm) cc_final: 0.8069 (tt) REVERT: A 63 ILE cc_start: 0.7973 (mm) cc_final: 0.7755 (mm) REVERT: A 209 ARG cc_start: 0.6678 (mmt90) cc_final: 0.6260 (mmm-85) REVERT: A 221 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: A 231 LEU cc_start: 0.8673 (mm) cc_final: 0.8310 (tm) REVERT: A 302 ASP cc_start: 0.7925 (t0) cc_final: 0.7503 (t0) REVERT: C 23 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7206 (mp) REVERT: C 32 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.7221 (tmm-80) REVERT: C 242 ARG cc_start: 0.8421 (mpt180) cc_final: 0.8021 (mpt-90) REVERT: C 252 SER cc_start: 0.8854 (m) cc_final: 0.8517 (p) REVERT: C 287 TYR cc_start: 0.8053 (m-10) cc_final: 0.7730 (m-10) REVERT: C 302 TYR cc_start: 0.8929 (t80) cc_final: 0.8549 (t80) REVERT: C 304 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 306 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8754 (tp40) REVERT: C 309 ASP cc_start: 0.9241 (t0) cc_final: 0.8976 (m-30) REVERT: C 318 GLU cc_start: 0.7773 (pt0) cc_final: 0.7082 (pm20) REVERT: C 325 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6986 (t) REVERT: C 341 ASP cc_start: 0.7883 (t0) cc_final: 0.7668 (t0) REVERT: B 19 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8451 (ttp80) REVERT: B 75 GLN cc_start: 0.8897 (mm110) cc_final: 0.8352 (mp10) REVERT: B 127 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8566 (mtmm) REVERT: B 217 MET cc_start: 0.8113 (ptt) cc_final: 0.7718 (pmt) REVERT: B 280 LYS cc_start: 0.8948 (tttp) cc_final: 0.8701 (ttmm) REVERT: B 292 PHE cc_start: 0.8773 (m-10) cc_final: 0.8283 (m-10) REVERT: B 332 TRP cc_start: 0.8516 (m-10) cc_final: 0.7702 (m-10) REVERT: G 22 GLU cc_start: 0.7479 (tt0) cc_final: 0.7259 (tm-30) REVERT: G 27 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7716 (mtt-85) REVERT: G 46 LYS cc_start: 0.9574 (ptmm) cc_final: 0.9323 (pptt) REVERT: G 48 ASP cc_start: 0.8641 (t0) cc_final: 0.8131 (t0) REVERT: S 1 ASP cc_start: 0.7755 (t70) cc_final: 0.7510 (t70) REVERT: S 82 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8245 (mm-40) REVERT: S 90 ASP cc_start: 0.8392 (t0) cc_final: 0.8174 (m-30) REVERT: S 140 MET cc_start: 0.8432 (mmm) cc_final: 0.8083 (tpt) REVERT: S 183 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8730 (mt0) REVERT: S 208 SER cc_start: 0.8885 (p) cc_final: 0.8630 (t) REVERT: S 220 GLU cc_start: 0.9110 (pp20) cc_final: 0.8726 (pp20) REVERT: S 223 ASP cc_start: 0.8651 (m-30) cc_final: 0.8081 (m-30) REVERT: S 246 GLU cc_start: 0.8708 (tp30) cc_final: 0.7514 (pm20) outliers start: 37 outliers final: 28 residues processed: 212 average time/residue: 1.0010 time to fit residues: 228.6860 Evaluate side-chains 205 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 LEU 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 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE 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 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR 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 S residue 2 VAL Chi-restraints excluded: chain S residue 63 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 46 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 chunk 16 optimal weight: 0.0970 chunk 75 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079591 restraints weight = 18289.149| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.91 r_work: 0.2986 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 1.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9160 Z= 0.216 Angle : 0.853 15.416 12434 Z= 0.420 Chirality : 0.044 0.252 1421 Planarity : 0.004 0.041 1571 Dihedral : 4.527 24.246 1249 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.41 % Allowed : 34.95 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1127 helix: 1.44 (0.27), residues: 390 sheet: -1.35 (0.33), residues: 256 loop : -1.88 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 19 HIS 0.004 0.001 HIS B 54 PHE 0.010 0.001 PHE S 108 TYR 0.030 0.001 TYR C 296 ARG 0.011 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7172.85 seconds wall clock time: 125 minutes 5.85 seconds (7505.85 seconds total)