Starting phenix.real_space_refine on Thu Feb 13 13:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k26_61991/02_2025/9k26_61991_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k26_61991/02_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_61991/02_2025/9k26_61991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k26_61991/02_2025/9k26_61991.map" model { file = "/net/cci-nas-00/data/ceres_data/9k26_61991/02_2025/9k26_61991_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k26_61991/02_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-5592/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: 5.66, per 1000 atoms: 0.63 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 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: 0.99 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: 2.55 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2375 1.33 - 1.45: 1723 1.45 - 1.57: 4984 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 9160 Sorted by residual: bond pdb=" N ILE B 338 " pdb=" CA ILE B 338 " ideal model delta sigma weight residual 1.460 1.492 -0.031 1.10e-02 8.26e+03 8.15e+00 bond pdb=" N ILE S 189 " pdb=" CA ILE S 189 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.17e-02 7.31e+03 7.59e+00 bond pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" CA GLU A 213 " pdb=" C GLU A 213 " ideal model delta sigma weight residual 1.530 1.500 0.030 1.14e-02 7.69e+03 6.97e+00 bond pdb=" N SER S 146 " pdb=" CA SER S 146 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.25e-02 6.40e+03 6.35e+00 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 12154 2.20 - 4.40: 250 4.40 - 6.60: 23 6.60 - 8.80: 5 8.80 - 11.00: 2 Bond angle restraints: 12434 Sorted by residual: angle pdb=" N PHE A 214 " pdb=" CA PHE A 214 " pdb=" C PHE A 214 " ideal model delta sigma weight residual 110.30 99.30 11.00 1.50e+00 4.44e-01 5.37e+01 angle pdb=" C PHE A 214 " pdb=" CA PHE A 214 " pdb=" CB PHE A 214 " ideal model delta sigma weight residual 110.06 118.00 -7.94 1.39e+00 5.18e-01 3.26e+01 angle pdb=" N VAL S 149 " pdb=" CA VAL S 149 " pdb=" C VAL S 149 " ideal model delta sigma weight residual 108.45 115.20 -6.75 1.48e+00 4.57e-01 2.08e+01 angle pdb=" N GLN A 218 " pdb=" CA GLN A 218 " pdb=" C GLN A 218 " ideal model delta sigma weight residual 111.52 106.42 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" N CYS A 329 " pdb=" CA CYS A 329 " pdb=" C CYS A 329 " ideal model delta sigma weight residual 113.41 117.70 -4.29 1.22e+00 6.72e-01 1.24e+01 ... (remaining 12429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 5034 21.29 - 42.58: 339 42.58 - 63.86: 29 63.86 - 85.15: 9 85.15 - 106.44: 1 Dihedral angle restraints: 5412 sinusoidal: 2088 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ALA S 143 " pdb=" C ALA S 143 " pdb=" N THR S 144 " pdb=" CA THR S 144 " ideal model delta harmonic sigma weight residual 180.00 73.56 106.44 0 5.00e+00 4.00e-02 4.53e+02 dihedral pdb=" CA GLN S 142 " pdb=" C GLN S 142 " pdb=" N ALA S 143 " pdb=" CA ALA S 143 " ideal model delta harmonic sigma weight residual -180.00 -117.91 -62.09 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA THR S 144 " pdb=" C THR S 144 " pdb=" N SER S 145 " pdb=" CA SER S 145 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1081 0.049 - 0.097: 260 0.097 - 0.146: 64 0.146 - 0.195: 13 0.195 - 0.244: 3 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA ALA A 328 " pdb=" N ALA A 328 " pdb=" C ALA A 328 " pdb=" CB ALA A 328 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE S 58 " pdb=" CA ILE S 58 " pdb=" CG1 ILE S 58 " pdb=" CG2 ILE S 58 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.61e-01 ... (remaining 1418 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER S 146 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C SER S 146 " 0.039 2.00e-02 2.50e+03 pdb=" O SER S 146 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL S 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.015 2.00e-02 2.50e+03 1.18e-02 3.49e+00 pdb=" CG TRP B 332 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU S 166 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LEU S 166 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU S 166 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS S 167 " 0.009 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 84 2.58 - 3.16: 7544 3.16 - 3.74: 13941 3.74 - 4.32: 18261 4.32 - 4.90: 31444 Nonbonded interactions: 71274 Sorted by model distance: nonbonded pdb=" NE2 HIS A 321 " pdb=" O PHE F 31 " model vdw 1.994 3.120 nonbonded pdb=" OE1 GLN A 141 " pdb=" N NH2 F 33 " model vdw 2.053 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.181 3.040 nonbonded pdb=" OE2 GLU C 318 " pdb=" OH TYR C 320 " model vdw 2.202 3.040 nonbonded pdb=" O LEU A 229 " pdb=" OG1 THR A 233 " model vdw 2.206 3.040 ... (remaining 71269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- 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 : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8145 (mm) cc_final: 0.7503 (tt) REVERT: A 113 CYS cc_start: 0.8362 (m) cc_final: 0.7797 (m) REVERT: A 192 LEU cc_start: 0.8178 (mt) cc_final: 0.7951 (mm) REVERT: A 209 ARG cc_start: 0.6503 (mmt90) cc_final: 0.6273 (mmm-85) REVERT: A 320 CYS cc_start: 0.7764 (m) cc_final: 0.7506 (m) REVERT: A 322 TRP cc_start: 0.8997 (t60) cc_final: 0.8651 (t60) REVERT: C 197 LYS cc_start: 0.6058 (mtpt) cc_final: 0.5719 (ttpp) REVERT: C 285 ILE cc_start: 0.6911 (mt) cc_final: 0.6657 (mp) REVERT: B 10 GLU cc_start: 0.8392 (pp20) cc_final: 0.8151 (pp20) REVERT: B 292 PHE cc_start: 0.8557 (m-10) cc_final: 0.8349 (m-80) outliers start: 7 outliers final: 6 residues processed: 338 average time/residue: 0.9663 time to fit residues: 353.5582 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 : 0.964 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092300 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 : 1.005 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: 0.8216 (mm) cc_final: 0.7658 (tt) REVERT: A 209 ARG cc_start: 0.6691 (mmt90) cc_final: 0.6360 (mmm-85) REVERT: A 219 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8910 (tm-30) REVERT: A 221 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 231 LEU cc_start: 0.8800 (mm) cc_final: 0.8406 (tm) REVERT: A 270 ARG cc_start: 0.8193 (mmp-170) cc_final: 0.7531 (tpt170) REVERT: A 320 CYS cc_start: 0.7482 (m) cc_final: 0.7166 (m) REVERT: A 325 MET cc_start: 0.8841 (tpp) cc_final: 0.8640 (tpp) REVERT: F 19 TRP cc_start: 0.8696 (p-90) cc_final: 0.8433 (p-90) REVERT: F 30 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7484 (mtt180) REVERT: C 222 ILE cc_start: 0.8015 (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: 0.8020 (pp20) REVERT: B 12 GLU cc_start: 0.8922 (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: 0.7926 (ptt) cc_final: 0.7565 (pmt) REVERT: B 226 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8777 (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: 0.8667 (mmmm) cc_final: 0.8459 (mmmm) REVERT: G 9 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7825 (tt) REVERT: G 22 GLU cc_start: 0.7499 (tt0) cc_final: 0.7089 (tt0) REVERT: G 48 ASP cc_start: 0.8328 (t70) cc_final: 0.8025 (t0) REVERT: S 38 ARG cc_start: 0.7468 (ptt180) cc_final: 0.6847 (ptp90) REVERT: S 67 ARG cc_start: 0.5610 (ttp80) cc_final: 0.5231 (ttp-110) REVERT: S 100 ILE cc_start: 0.8492 (tt) cc_final: 0.8199 (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: 1.0548 time to fit residues: 336.7323 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 : 1.047 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.119794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089862 restraints weight = 18138.969| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.07 r_work: 0.3183 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.7438 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= 0.206 Angle : 0.721 11.682 12434 Z= 0.364 Chirality : 0.043 0.173 1421 Planarity : 0.004 0.038 1571 Dihedral : 6.747 151.381 1257 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.38 % Allowed : 24.51 % Favored : 70.11 % 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: -1.17 (0.25), residues: 1127 helix: 1.26 (0.26), residues: 389 sheet: -1.42 (0.32), residues: 257 loop : -2.14 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 332 HIS 0.005 0.001 HIS A 339 PHE 0.018 0.001 PHE F 31 TYR 0.022 0.002 TYR C 296 ARG 0.007 0.001 ARG S 160 *********************** 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 273 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 221 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8349 (mm) cc_final: 0.7634 (tt) REVERT: A 129 PHE cc_start: 0.7937 (m-80) cc_final: 0.7694 (m-80) REVERT: A 209 ARG cc_start: 0.6614 (mmt90) cc_final: 0.6253 (mmm-85) REVERT: A 214 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6449 (m-10) REVERT: A 221 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: A 231 LEU cc_start: 0.8755 (mm) cc_final: 0.8391 (tm) REVERT: A 270 ARG cc_start: 0.8147 (mmp-170) cc_final: 0.7434 (tpt170) REVERT: A 303 LEU cc_start: 0.8125 (pt) cc_final: 0.7748 (tm) REVERT: A 320 CYS cc_start: 0.7301 (m) cc_final: 0.7047 (m) REVERT: F 16 ASN cc_start: 0.8806 (t0) cc_final: 0.8505 (t0) REVERT: C 23 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7146 (mp) REVERT: C 32 ARG cc_start: 0.6720 (tmm-80) cc_final: 0.6464 (tmm-80) REVERT: C 296 TYR cc_start: 0.7200 (t80) cc_final: 0.6678 (t80) REVERT: C 306 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8724 (tp40) REVERT: C 309 ASP cc_start: 0.9226 (t0) cc_final: 0.8692 (m-30) REVERT: C 313 ARG cc_start: 0.7552 (mpp80) cc_final: 0.7347 (mpp80) REVERT: C 344 ILE cc_start: 0.7381 (tt) cc_final: 0.7121 (pp) REVERT: B 19 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8376 (ttp80) REVERT: B 42 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8064 (tmt170) REVERT: B 127 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8362 (mtmm) REVERT: B 163 ASP cc_start: 0.8389 (t0) cc_final: 0.8047 (t0) REVERT: B 217 MET cc_start: 0.7837 (ptt) cc_final: 0.7446 (pmt) REVERT: B 226 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8764 (mt-10) REVERT: B 228 ASP cc_start: 0.6606 (m-30) cc_final: 0.5694 (m-30) REVERT: B 280 LYS cc_start: 0.8999 (tttp) cc_final: 0.8668 (ttmm) REVERT: B 292 PHE cc_start: 0.8986 (m-10) cc_final: 0.8534 (m-80) REVERT: G 9 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7793 (tt) REVERT: G 22 GLU cc_start: 0.7360 (tt0) cc_final: 0.7031 (tt0) REVERT: G 47 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8849 (tm-30) REVERT: G 48 ASP cc_start: 0.8346 (t70) cc_final: 0.7890 (t0) REVERT: S 87 ARG cc_start: 0.7824 (mtm180) cc_final: 0.7382 (mtm110) REVERT: S 105 SER cc_start: 0.9173 (t) cc_final: 0.8923 (p) outliers start: 52 outliers final: 24 residues processed: 253 average time/residue: 1.0592 time to fit residues: 287.7985 Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 215 TRP Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain C residue 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 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 331 SER Chi-restraints excluded: chain G residue 9 ILE 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 144 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 180 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 213 HIS B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.110510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079696 restraints weight = 18110.724| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.99 r_work: 0.2993 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9160 Z= 0.281 Angle : 0.719 10.897 12434 Z= 0.369 Chirality : 0.044 0.173 1421 Planarity : 0.004 0.034 1571 Dihedral : 5.186 37.401 1257 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 6.10 % Allowed : 25.23 % Favored : 68.67 % 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: -1.13 (0.25), residues: 1127 helix: 1.43 (0.27), residues: 388 sheet: -1.55 (0.31), residues: 266 loop : -2.14 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 19 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.002 PHE S 108 TYR 0.019 0.002 TYR S 59 ARG 0.008 0.001 ARG S 160 *********************** 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 270 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 1.017 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: 0.8388 (mm) cc_final: 0.7703 (tt) REVERT: A 129 PHE cc_start: 0.8175 (m-80) cc_final: 0.7830 (m-80) REVERT: A 209 ARG cc_start: 0.6569 (mmt90) cc_final: 0.6150 (mmm-85) REVERT: A 214 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: A 221 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: A 231 LEU cc_start: 0.8796 (mm) cc_final: 0.8362 (tm) REVERT: A 270 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7322 (tpt170) REVERT: A 302 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7580 (t0) REVERT: A 317 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7762 (tp40) REVERT: A 325 MET cc_start: 0.8679 (tpp) cc_final: 0.7956 (mpp) REVERT: C 23 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7318 (mp) REVERT: C 32 ARG cc_start: 0.7540 (tmm-80) cc_final: 0.7019 (tmm-80) REVERT: C 276 GLU cc_start: 0.9020 (tp30) cc_final: 0.8619 (pt0) REVERT: C 290 TYR cc_start: 0.7054 (t80) cc_final: 0.6454 (t80) REVERT: C 296 TYR cc_start: 0.7562 (t80) cc_final: 0.7025 (t80) REVERT: C 306 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8743 (tp40) REVERT: C 309 ASP cc_start: 0.9356 (t0) cc_final: 0.8916 (m-30) REVERT: C 318 GLU cc_start: 0.7310 (pt0) cc_final: 0.6706 (pm20) REVERT: B 19 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8336 (ttp80) REVERT: B 127 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8470 (mtmm) REVERT: B 217 MET cc_start: 0.7744 (ptt) cc_final: 0.7377 (pmt) REVERT: B 226 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8647 (mt-10) REVERT: B 280 LYS cc_start: 0.9049 (tttp) cc_final: 0.8787 (ttmm) REVERT: B 292 PHE cc_start: 0.8951 (m-10) cc_final: 0.8425 (m-10) REVERT: B 332 TRP cc_start: 0.8434 (m-10) cc_final: 0.8156 (m-10) REVERT: G 9 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (tt) REVERT: G 21 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: G 22 GLU cc_start: 0.7235 (tt0) cc_final: 0.6797 (tm-30) REVERT: G 28 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.6526 (pp) REVERT: G 36 ASP cc_start: 0.8569 (t0) cc_final: 0.8280 (t0) REVERT: G 47 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8476 (tm-30) REVERT: S 82 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7933 (mm-40) REVERT: S 93 MET cc_start: 0.7127 (tmm) cc_final: 0.6441 (tpt) REVERT: S 105 SER cc_start: 0.9028 (t) cc_final: 0.8798 (p) REVERT: S 220 GLU cc_start: 0.8552 (pp20) cc_final: 0.8343 (pp20) REVERT: S 223 ASP cc_start: 0.8138 (m-30) cc_final: 0.7698 (m-30) REVERT: S 246 GLU cc_start: 0.8621 (tp30) cc_final: 0.6688 (pm20) outliers start: 59 outliers final: 31 residues processed: 252 average time/residue: 1.1234 time to fit residues: 302.8703 Evaluate side-chains 225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 232 VAL 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 23 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 263 SER 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 210 LEU Chi-restraints excluded: chain B residue 255 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 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 20 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 139 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: 2.9990 chunk 43 optimal weight: 0.0040 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 256 ASN B 142 HIS S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081450 restraints weight = 17995.286| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.93 r_work: 0.3016 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.9064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9160 Z= 0.209 Angle : 0.730 14.839 12434 Z= 0.365 Chirality : 0.044 0.203 1421 Planarity : 0.004 0.053 1571 Dihedral : 4.949 37.073 1254 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 6.31 % Allowed : 27.40 % Favored : 66.29 % 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: 1.49 (0.27), residues: 387 sheet: -1.36 (0.32), residues: 260 loop : -2.10 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 227 HIS 0.004 0.001 HIS A 339 PHE 0.013 0.001 PHE S 108 TYR 0.022 0.001 TYR A 311 ARG 0.008 0.001 ARG S 160 *********************** 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 271 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 1.028 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: 0.8420 (mm) cc_final: 0.7715 (tt) REVERT: A 209 ARG cc_start: 0.6556 (mmt90) cc_final: 0.6151 (mmm-85) REVERT: A 218 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7876 (mm-40) REVERT: A 221 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: A 231 LEU cc_start: 0.8745 (mm) cc_final: 0.8386 (tm) REVERT: A 268 TRP cc_start: 0.8611 (m100) cc_final: 0.7416 (m-90) REVERT: A 270 ARG cc_start: 0.8142 (mmp-170) cc_final: 0.7349 (tpt170) REVERT: A 302 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7713 (t0) REVERT: A 317 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7570 (tp40) REVERT: A 325 MET cc_start: 0.8640 (tpp) cc_final: 0.7944 (mpp) REVERT: F 16 ASN cc_start: 0.8800 (t0) cc_final: 0.8385 (t0) REVERT: F 19 TRP cc_start: 0.8810 (t60) cc_final: 0.8594 (p-90) REVERT: F 31 PHE cc_start: 0.8193 (m-10) cc_final: 0.7895 (m-80) REVERT: C 23 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7303 (mp) REVERT: C 32 ARG cc_start: 0.7291 (tmm-80) cc_final: 0.6916 (tmm-80) REVERT: C 276 GLU cc_start: 0.9029 (tp30) cc_final: 0.8624 (pt0) REVERT: C 287 TYR cc_start: 0.7249 (m-10) cc_final: 0.7041 (m-10) REVERT: C 290 TYR cc_start: 0.7145 (t80) cc_final: 0.6697 (t80) REVERT: C 306 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8780 (tp40) REVERT: C 309 ASP cc_start: 0.9367 (t0) cc_final: 0.9001 (m-30) REVERT: C 318 GLU cc_start: 0.7376 (pt0) cc_final: 0.6798 (pm20) REVERT: B 19 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8334 (ttp80) REVERT: B 42 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7838 (tmt170) REVERT: B 217 MET cc_start: 0.7909 (ptt) cc_final: 0.7505 (pmt) REVERT: B 260 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7865 (tp30) REVERT: B 280 LYS cc_start: 0.9037 (tttp) cc_final: 0.8733 (ttmm) REVERT: B 292 PHE cc_start: 0.8917 (m-10) cc_final: 0.8431 (m-10) REVERT: B 332 TRP cc_start: 0.8360 (m-10) cc_final: 0.8050 (m-10) REVERT: G 9 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7834 (tt) REVERT: G 22 GLU cc_start: 0.7258 (tt0) cc_final: 0.6911 (tm-30) REVERT: G 36 ASP cc_start: 0.8625 (t0) cc_final: 0.8410 (t0) REVERT: G 48 ASP cc_start: 0.8259 (t0) cc_final: 0.8012 (t0) REVERT: S 82 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8190 (mm-40) REVERT: S 93 MET cc_start: 0.7023 (tmm) cc_final: 0.6412 (tpt) REVERT: S 141 THR cc_start: 0.8935 (t) cc_final: 0.8451 (p) REVERT: S 223 ASP cc_start: 0.8242 (m-30) cc_final: 0.7734 (m-30) REVERT: S 246 GLU cc_start: 0.8709 (tp30) cc_final: 0.6922 (pm20) outliers start: 61 outliers final: 28 residues processed: 251 average time/residue: 1.1656 time to fit residues: 312.4377 Evaluate side-chains 225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP 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 302 ASP Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 354 PHE 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 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 G residue 42 GLU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET 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: 20.0000 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072578 restraints weight = 18197.517| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.80 r_work: 0.2854 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 1.0118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9160 Z= 0.411 Angle : 0.831 13.595 12434 Z= 0.423 Chirality : 0.048 0.196 1421 Planarity : 0.005 0.047 1571 Dihedral : 5.479 37.822 1254 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.34 % Allowed : 28.34 % Favored : 64.32 % 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: -1.13 (0.25), residues: 1127 helix: 1.43 (0.27), residues: 382 sheet: -1.59 (0.31), residues: 265 loop : -2.06 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 111 HIS 0.004 0.001 HIS A 339 PHE 0.021 0.002 PHE C 199 TYR 0.020 0.002 TYR S 50 ARG 0.010 0.001 ARG S 160 *********************** 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 264 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 1.111 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: A 62 LEU cc_start: 0.8575 (mm) cc_final: 0.7947 (tt) REVERT: A 129 PHE cc_start: 0.8309 (m-80) cc_final: 0.8079 (m-80) REVERT: A 209 ARG cc_start: 0.6645 (mmt90) cc_final: 0.6190 (mmm-85) REVERT: A 218 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8033 (mm-40) REVERT: A 221 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: A 231 LEU cc_start: 0.8846 (mm) cc_final: 0.8364 (tm) REVERT: A 261 VAL cc_start: 0.8755 (p) cc_final: 0.8532 (m) REVERT: A 270 ARG cc_start: 0.8118 (mmp-170) cc_final: 0.7239 (tpt170) REVERT: A 302 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7711 (t0) REVERT: F 16 ASN cc_start: 0.8808 (t0) cc_final: 0.8488 (t0) REVERT: F 31 PHE cc_start: 0.8367 (m-10) cc_final: 0.8097 (m-80) REVERT: C 23 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7237 (mp) REVERT: C 32 ARG cc_start: 0.8214 (tmm-80) cc_final: 0.7940 (tmm-80) REVERT: C 252 SER cc_start: 0.9016 (m) cc_final: 0.8644 (p) REVERT: C 287 TYR cc_start: 0.7954 (m-10) cc_final: 0.7695 (m-10) REVERT: C 306 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8710 (tp40) REVERT: C 309 ASP cc_start: 0.9372 (t0) cc_final: 0.9029 (m-30) REVERT: C 313 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7752 (mpp80) REVERT: C 318 GLU cc_start: 0.7722 (pt0) cc_final: 0.7027 (pm20) REVERT: C 341 ASP cc_start: 0.7853 (t0) cc_final: 0.7635 (t0) REVERT: B 19 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8453 (tmm-80) REVERT: B 42 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.8024 (ttt-90) REVERT: B 59 TYR cc_start: 0.8510 (m-80) cc_final: 0.8163 (m-80) REVERT: B 130 GLU cc_start: 0.8998 (mp0) cc_final: 0.8797 (mp0) REVERT: B 217 MET cc_start: 0.7695 (ptt) cc_final: 0.7243 (pmt) REVERT: B 255 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7718 (mp) REVERT: B 280 LYS cc_start: 0.8961 (tttp) cc_final: 0.8638 (ttmm) REVERT: B 292 PHE cc_start: 0.8928 (m-10) cc_final: 0.8404 (m-10) REVERT: G 9 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8140 (tt) REVERT: G 21 MET cc_start: 0.8928 (ttp) cc_final: 0.8542 (ttt) REVERT: G 22 GLU cc_start: 0.7522 (tt0) cc_final: 0.7247 (tm-30) REVERT: G 47 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8720 (tm-30) REVERT: G 48 ASP cc_start: 0.8358 (t0) cc_final: 0.7939 (t0) REVERT: S 82 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8232 (mm-40) REVERT: S 93 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7057 (tpt) REVERT: S 220 GLU cc_start: 0.8991 (pp20) cc_final: 0.8536 (pp20) REVERT: S 223 ASP cc_start: 0.8845 (m-30) cc_final: 0.7985 (m-30) REVERT: S 246 GLU cc_start: 0.8762 (tp30) cc_final: 0.7123 (pm20) REVERT: S 247 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7105 (tt) outliers start: 71 outliers final: 34 residues processed: 244 average time/residue: 1.1389 time to fit residues: 297.2136 Evaluate side-chains 216 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 289 VAL Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain F residue 19 TRP 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 354 PHE Chi-restraints excluded: chain B residue 25 CYS 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 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 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 20 LEU 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 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 7.9990 chunk 101 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- 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 256 ASN B 110 ASN B 142 HIS B 220 GLN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076792 restraints weight = 18070.338| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.81 r_work: 0.2947 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 1.0254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9160 Z= 0.214 Angle : 0.779 12.563 12434 Z= 0.388 Chirality : 0.044 0.240 1421 Planarity : 0.004 0.040 1571 Dihedral : 4.895 37.053 1251 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.76 % Allowed : 32.16 % Favored : 63.08 % 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: 1.45 (0.27), residues: 388 sheet: -1.46 (0.31), residues: 269 loop : -1.93 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 127 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE C 199 TYR 0.025 0.001 TYR C 296 ARG 0.011 0.001 ARG S 160 *********************** 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 242 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.209 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: A 62 LEU cc_start: 0.8621 (mm) cc_final: 0.8004 (tt) REVERT: A 129 PHE cc_start: 0.8196 (m-80) cc_final: 0.7918 (m-80) REVERT: A 209 ARG cc_start: 0.6616 (mmt90) cc_final: 0.6225 (mmm-85) REVERT: A 218 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7977 (mm-40) REVERT: A 221 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: A 231 LEU cc_start: 0.8772 (mm) cc_final: 0.8396 (tm) REVERT: A 261 VAL cc_start: 0.8737 (p) cc_final: 0.8529 (m) REVERT: A 302 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7648 (t0) REVERT: F 16 ASN cc_start: 0.8790 (t0) cc_final: 0.8551 (t0) REVERT: F 31 PHE cc_start: 0.8094 (m-10) cc_final: 0.7851 (m-80) REVERT: C 23 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7243 (mp) REVERT: C 32 ARG cc_start: 0.7496 (tmm-80) cc_final: 0.7222 (tmm-80) REVERT: C 247 MET cc_start: 0.9072 (ttm) cc_final: 0.8767 (mtp) REVERT: C 252 SER cc_start: 0.8997 (m) cc_final: 0.8591 (p) REVERT: C 287 TYR cc_start: 0.7861 (m-10) cc_final: 0.7601 (m-10) REVERT: C 302 TYR cc_start: 0.8879 (t80) cc_final: 0.8596 (t80) REVERT: C 306 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8751 (tp40) REVERT: C 309 ASP cc_start: 0.9327 (t0) cc_final: 0.8987 (m-30) REVERT: C 318 GLU cc_start: 0.7659 (pt0) cc_final: 0.7016 (pm20) REVERT: C 341 ASP cc_start: 0.7836 (t0) cc_final: 0.7599 (t0) REVERT: B 19 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8460 (tmm-80) REVERT: B 42 ARG cc_start: 0.8209 (ttt-90) cc_final: 0.7942 (tmt170) REVERT: B 59 TYR cc_start: 0.8311 (m-80) cc_final: 0.8043 (m-80) REVERT: B 127 LYS cc_start: 0.9021 (mtmp) cc_final: 0.8733 (mtmp) REVERT: B 217 MET cc_start: 0.7943 (ptt) cc_final: 0.7490 (pmt) REVERT: B 280 LYS cc_start: 0.8930 (tttp) cc_final: 0.8697 (tttm) REVERT: B 292 PHE cc_start: 0.8947 (m-10) cc_final: 0.8444 (m-10) REVERT: B 332 TRP cc_start: 0.8584 (m-10) cc_final: 0.7795 (m-10) REVERT: G 9 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8245 (tt) REVERT: G 22 GLU cc_start: 0.7445 (tt0) cc_final: 0.7144 (tm-30) REVERT: G 46 LYS cc_start: 0.9447 (ptpp) cc_final: 0.9245 (pptt) REVERT: G 48 ASP cc_start: 0.8532 (t0) cc_final: 0.8250 (t0) REVERT: S 39 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: S 82 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8210 (mm-40) REVERT: S 93 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.7013 (tmt) REVERT: S 160 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8018 (mtp85) REVERT: S 192 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (tmm) REVERT: S 220 GLU cc_start: 0.8910 (pp20) cc_final: 0.8581 (pp20) REVERT: S 223 ASP cc_start: 0.8651 (m-30) cc_final: 0.8042 (m-30) REVERT: S 246 GLU cc_start: 0.8765 (tp30) cc_final: 0.7378 (pm20) REVERT: S 247 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7192 (tt) outliers start: 46 outliers final: 29 residues processed: 231 average time/residue: 1.1271 time to fit residues: 278.7486 Evaluate side-chains 217 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 315 LEU 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 148 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 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 20 LEU Chi-restraints excluded: chain S residue 39 GLN 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 149 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 220 GLN B 259 GLN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077223 restraints weight = 18457.482| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.93 r_work: 0.2942 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 1.0377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9160 Z= 0.227 Angle : 0.801 12.682 12434 Z= 0.398 Chirality : 0.044 0.232 1421 Planarity : 0.004 0.036 1571 Dihedral : 4.735 36.576 1251 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 5.17 % Allowed : 32.26 % Favored : 62.56 % 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: -0.83 (0.25), residues: 1127 helix: 1.55 (0.27), residues: 390 sheet: -1.37 (0.31), residues: 276 loop : -1.88 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 19 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE C 199 TYR 0.011 0.001 TYR S 190 ARG 0.008 0.001 ARG S 160 *********************** 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 236 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.974 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: A 62 LEU cc_start: 0.8683 (mm) cc_final: 0.8085 (tt) REVERT: A 129 PHE cc_start: 0.8221 (m-80) cc_final: 0.7981 (m-80) REVERT: A 209 ARG cc_start: 0.6608 (mmt90) cc_final: 0.6204 (mmm-85) REVERT: A 218 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7814 (mm-40) REVERT: A 221 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: A 231 LEU cc_start: 0.8738 (mm) cc_final: 0.8368 (tm) REVERT: A 302 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7877 (t0) REVERT: F 16 ASN cc_start: 0.8895 (t0) cc_final: 0.8596 (t0) REVERT: C 23 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7231 (mp) REVERT: C 32 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7212 (tmm-80) REVERT: C 247 MET cc_start: 0.9061 (ttm) cc_final: 0.8744 (mtp) REVERT: C 252 SER cc_start: 0.8868 (m) cc_final: 0.8537 (p) REVERT: C 287 TYR cc_start: 0.7800 (m-10) cc_final: 0.7556 (m-10) REVERT: C 302 TYR cc_start: 0.8876 (t80) cc_final: 0.8610 (t80) REVERT: C 306 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8784 (tp40) REVERT: C 309 ASP cc_start: 0.9298 (t0) cc_final: 0.8984 (m-30) REVERT: C 318 GLU cc_start: 0.7684 (pt0) cc_final: 0.6984 (pm20) REVERT: C 325 CYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7183 (t) REVERT: C 341 ASP cc_start: 0.7868 (t0) cc_final: 0.7630 (t0) REVERT: B 19 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8502 (ttp80) REVERT: B 42 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7906 (tmt170) REVERT: B 59 TYR cc_start: 0.8284 (m-80) cc_final: 0.8058 (m-80) REVERT: B 217 MET cc_start: 0.8041 (ptt) cc_final: 0.7632 (pmt) REVERT: B 280 LYS cc_start: 0.8911 (tttp) cc_final: 0.8501 (ttmm) REVERT: B 292 PHE cc_start: 0.8932 (m-10) cc_final: 0.8447 (m-10) REVERT: G 9 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8203 (tt) REVERT: G 22 GLU cc_start: 0.7443 (tt0) cc_final: 0.7210 (tm-30) REVERT: G 48 ASP cc_start: 0.8537 (t0) cc_final: 0.8058 (t0) REVERT: S 82 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8243 (mm-40) REVERT: S 93 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6963 (tmt) REVERT: S 192 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8127 (tmm) REVERT: S 220 GLU cc_start: 0.8995 (pp20) cc_final: 0.8744 (pp20) REVERT: S 223 ASP cc_start: 0.8606 (m-30) cc_final: 0.8043 (m-30) REVERT: S 246 GLU cc_start: 0.8745 (tp30) cc_final: 0.7445 (pm20) outliers start: 50 outliers final: 33 residues processed: 224 average time/residue: 1.0688 time to fit residues: 256.9088 Evaluate side-chains 217 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 158 ASP 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 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 315 LEU 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 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 255 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 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 20 LEU 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 149 VAL Chi-restraints excluded: chain S residue 192 MET 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: 4.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 74 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078140 restraints weight = 18239.472| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.91 r_work: 0.2958 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 1.0472 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 : 0.821 14.531 12434 Z= 0.405 Chirality : 0.044 0.257 1421 Planarity : 0.004 0.034 1571 Dihedral : 4.706 36.314 1251 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.96 % Allowed : 32.68 % Favored : 62.36 % 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: -0.82 (0.25), residues: 1127 helix: 1.58 (0.27), residues: 389 sheet: -1.35 (0.31), residues: 272 loop : -1.88 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 127 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE A 138 TYR 0.028 0.001 TYR C 296 ARG 0.006 0.001 ARG F 23 *********************** 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 239 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 1.040 Fit side-chains 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: A 62 LEU cc_start: 0.8688 (mm) cc_final: 0.8116 (tt) REVERT: A 209 ARG cc_start: 0.6567 (mmt90) cc_final: 0.6186 (mmm-85) REVERT: A 218 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7876 (mm-40) REVERT: A 221 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: A 231 LEU cc_start: 0.8663 (mm) cc_final: 0.8309 (tm) REVERT: A 302 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7742 (t0) REVERT: F 19 TRP cc_start: 0.8912 (t60) cc_final: 0.8639 (p-90) REVERT: C 23 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7200 (mp) REVERT: C 32 ARG cc_start: 0.7394 (tmm-80) cc_final: 0.7125 (tmm-80) REVERT: C 247 MET cc_start: 0.9046 (ttm) cc_final: 0.8783 (mtp) REVERT: C 252 SER cc_start: 0.8851 (m) cc_final: 0.8514 (p) REVERT: C 287 TYR cc_start: 0.7805 (m-10) cc_final: 0.7523 (m-10) REVERT: C 302 TYR cc_start: 0.8875 (t80) cc_final: 0.8576 (t80) REVERT: C 304 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 306 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8759 (tp40) REVERT: C 309 ASP cc_start: 0.9267 (t0) cc_final: 0.8973 (m-30) REVERT: C 318 GLU cc_start: 0.7718 (pt0) cc_final: 0.7004 (pm20) REVERT: C 325 CYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7097 (t) REVERT: C 341 ASP cc_start: 0.7840 (t0) cc_final: 0.7609 (t0) REVERT: B 58 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7703 (pp) REVERT: B 217 MET cc_start: 0.8089 (ptt) cc_final: 0.7682 (pmt) REVERT: B 260 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7951 (tp30) REVERT: B 280 LYS cc_start: 0.8908 (tttp) cc_final: 0.8481 (ttmm) REVERT: B 292 PHE cc_start: 0.8910 (m-10) cc_final: 0.8427 (m-10) REVERT: B 332 TRP cc_start: 0.8413 (m-10) cc_final: 0.7591 (m-10) REVERT: G 9 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8181 (tt) REVERT: G 22 GLU cc_start: 0.7423 (tt0) cc_final: 0.7214 (tm-30) REVERT: G 27 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: G 47 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8549 (tm-30) REVERT: G 48 ASP cc_start: 0.8474 (t0) cc_final: 0.7998 (t0) REVERT: S 39 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: S 82 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8244 (mm-40) REVERT: S 160 ARG cc_start: 0.8595 (mtm110) cc_final: 0.8039 (mtp-110) REVERT: S 174 LEU cc_start: 0.8393 (tp) cc_final: 0.8166 (tm) REVERT: S 192 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8152 (tmm) REVERT: S 208 SER cc_start: 0.8911 (p) cc_final: 0.8687 (m) REVERT: S 212 PHE cc_start: 0.8262 (m-10) cc_final: 0.7882 (m-10) REVERT: S 223 ASP cc_start: 0.8621 (m-30) cc_final: 0.8267 (m-30) REVERT: S 246 GLU cc_start: 0.8749 (tp30) cc_final: 0.7593 (pm20) outliers start: 48 outliers final: 34 residues processed: 228 average time/residue: 1.0545 time to fit residues: 258.3097 Evaluate side-chains 219 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP 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 192 LEU Chi-restraints excluded: chain A residue 198 THR 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 302 ASP Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain A residue 315 LEU 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 25 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 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 20 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 192 MET 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: 0.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076538 restraints weight = 18076.802| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.83 r_work: 0.2949 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 1.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9160 Z= 0.242 Angle : 0.855 15.057 12434 Z= 0.420 Chirality : 0.045 0.256 1421 Planarity : 0.004 0.034 1571 Dihedral : 4.697 36.384 1251 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.55 % Allowed : 33.92 % Favored : 61.53 % 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: -0.80 (0.25), residues: 1127 helix: 1.53 (0.27), residues: 391 sheet: -1.20 (0.31), residues: 275 loop : -1.92 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 127 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE S 108 TYR 0.020 0.001 TYR C 290 ARG 0.006 0.001 ARG F 23 ********************** 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 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.975 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 62 LEU cc_start: 0.8696 (mm) cc_final: 0.8120 (tt) REVERT: A 209 ARG cc_start: 0.6594 (mmt90) cc_final: 0.6275 (mmm-85) REVERT: A 218 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7728 (mm-40) REVERT: A 221 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: A 231 LEU cc_start: 0.8675 (mm) cc_final: 0.8318 (tm) REVERT: A 302 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7698 (t0) REVERT: F 19 TRP cc_start: 0.8934 (t60) cc_final: 0.8667 (p-90) REVERT: C 23 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7194 (mp) REVERT: C 32 ARG cc_start: 0.7444 (tmm-80) cc_final: 0.7175 (tmm-80) REVERT: C 247 MET cc_start: 0.9072 (ttm) cc_final: 0.8817 (mtp) REVERT: C 252 SER cc_start: 0.8890 (m) cc_final: 0.8562 (p) REVERT: C 287 TYR cc_start: 0.7825 (m-10) cc_final: 0.7511 (m-10) REVERT: C 302 TYR cc_start: 0.8887 (t80) cc_final: 0.8544 (t80) REVERT: C 304 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 306 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8740 (tp40) REVERT: C 309 ASP cc_start: 0.9246 (t0) cc_final: 0.8959 (m-30) REVERT: C 318 GLU cc_start: 0.7715 (pt0) cc_final: 0.7012 (pm20) REVERT: C 325 CYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7079 (t) REVERT: C 341 ASP cc_start: 0.7883 (t0) cc_final: 0.7666 (t0) REVERT: B 19 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8584 (ttp80) REVERT: B 59 TYR cc_start: 0.8249 (m-80) cc_final: 0.7811 (m-80) REVERT: B 217 MET cc_start: 0.8127 (ptt) cc_final: 0.7715 (pmt) REVERT: B 255 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7146 (mp) REVERT: B 280 LYS cc_start: 0.8921 (tttp) cc_final: 0.8476 (ttmm) REVERT: B 292 PHE cc_start: 0.8912 (m-10) cc_final: 0.8411 (m-10) REVERT: B 332 TRP cc_start: 0.8392 (m-10) cc_final: 0.7663 (m-10) REVERT: G 27 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7855 (mtt-85) REVERT: G 46 LYS cc_start: 0.9571 (ptmm) cc_final: 0.9322 (pptt) REVERT: G 48 ASP cc_start: 0.8569 (t0) cc_final: 0.8089 (t0) REVERT: S 39 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: S 82 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8255 (mm-40) REVERT: S 93 MET cc_start: 0.7841 (tmt) cc_final: 0.7631 (ttp) REVERT: S 174 LEU cc_start: 0.8440 (tp) cc_final: 0.8138 (tm) REVERT: S 192 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8215 (tmm) REVERT: S 208 SER cc_start: 0.8950 (p) cc_final: 0.8665 (t) REVERT: S 212 PHE cc_start: 0.8289 (m-10) cc_final: 0.7862 (m-10) REVERT: S 220 GLU cc_start: 0.9093 (pp20) cc_final: 0.8579 (pp20) REVERT: S 223 ASP cc_start: 0.8764 (m-30) cc_final: 0.8258 (m-30) REVERT: S 246 GLU cc_start: 0.8714 (tp30) cc_final: 0.7920 (pm20) outliers start: 44 outliers final: 31 residues processed: 218 average time/residue: 1.0547 time to fit residues: 247.4701 Evaluate side-chains 217 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP 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 192 LEU Chi-restraints excluded: chain A residue 198 THR 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 302 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 25 CYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 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 S residue 2 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 192 MET 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: 0.6980 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN B 142 HIS B 259 GLN S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076805 restraints weight = 18054.915| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.85 r_work: 0.2952 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 1.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9160 Z= 0.236 Angle : 0.845 14.528 12434 Z= 0.416 Chirality : 0.045 0.256 1421 Planarity : 0.004 0.035 1571 Dihedral : 4.524 23.335 1249 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.45 % Allowed : 34.44 % Favored : 61.12 % 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: -0.77 (0.26), residues: 1127 helix: 1.52 (0.27), residues: 392 sheet: -1.17 (0.31), residues: 275 loop : -1.89 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 127 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE C 199 TYR 0.029 0.002 TYR C 296 ARG 0.007 0.001 ARG C 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6928.48 seconds wall clock time: 123 minutes 20.15 seconds (7400.15 seconds total)