Starting phenix.real_space_refine on Thu Feb 13 11:13:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uun_20883/02_2025/6uun_20883.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uun_20883/02_2025/6uun_20883.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/6uun_20883/02_2025/6uun_20883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uun_20883/02_2025/6uun_20883.map" model { file = "/net/cci-nas-00/data/ceres_data/6uun_20883/02_2025/6uun_20883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uun_20883/02_2025/6uun_20883.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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5693 2.51 5 N 1580 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8980 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 627 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 260 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2565 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 232 Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8980 At special positions: 0 Unit cell: (84.66, 95.45, 160.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1643 8.00 N 1580 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 16 " - pdb=" SG CYS P 21 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 41.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.668A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.905A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.572A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.542A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 106 removed outlier: 3.508A pdb=" N TYR E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.638A pdb=" N ILE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 155 Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 156 through 167 removed outlier: 3.610A pdb=" N LEU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.593A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'P' and resid 20 through 22 No H-bonds generated for 'chain 'P' and resid 20 through 22' Processing helix chain 'P' and resid 23 through 34 removed outlier: 4.326A pdb=" N GLN P 32 " --> pdb=" O HIS P 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'R' and resid 36 through 55 removed outlier: 3.708A pdb=" N ASP R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 167 removed outlier: 3.955A pdb=" N ASN R 128 " --> pdb=" O TYR R 124 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS R 132 " --> pdb=" O ASN R 128 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU R 133 " --> pdb=" O VAL R 129 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.515A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR R 227 " --> pdb=" O MET R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 Processing helix chain 'R' and resid 263 through 279 removed outlier: 3.570A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 290 through 294 Processing helix chain 'R' and resid 296 through 321 Processing helix chain 'R' and resid 333 through 345 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 364 through 375 Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 400 removed outlier: 4.056A pdb=" N ASN R 400 " --> pdb=" O ARG R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.110A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.757A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.056A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.738A 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 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.516A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.517A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.544A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'R' and resid 68 through 69 Processing sheet with id=AB4, first strand: chain 'R' and resid 82 through 87 removed outlier: 4.095A pdb=" N THR R 82 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS R 105 " --> pdb=" O THR R 82 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1287 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: 2.38 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2765 1.34 - 1.45: 1409 1.45 - 1.57: 4896 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9154 Sorted by residual: bond pdb=" N VAL R 198 " pdb=" CA VAL R 198 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.17e-02 7.31e+03 8.67e+00 bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" N VAL R 135 " pdb=" CA VAL R 135 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 9149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11731 1.53 - 3.06: 621 3.06 - 4.59: 72 4.59 - 6.13: 12 6.13 - 7.66: 3 Bond angle restraints: 12439 Sorted by residual: angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 112.72 105.06 7.66 1.14e+00 7.69e-01 4.51e+01 angle pdb=" C LEU E 156 " pdb=" N ILE E 157 " pdb=" CA ILE E 157 " ideal model delta sigma weight residual 120.33 123.99 -3.66 8.00e-01 1.56e+00 2.09e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.01 107.74 5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CA ASN R 281 " pdb=" C ASN R 281 " pdb=" O ASN R 281 " ideal model delta sigma weight residual 121.54 117.06 4.48 1.16e+00 7.43e-01 1.49e+01 angle pdb=" N CYS R 282 " pdb=" CA CYS R 282 " pdb=" C CYS R 282 " ideal model delta sigma weight residual 113.56 108.68 4.88 1.39e+00 5.18e-01 1.23e+01 ... (remaining 12434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5073 17.66 - 35.32: 292 35.32 - 52.97: 51 52.97 - 70.63: 13 70.63 - 88.29: 5 Dihedral angle restraints: 5434 sinusoidal: 1935 harmonic: 3499 Sorted by residual: dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -139.41 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 142.77 -49.77 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS P 16 " pdb=" SG CYS P 16 " pdb=" SG CYS P 21 " pdb=" CB CYS P 21 " ideal model delta sinusoidal sigma weight residual -86.00 -43.45 -42.55 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 5431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1102 0.055 - 0.111: 258 0.111 - 0.166: 54 0.166 - 0.221: 18 0.221 - 0.277: 6 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1435 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C THR R 196 " -0.025 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO G 55 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG B 52 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1423 2.76 - 3.30: 8778 3.30 - 3.83: 14872 3.83 - 4.37: 18007 4.37 - 4.90: 30630 Nonbonded interactions: 73710 Sorted by model distance: nonbonded pdb=" O ASN R 398 " pdb=" ND2 ASN R 398 " model vdw 2.226 3.120 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.270 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.275 3.120 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.283 3.120 ... (remaining 73705 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.005 0.039 9154 Z= 0.351 Angle : 0.729 7.657 12439 Z= 0.515 Chirality : 0.055 0.277 1438 Planarity : 0.003 0.036 1597 Dihedral : 11.918 88.291 3135 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.45 % Allowed : 4.20 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.59 (0.23), residues: 1176 helix: 0.35 (0.25), residues: 433 sheet: -1.39 (0.32), residues: 223 loop : -2.11 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR P 31 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7834 (mt0) cc_final: 0.7143 (tp-100) REVERT: A 34 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7979 (ttmm) REVERT: A 274 ASP cc_start: 0.7228 (t0) cc_final: 0.6908 (t70) REVERT: B 111 TYR cc_start: 0.8834 (m-80) cc_final: 0.8547 (m-80) REVERT: B 124 TYR cc_start: 0.8821 (m-80) cc_final: 0.8550 (m-80) REVERT: B 325 MET cc_start: 0.8077 (tpp) cc_final: 0.7685 (tpt) REVERT: E 167 ARG cc_start: 0.4151 (mpt180) cc_final: 0.3350 (mmm-85) REVERT: G 42 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6530 (mm-30) REVERT: N 80 TYR cc_start: 0.8083 (m-80) cc_final: 0.7666 (m-80) REVERT: N 87 LYS cc_start: 0.7990 (mttp) cc_final: 0.7278 (mtpm) REVERT: R 134 LYS cc_start: 0.6307 (ttpt) cc_final: 0.6106 (mmtt) REVERT: R 139 LEU cc_start: 0.6457 (mm) cc_final: 0.6232 (mm) REVERT: R 213 LYS cc_start: 0.6557 (mtmt) cc_final: 0.6256 (mttt) REVERT: R 332 MET cc_start: 0.6557 (mmp) cc_final: 0.6302 (pmm) REVERT: R 381 SER cc_start: 0.7836 (t) cc_final: 0.7489 (m) outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 1.3665 time to fit residues: 268.6799 Evaluate side-chains 135 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 127 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 31 GLN A 35 GLN A 262 GLN A 377 ASN A 390 GLN B 6 GLN B 32 GLN B 175 GLN B 237 ASN B 340 ASN N 31 ASN N 35 ASN N 74 ASN N 120 GLN P 24 GLN R 172 GLN R 179 ASN R 219 HIS R 281 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 398 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.177489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119396 restraints weight = 10224.499| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.81 r_work: 0.3239 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9154 Z= 0.244 Angle : 0.557 6.399 12439 Z= 0.298 Chirality : 0.043 0.166 1438 Planarity : 0.004 0.039 1597 Dihedral : 4.638 59.637 1290 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.30 % Allowed : 12.16 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.66 (0.24), residues: 1176 helix: 1.21 (0.25), residues: 458 sheet: -1.17 (0.32), residues: 220 loop : -1.65 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.016 0.001 TYR R 277 ARG 0.006 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8322 (mt0) cc_final: 0.7448 (tp-100) REVERT: A 34 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8272 (ttmm) REVERT: A 223 ASP cc_start: 0.7880 (p0) cc_final: 0.7649 (t70) REVERT: B 17 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7507 (tt0) REVERT: B 97 SER cc_start: 0.8102 (p) cc_final: 0.7655 (t) REVERT: B 124 TYR cc_start: 0.9010 (m-80) cc_final: 0.8725 (m-80) REVERT: B 127 LYS cc_start: 0.8735 (mmpt) cc_final: 0.8458 (mmtm) REVERT: B 325 MET cc_start: 0.8446 (tpp) cc_final: 0.8049 (tpt) REVERT: E 167 ARG cc_start: 0.4569 (mpt180) cc_final: 0.3650 (mmm-85) REVERT: N 65 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8328 (ttpt) REVERT: N 80 TYR cc_start: 0.8516 (m-80) cc_final: 0.8251 (m-80) REVERT: R 134 LYS cc_start: 0.6000 (ttpt) cc_final: 0.5788 (mmtt) REVERT: R 139 LEU cc_start: 0.6583 (mm) cc_final: 0.6306 (mm) REVERT: R 182 PHE cc_start: 0.7343 (t80) cc_final: 0.6822 (t80) REVERT: R 213 LYS cc_start: 0.6886 (mtmt) cc_final: 0.6475 (mttt) REVERT: R 253 MET cc_start: 0.8052 (ttt) cc_final: 0.7701 (ttp) REVERT: R 269 ILE cc_start: 0.8006 (mm) cc_final: 0.7777 (mp) REVERT: R 332 MET cc_start: 0.6761 (mmp) cc_final: 0.6448 (pmm) REVERT: R 381 SER cc_start: 0.8066 (t) cc_final: 0.7704 (m) outliers start: 29 outliers final: 11 residues processed: 155 average time/residue: 1.3429 time to fit residues: 221.1417 Evaluate side-chains 142 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 215 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 52 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN R 370 HIS R 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122806 restraints weight = 10356.149| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.00 r_work: 0.3250 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9154 Z= 0.239 Angle : 0.526 6.329 12439 Z= 0.282 Chirality : 0.043 0.147 1438 Planarity : 0.004 0.039 1597 Dihedral : 4.619 57.078 1290 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.75 % Allowed : 13.75 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1176 helix: 1.48 (0.25), residues: 460 sheet: -1.05 (0.32), residues: 217 loop : -1.45 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR B 105 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.980 Fit side-chains REVERT: A 21 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 31 GLN cc_start: 0.8255 (mt0) cc_final: 0.7395 (tp-100) REVERT: A 34 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8235 (ttmt) REVERT: A 223 ASP cc_start: 0.8028 (p0) cc_final: 0.7796 (t70) REVERT: A 266 LEU cc_start: 0.8720 (tp) cc_final: 0.8377 (tp) REVERT: B 17 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7476 (tt0) REVERT: B 97 SER cc_start: 0.8210 (p) cc_final: 0.7782 (t) REVERT: B 127 LYS cc_start: 0.8782 (mmpt) cc_final: 0.8505 (mmtm) REVERT: B 325 MET cc_start: 0.8402 (tpp) cc_final: 0.7931 (tpt) REVERT: E 167 ARG cc_start: 0.4802 (mpt180) cc_final: 0.3848 (mmm-85) REVERT: N 65 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: N 73 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7232 (t0) REVERT: N 80 TYR cc_start: 0.8547 (m-80) cc_final: 0.8219 (m-80) REVERT: N 105 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7655 (ttp-110) REVERT: N 106 ASP cc_start: 0.8853 (p0) cc_final: 0.8625 (p0) REVERT: R 127 CYS cc_start: 0.4823 (OUTLIER) cc_final: 0.4194 (p) REVERT: R 134 LYS cc_start: 0.6254 (ttpt) cc_final: 0.5999 (mmtt) REVERT: R 165 TYR cc_start: 0.6363 (t80) cc_final: 0.6081 (t80) REVERT: R 213 LYS cc_start: 0.6893 (mtmt) cc_final: 0.6486 (mttt) REVERT: R 253 MET cc_start: 0.7988 (ttt) cc_final: 0.7641 (ttp) REVERT: R 332 MET cc_start: 0.6887 (mmp) cc_final: 0.6385 (pmm) REVERT: R 370 HIS cc_start: 0.6575 (m-70) cc_final: 0.6171 (m90) REVERT: R 381 SER cc_start: 0.8055 (t) cc_final: 0.7670 (m) outliers start: 33 outliers final: 14 residues processed: 152 average time/residue: 1.3156 time to fit residues: 212.6534 Evaluate side-chains 147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.177446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120217 restraints weight = 10339.324| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.74 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9154 Z= 0.278 Angle : 0.552 6.335 12439 Z= 0.295 Chirality : 0.043 0.165 1438 Planarity : 0.004 0.037 1597 Dihedral : 4.740 56.963 1290 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.98 % Allowed : 15.23 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1176 helix: 1.51 (0.25), residues: 466 sheet: -1.15 (0.32), residues: 217 loop : -1.33 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.005 0.001 HIS R 270 PHE 0.015 0.002 PHE A 212 TYR 0.017 0.001 TYR B 105 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: A 31 GLN cc_start: 0.8291 (mt0) cc_final: 0.7472 (tp-100) REVERT: A 34 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8315 (ttmt) REVERT: A 266 LEU cc_start: 0.8726 (tp) cc_final: 0.8401 (tp) REVERT: A 333 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.3563 (ttt180) REVERT: B 17 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7596 (tt0) REVERT: B 97 SER cc_start: 0.8198 (p) cc_final: 0.7773 (t) REVERT: B 127 LYS cc_start: 0.8781 (mmpt) cc_final: 0.8541 (mmtm) REVERT: B 325 MET cc_start: 0.8415 (tpp) cc_final: 0.7986 (tpt) REVERT: E 167 ARG cc_start: 0.4939 (mpt180) cc_final: 0.3861 (mmm-85) REVERT: N 5 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7399 (tp40) REVERT: N 73 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7246 (t0) REVERT: N 80 TYR cc_start: 0.8579 (m-80) cc_final: 0.8315 (m-80) REVERT: N 105 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7688 (ttp-110) REVERT: R 127 CYS cc_start: 0.4481 (OUTLIER) cc_final: 0.3987 (p) REVERT: R 134 LYS cc_start: 0.6400 (ttpt) cc_final: 0.6123 (mmtt) REVERT: R 165 TYR cc_start: 0.6392 (t80) cc_final: 0.6120 (t80) REVERT: R 213 LYS cc_start: 0.7109 (mtmt) cc_final: 0.6625 (mttt) REVERT: R 253 MET cc_start: 0.8037 (ttt) cc_final: 0.7719 (ttp) REVERT: R 332 MET cc_start: 0.6905 (mmp) cc_final: 0.6339 (pmm) REVERT: R 370 HIS cc_start: 0.6658 (m-70) cc_final: 0.6272 (m90) REVERT: R 381 SER cc_start: 0.8211 (t) cc_final: 0.7814 (m) outliers start: 35 outliers final: 19 residues processed: 150 average time/residue: 1.1947 time to fit residues: 191.5390 Evaluate side-chains 149 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135639 restraints weight = 10321.186| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.46 r_work: 0.3231 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9154 Z= 0.206 Angle : 0.513 6.474 12439 Z= 0.274 Chirality : 0.042 0.170 1438 Planarity : 0.003 0.033 1597 Dihedral : 4.571 55.568 1290 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.43 % Allowed : 15.11 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.06 (0.24), residues: 1176 helix: 1.64 (0.25), residues: 466 sheet: -1.02 (0.31), residues: 216 loop : -1.21 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 PHE 0.016 0.001 PHE R 228 TYR 0.012 0.001 TYR R 278 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 1.093 Fit side-chains REVERT: A 17 LYS cc_start: 0.7602 (mmmm) cc_final: 0.7390 (mmmm) REVERT: A 21 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 31 GLN cc_start: 0.8363 (mt0) cc_final: 0.7528 (tp-100) REVERT: A 34 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8301 (ttmt) REVERT: A 209 GLU cc_start: 0.7971 (mp0) cc_final: 0.7754 (mp0) REVERT: A 266 LEU cc_start: 0.8709 (tp) cc_final: 0.8384 (tp) REVERT: A 333 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.3604 (ttt180) REVERT: B 17 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7550 (tt0) REVERT: B 97 SER cc_start: 0.8231 (p) cc_final: 0.7828 (t) REVERT: B 127 LYS cc_start: 0.8752 (mmpt) cc_final: 0.8530 (mmtm) REVERT: B 325 MET cc_start: 0.8412 (tpp) cc_final: 0.7856 (tpt) REVERT: E 167 ARG cc_start: 0.4908 (mpt180) cc_final: 0.3815 (mmm-85) REVERT: N 5 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7287 (tp40) REVERT: N 65 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: N 73 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7272 (t0) REVERT: N 80 TYR cc_start: 0.8618 (m-80) cc_final: 0.8360 (m-80) REVERT: N 89 GLU cc_start: 0.7482 (pt0) cc_final: 0.6946 (pp20) REVERT: P 31 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.6152 (t80) REVERT: R 127 CYS cc_start: 0.4294 (OUTLIER) cc_final: 0.3771 (p) REVERT: R 134 LYS cc_start: 0.6374 (ttpt) cc_final: 0.6091 (mmtt) REVERT: R 165 TYR cc_start: 0.6359 (t80) cc_final: 0.6071 (t80) REVERT: R 213 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6605 (mttt) REVERT: R 253 MET cc_start: 0.8030 (ttt) cc_final: 0.7714 (ttp) REVERT: R 332 MET cc_start: 0.6897 (mmp) cc_final: 0.6236 (pmm) REVERT: R 370 HIS cc_start: 0.6651 (m-70) cc_final: 0.6266 (m90) REVERT: R 381 SER cc_start: 0.8169 (t) cc_final: 0.7764 (m) outliers start: 39 outliers final: 22 residues processed: 154 average time/residue: 1.2385 time to fit residues: 203.5453 Evaluate side-chains 156 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 250 GLN Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 73 optimal weight: 0.0470 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 72 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.138310 restraints weight = 10312.977| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.07 r_work: 0.3289 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9154 Z= 0.142 Angle : 0.480 6.664 12439 Z= 0.256 Chirality : 0.041 0.148 1438 Planarity : 0.003 0.032 1597 Dihedral : 4.324 52.509 1290 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.52 % Allowed : 16.25 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.30 (0.25), residues: 1176 helix: 1.93 (0.25), residues: 458 sheet: -0.81 (0.32), residues: 217 loop : -0.96 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 99 HIS 0.003 0.001 HIS R 270 PHE 0.015 0.001 PHE R 228 TYR 0.010 0.001 TYR R 278 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.013 Fit side-chains REVERT: A 17 LYS cc_start: 0.7461 (mmmm) cc_final: 0.7232 (mmmm) REVERT: A 21 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: A 31 GLN cc_start: 0.8343 (mt0) cc_final: 0.7546 (tp-100) REVERT: A 34 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8192 (tttt) REVERT: A 230 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 333 ARG cc_start: 0.5880 (OUTLIER) cc_final: 0.3558 (ttt180) REVERT: B 17 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7533 (tt0) REVERT: B 97 SER cc_start: 0.8226 (p) cc_final: 0.7852 (t) REVERT: B 127 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8541 (mmtm) REVERT: B 325 MET cc_start: 0.8359 (tpp) cc_final: 0.7843 (tpt) REVERT: E 167 ARG cc_start: 0.4830 (mpt180) cc_final: 0.3891 (mmm-85) REVERT: G 47 GLU cc_start: 0.8356 (pt0) cc_final: 0.8081 (pt0) REVERT: N 65 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8152 (ttpt) REVERT: N 73 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7245 (t0) REVERT: N 80 TYR cc_start: 0.8592 (m-80) cc_final: 0.8335 (m-80) REVERT: N 89 GLU cc_start: 0.7433 (pt0) cc_final: 0.6945 (pp20) REVERT: R 127 CYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3706 (p) REVERT: R 134 LYS cc_start: 0.6438 (ttpt) cc_final: 0.6122 (mmtt) REVERT: R 213 LYS cc_start: 0.7175 (mtmt) cc_final: 0.6676 (mttt) REVERT: R 253 MET cc_start: 0.7984 (ttt) cc_final: 0.7664 (ttp) REVERT: R 332 MET cc_start: 0.6718 (mmp) cc_final: 0.6254 (pmm) REVERT: R 370 HIS cc_start: 0.6616 (m-70) cc_final: 0.6266 (m90) REVERT: R 373 MET cc_start: 0.7240 (ttp) cc_final: 0.6867 (ttp) REVERT: R 381 SER cc_start: 0.8089 (t) cc_final: 0.7710 (m) outliers start: 31 outliers final: 19 residues processed: 161 average time/residue: 1.2439 time to fit residues: 214.0527 Evaluate side-chains 158 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 0.0370 chunk 98 optimal weight: 10.0000 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119007 restraints weight = 10463.039| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.85 r_work: 0.3224 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.205 Angle : 0.516 6.723 12439 Z= 0.274 Chirality : 0.042 0.145 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.424 53.674 1288 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.20 % Allowed : 17.61 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.24 (0.25), residues: 1176 helix: 1.86 (0.25), residues: 464 sheet: -0.90 (0.31), residues: 217 loop : -0.96 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS R 270 PHE 0.014 0.001 PHE R 228 TYR 0.013 0.001 TYR B 105 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.966 Fit side-chains REVERT: A 17 LYS cc_start: 0.7396 (mmmm) cc_final: 0.7131 (mmmm) REVERT: A 21 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 31 GLN cc_start: 0.8348 (mt0) cc_final: 0.7496 (tp-100) REVERT: A 34 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8142 (tttt) REVERT: A 333 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.3495 (ttt180) REVERT: B 17 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7512 (tt0) REVERT: B 127 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8496 (mmtm) REVERT: B 325 MET cc_start: 0.8394 (tpp) cc_final: 0.7940 (tpt) REVERT: E 151 ILE cc_start: 0.5249 (OUTLIER) cc_final: 0.4953 (OUTLIER) REVERT: E 167 ARG cc_start: 0.4794 (mpt180) cc_final: 0.3696 (mmm-85) REVERT: G 47 GLU cc_start: 0.8334 (pt0) cc_final: 0.8032 (pt0) REVERT: N 65 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: N 80 TYR cc_start: 0.8624 (m-80) cc_final: 0.8403 (m-80) REVERT: N 89 GLU cc_start: 0.7372 (pt0) cc_final: 0.6857 (pp20) REVERT: R 127 CYS cc_start: 0.4051 (OUTLIER) cc_final: 0.3693 (p) REVERT: R 134 LYS cc_start: 0.6330 (ttpt) cc_final: 0.6036 (mmtt) REVERT: R 182 PHE cc_start: 0.7562 (t80) cc_final: 0.7069 (t80) REVERT: R 213 LYS cc_start: 0.7093 (mtmt) cc_final: 0.6590 (mttt) REVERT: R 253 MET cc_start: 0.7982 (ttt) cc_final: 0.7654 (ttp) REVERT: R 332 MET cc_start: 0.6827 (mmp) cc_final: 0.6220 (pmm) REVERT: R 370 HIS cc_start: 0.6542 (m-70) cc_final: 0.6190 (m90) REVERT: R 381 SER cc_start: 0.8015 (t) cc_final: 0.7603 (m) outliers start: 37 outliers final: 22 residues processed: 154 average time/residue: 1.3325 time to fit residues: 218.8288 Evaluate side-chains 156 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.176836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119494 restraints weight = 10604.470| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.85 r_work: 0.3229 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9154 Z= 0.185 Angle : 0.510 6.687 12439 Z= 0.270 Chirality : 0.041 0.146 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.388 53.444 1288 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.64 % Allowed : 17.73 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.32 (0.25), residues: 1176 helix: 1.90 (0.25), residues: 464 sheet: -0.80 (0.32), residues: 215 loop : -0.93 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 228 TYR 0.011 0.001 TYR B 111 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.047 Fit side-chains REVERT: A 17 LYS cc_start: 0.7338 (mmmm) cc_final: 0.7071 (mmmm) REVERT: A 21 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: A 31 GLN cc_start: 0.8326 (mt0) cc_final: 0.7473 (tp-100) REVERT: A 34 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8087 (tttt) REVERT: A 266 LEU cc_start: 0.8628 (tp) cc_final: 0.8261 (tp) REVERT: A 333 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.3490 (ttt180) REVERT: B 17 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7499 (tt0) REVERT: B 127 LYS cc_start: 0.8744 (mmpt) cc_final: 0.8514 (mmtm) REVERT: B 325 MET cc_start: 0.8396 (tpp) cc_final: 0.7828 (tpt) REVERT: E 151 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.5046 (mt) REVERT: E 167 ARG cc_start: 0.4804 (mpt180) cc_final: 0.3798 (mmm-85) REVERT: G 47 GLU cc_start: 0.8292 (pt0) cc_final: 0.7967 (pt0) REVERT: N 5 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7304 (tp40) REVERT: N 65 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8102 (ttpt) REVERT: N 73 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7256 (t0) REVERT: N 80 TYR cc_start: 0.8634 (m-80) cc_final: 0.8426 (m-80) REVERT: N 89 GLU cc_start: 0.7362 (pt0) cc_final: 0.6851 (pp20) REVERT: N 105 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7558 (ttp-110) REVERT: R 127 CYS cc_start: 0.4000 (OUTLIER) cc_final: 0.3655 (p) REVERT: R 134 LYS cc_start: 0.6372 (ttpt) cc_final: 0.6051 (mmtt) REVERT: R 182 PHE cc_start: 0.7567 (t80) cc_final: 0.7085 (t80) REVERT: R 213 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6632 (mttt) REVERT: R 253 MET cc_start: 0.7969 (ttt) cc_final: 0.7632 (ttp) REVERT: R 332 MET cc_start: 0.6838 (mmp) cc_final: 0.6117 (pmm) REVERT: R 370 HIS cc_start: 0.6534 (m-70) cc_final: 0.6171 (m90) REVERT: R 381 SER cc_start: 0.8024 (t) cc_final: 0.7598 (m) outliers start: 32 outliers final: 21 residues processed: 152 average time/residue: 1.2466 time to fit residues: 202.5148 Evaluate side-chains 154 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.178297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136224 restraints weight = 10316.345| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.26 r_work: 0.3232 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9154 Z= 0.220 Angle : 0.528 6.922 12439 Z= 0.280 Chirality : 0.042 0.153 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.456 53.763 1288 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 18.07 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1176 helix: 1.89 (0.25), residues: 464 sheet: -0.91 (0.32), residues: 217 loop : -0.86 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE R 228 TYR 0.012 0.001 TYR B 105 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.944 Fit side-chains REVERT: A 17 LYS cc_start: 0.7380 (mmmm) cc_final: 0.7144 (mmmm) REVERT: A 21 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 31 GLN cc_start: 0.8366 (mt0) cc_final: 0.7546 (tp-100) REVERT: A 34 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8188 (tttt) REVERT: A 266 LEU cc_start: 0.8682 (tp) cc_final: 0.8320 (tp) REVERT: A 333 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.3567 (ttt180) REVERT: B 17 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7503 (tt0) REVERT: B 127 LYS cc_start: 0.8764 (mmpt) cc_final: 0.8558 (mmtm) REVERT: B 325 MET cc_start: 0.8465 (tpp) cc_final: 0.8005 (tpt) REVERT: E 151 ILE cc_start: 0.5554 (OUTLIER) cc_final: 0.5257 (mt) REVERT: E 167 ARG cc_start: 0.4817 (mpt180) cc_final: 0.3848 (mmm-85) REVERT: G 47 GLU cc_start: 0.8321 (pt0) cc_final: 0.8071 (pt0) REVERT: N 5 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7308 (tp40) REVERT: N 65 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: N 73 ASP cc_start: 0.7715 (t70) cc_final: 0.7331 (t0) REVERT: N 80 TYR cc_start: 0.8665 (m-80) cc_final: 0.8419 (m-80) REVERT: N 89 GLU cc_start: 0.7467 (pt0) cc_final: 0.6957 (pp20) REVERT: N 105 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7498 (ttp-110) REVERT: R 127 CYS cc_start: 0.3990 (OUTLIER) cc_final: 0.3680 (p) REVERT: R 134 LYS cc_start: 0.6393 (ttpt) cc_final: 0.6057 (mmtt) REVERT: R 182 PHE cc_start: 0.7689 (t80) cc_final: 0.7205 (t80) REVERT: R 213 LYS cc_start: 0.7182 (mtmt) cc_final: 0.6686 (mttt) REVERT: R 253 MET cc_start: 0.7966 (ttt) cc_final: 0.7747 (ttt) REVERT: R 332 MET cc_start: 0.6870 (mmp) cc_final: 0.6152 (pmm) REVERT: R 370 HIS cc_start: 0.6608 (m-70) cc_final: 0.6257 (m90) REVERT: R 381 SER cc_start: 0.8194 (t) cc_final: 0.7765 (m) outliers start: 29 outliers final: 21 residues processed: 147 average time/residue: 1.2200 time to fit residues: 191.8083 Evaluate side-chains 151 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 0.0060 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136171 restraints weight = 10424.549| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.25 r_work: 0.3230 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9154 Z= 0.232 Angle : 0.536 7.279 12439 Z= 0.285 Chirality : 0.042 0.156 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.492 53.919 1288 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.52 % Allowed : 17.95 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.29 (0.25), residues: 1176 helix: 1.86 (0.25), residues: 464 sheet: -0.92 (0.32), residues: 216 loop : -0.87 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 105 ARG 0.002 0.000 ARG N 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.055 Fit side-chains REVERT: A 17 LYS cc_start: 0.7478 (mmmm) cc_final: 0.7227 (mmmm) REVERT: A 21 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 31 GLN cc_start: 0.8362 (mt0) cc_final: 0.7547 (tp-100) REVERT: A 34 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8218 (tttt) REVERT: A 209 GLU cc_start: 0.7959 (mp0) cc_final: 0.7724 (mm-30) REVERT: A 266 LEU cc_start: 0.8683 (tp) cc_final: 0.8327 (tp) REVERT: A 333 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.3585 (ttt180) REVERT: B 17 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7494 (tt0) REVERT: B 127 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8567 (mmtm) REVERT: B 325 MET cc_start: 0.8490 (tpp) cc_final: 0.7940 (tpt) REVERT: E 151 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.5276 (mt) REVERT: E 167 ARG cc_start: 0.4927 (mpt180) cc_final: 0.3930 (mmm-85) REVERT: G 21 MET cc_start: 0.8048 (ttp) cc_final: 0.7729 (mtp) REVERT: G 47 GLU cc_start: 0.8331 (pt0) cc_final: 0.8093 (pt0) REVERT: N 5 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7311 (tp40) REVERT: N 65 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8166 (ttpt) REVERT: N 73 ASP cc_start: 0.7706 (t70) cc_final: 0.7315 (t0) REVERT: N 80 TYR cc_start: 0.8654 (m-80) cc_final: 0.8445 (m-80) REVERT: N 89 GLU cc_start: 0.7492 (pt0) cc_final: 0.6988 (pp20) REVERT: N 105 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7507 (ttp-110) REVERT: R 127 CYS cc_start: 0.3810 (OUTLIER) cc_final: 0.3556 (p) REVERT: R 134 LYS cc_start: 0.6375 (ttpt) cc_final: 0.6056 (mmtt) REVERT: R 165 TYR cc_start: 0.6399 (t80) cc_final: 0.6068 (t80) REVERT: R 182 PHE cc_start: 0.7686 (t80) cc_final: 0.7197 (t80) REVERT: R 213 LYS cc_start: 0.7181 (mtmt) cc_final: 0.6695 (mttt) REVERT: R 253 MET cc_start: 0.8027 (ttt) cc_final: 0.7817 (ttt) REVERT: R 370 HIS cc_start: 0.6612 (m-70) cc_final: 0.6259 (m90) REVERT: R 381 SER cc_start: 0.8198 (t) cc_final: 0.7798 (m) outliers start: 31 outliers final: 22 residues processed: 147 average time/residue: 1.2682 time to fit residues: 200.5192 Evaluate side-chains 152 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 215 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122965 restraints weight = 10364.771| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.75 r_work: 0.3297 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9154 Z= 0.179 Angle : 0.511 7.115 12439 Z= 0.271 Chirality : 0.041 0.150 1438 Planarity : 0.003 0.030 1597 Dihedral : 4.388 53.205 1288 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.95 % Allowed : 18.86 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.46 (0.25), residues: 1176 helix: 2.04 (0.25), residues: 458 sheet: -0.87 (0.32), residues: 214 loop : -0.75 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 228 TYR 0.011 0.001 TYR R 278 ARG 0.002 0.000 ARG N 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7465.05 seconds wall clock time: 132 minutes 9.96 seconds (7929.96 seconds total)