Starting phenix.real_space_refine on Mon Jan 20 22:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrk_60399/01_2025/8zrk_60399_neut_trim.cif" } resolution = 2.82 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= 0.034 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 5093 2.51 5 N 1389 2.21 5 O 1483 1.98 5 H 7877 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15895 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3876 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 5015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5015 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1855 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4232 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 7, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'A1D8Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.78, per 1000 atoms: 0.55 Number of scatterers: 15895 At special positions: 0 Unit cell: (83.3, 102.85, 130.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 O 1483 8.00 N 1389 7.00 C 5093 6.00 H 7877 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 42.7% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.641A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.586A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.907A 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 293 through 303 removed outlier: 3.570A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.543A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.097A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.722A 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 28 through 32 removed outlier: 3.654A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.898A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 36 Processing helix chain 'R' and resid 40 through 61 removed outlier: 4.027A pdb=" N THR R 44 " --> pdb=" O SER R 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 109 removed outlier: 3.540A pdb=" N ALA R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 97 " --> pdb=" O VAL R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 removed outlier: 3.598A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 139 removed outlier: 3.705A pdb=" N PHE R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 removed outlier: 3.547A pdb=" N VAL R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 173 removed outlier: 3.988A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 210 removed outlier: 3.614A pdb=" N LEU R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 183 " --> pdb=" O LEU R 179 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR R 185 " --> pdb=" O PHE R 181 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU R 189 " --> pdb=" O TYR R 185 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS R 190 " --> pdb=" O CYS R 186 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA R 192 " --> pdb=" O MET R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 236 Processing helix chain 'R' and resid 238 through 251 removed outlier: 3.655A pdb=" N THR R 244 " --> pdb=" O PRO R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 280 removed outlier: 3.743A pdb=" N VAL R 269 " --> pdb=" O TRP R 265 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU R 274 " --> pdb=" O GLY R 270 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.496A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.704A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 7.294A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.803A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.534A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.514A 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: 6.500A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.523A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.045A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1116 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: 6.35 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 7849 1.04 - 1.24: 1086 1.24 - 1.44: 2482 1.44 - 1.64: 4557 1.64 - 1.84: 78 Bond restraints: 16052 Sorted by residual: bond pdb=" C10 A1D8Y R 401 " pdb=" C11 A1D8Y R 401 " ideal model delta sigma weight residual 1.543 1.437 0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C07 A1D8Y R 401 " pdb=" N08 A1D8Y R 401 " ideal model delta sigma weight residual 1.327 1.428 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C17 A1D8Y R 401 " pdb=" C18 A1D8Y R 401 " ideal model delta sigma weight residual 1.478 1.391 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C11 A1D8Y R 401 " pdb=" C30 A1D8Y R 401 " ideal model delta sigma weight residual 1.526 1.441 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" N ASN B 155 " pdb=" CA ASN B 155 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.00e+01 ... (remaining 16047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 28769 3.24 - 6.48: 91 6.48 - 9.73: 3 9.73 - 12.97: 1 12.97 - 16.21: 1 Bond angle restraints: 28865 Sorted by residual: angle pdb=" O24 A1D8Y R 401 " pdb=" S22 A1D8Y R 401 " pdb=" O25 A1D8Y R 401 " ideal model delta sigma weight residual 118.61 102.40 16.21 3.00e+00 1.11e-01 2.92e+01 angle pdb=" N SER R 79 " pdb=" CA SER R 79 " pdb=" C SER R 79 " ideal model delta sigma weight residual 112.89 107.13 5.76 1.24e+00 6.50e-01 2.15e+01 angle pdb=" CA HIS A 357 " pdb=" C HIS A 357 " pdb=" O HIS A 357 " ideal model delta sigma weight residual 120.89 115.94 4.95 1.10e+00 8.26e-01 2.02e+01 angle pdb=" N LEU R 80 " pdb=" CA LEU R 80 " pdb=" C LEU R 80 " ideal model delta sigma weight residual 113.41 108.10 5.31 1.22e+00 6.72e-01 1.90e+01 angle pdb=" CA ARG R 287 " pdb=" C ARG R 287 " pdb=" O ARG R 287 " ideal model delta sigma weight residual 120.42 115.83 4.59 1.06e+00 8.90e-01 1.87e+01 ... (remaining 28860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 6917 25.08 - 50.17: 526 50.17 - 75.25: 108 75.25 - 100.33: 26 100.33 - 125.42: 5 Dihedral angle restraints: 7582 sinusoidal: 4051 harmonic: 3531 Sorted by residual: dihedral pdb=" CA ILE B 120 " pdb=" C ILE B 120 " pdb=" N CYS B 121 " pdb=" CA CYS B 121 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" C03 A1D8Y R 401 " pdb=" C02 A1D8Y R 401 " pdb=" C04 A1D8Y R 401 " pdb=" N32 A1D8Y R 401 " ideal model delta sinusoidal sigma weight residual -60.96 64.46 -125.42 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C01 A1D8Y R 401 " pdb=" C02 A1D8Y R 401 " pdb=" C04 A1D8Y R 401 " pdb=" N32 A1D8Y R 401 " ideal model delta sinusoidal sigma weight residual 62.39 -172.21 -125.40 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 7579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 952 0.040 - 0.080: 214 0.080 - 0.120: 82 0.120 - 0.160: 16 0.160 - 0.200: 1 Chirality restraints: 1265 Sorted by residual: chirality pdb=" C11 A1D8Y R 401 " pdb=" C10 A1D8Y R 401 " pdb=" C12 A1D8Y R 401 " pdb=" C30 A1D8Y R 401 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA LEU B 146 " pdb=" N LEU B 146 " pdb=" C LEU B 146 " pdb=" CB LEU B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 1262 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 155 " 0.216 2.00e-02 2.50e+03 3.83e-01 2.19e+03 pdb=" CG ASN B 155 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 155 " -0.213 2.00e-02 2.50e+03 pdb=" ND2 ASN B 155 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 155 " -0.624 2.00e-02 2.50e+03 pdb="HD22 ASN B 155 " 0.630 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN R 283 " 0.121 2.00e-02 2.50e+03 1.33e-01 2.64e+02 pdb=" CD GLN R 283 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN R 283 " -0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN R 283 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN R 283 " -0.196 2.00e-02 2.50e+03 pdb="HE22 GLN R 283 " 0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C LYS B 57 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS B 57 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 58 " -0.021 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 303 2.10 - 2.73: 26903 2.73 - 3.35: 44464 3.35 - 3.98: 56540 3.98 - 4.60: 89833 Nonbonded interactions: 218043 Sorted by model distance: nonbonded pdb=" OE1 GLU A 309 " pdb=" H GLU A 309 " model vdw 1.478 2.450 nonbonded pdb=" O SER B 147 " pdb=" HG CYS B 148 " model vdw 1.613 2.620 nonbonded pdb=" HG1 THR B 34 " pdb=" O LEU B 300 " model vdw 1.613 2.450 nonbonded pdb=" O SER A 252 " pdb=" HG SER A 252 " model vdw 1.617 2.450 nonbonded pdb=" O GLN B 75 " pdb=" HG SER B 98 " model vdw 1.627 2.450 ... (remaining 218038 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: 0.010 Normalize map: mean=0, sd=1: 3.040 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: 0.270 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8175 Z= 0.287 Angle : 0.654 16.210 11080 Z= 0.370 Chirality : 0.041 0.200 1265 Planarity : 0.004 0.054 1408 Dihedral : 18.739 125.415 2930 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.95 % Allowed : 24.73 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.27), residues: 1014 helix: 1.86 (0.26), residues: 413 sheet: 0.05 (0.37), residues: 220 loop : -1.14 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS A 362 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR R 134 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 145 MET cc_start: 0.6261 (ptm) cc_final: 0.5970 (ptp) REVERT: R 285 GLU cc_start: 0.7310 (mp0) cc_final: 0.6942 (mm-30) outliers start: 8 outliers final: 8 residues processed: 104 average time/residue: 2.7496 time to fit residues: 303.9330 Evaluate side-chains 98 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 248 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.190084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150181 restraints weight = 22319.467| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.00 r_work: 0.3644 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8175 Z= 0.177 Angle : 0.507 4.878 11080 Z= 0.275 Chirality : 0.040 0.159 1265 Planarity : 0.004 0.049 1408 Dihedral : 6.879 62.727 1155 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.37 % Allowed : 24.50 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.27), residues: 1014 helix: 2.11 (0.26), residues: 409 sheet: 0.22 (0.37), residues: 214 loop : -1.10 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR R 134 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: N 78 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7773 (m) outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 2.5424 time to fit residues: 292.5024 Evaluate side-chains 102 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.188873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149234 restraints weight = 22171.981| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.95 r_work: 0.3596 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8175 Z= 0.214 Angle : 0.512 4.568 11080 Z= 0.279 Chirality : 0.040 0.162 1265 Planarity : 0.004 0.049 1408 Dihedral : 5.026 42.357 1147 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.60 % Allowed : 24.50 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.27), residues: 1014 helix: 2.03 (0.26), residues: 409 sheet: 0.34 (0.36), residues: 216 loop : -1.20 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE B 151 TYR 0.014 0.001 TYR R 134 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.392 Fit side-chains REVERT: A 27 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6259 (mm-30) REVERT: A 309 GLU cc_start: 0.7516 (pm20) cc_final: 0.7275 (pm20) REVERT: B 228 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: B 318 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7990 (mp) REVERT: N 78 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7775 (m) REVERT: R 147 GLN cc_start: 0.8290 (mt0) cc_final: 0.7717 (mt0) REVERT: R 285 GLU cc_start: 0.7352 (mp0) cc_final: 0.6741 (mm-30) outliers start: 22 outliers final: 12 residues processed: 112 average time/residue: 2.5141 time to fit residues: 300.3041 Evaluate side-chains 109 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151118 restraints weight = 22362.887| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.96 r_work: 0.3538 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8175 Z= 0.143 Angle : 0.467 4.378 11080 Z= 0.252 Chirality : 0.039 0.152 1265 Planarity : 0.004 0.048 1408 Dihedral : 4.618 37.887 1144 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.37 % Allowed : 24.38 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.27), residues: 1014 helix: 2.33 (0.26), residues: 409 sheet: 0.53 (0.36), residues: 216 loop : -1.07 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR R 134 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.217 Fit side-chains REVERT: A 27 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6310 (mm-30) REVERT: A 253 TYR cc_start: 0.6218 (p90) cc_final: 0.6017 (p90) REVERT: B 228 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: N 78 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7727 (m) REVERT: R 147 GLN cc_start: 0.8261 (mt0) cc_final: 0.7737 (mt0) REVERT: R 285 GLU cc_start: 0.7190 (mp0) cc_final: 0.6947 (pm20) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 2.5685 time to fit residues: 304.1476 Evaluate side-chains 107 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.186484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146027 restraints weight = 22608.054| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.01 r_work: 0.3566 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8175 Z= 0.289 Angle : 0.553 4.719 11080 Z= 0.301 Chirality : 0.042 0.174 1265 Planarity : 0.004 0.050 1408 Dihedral : 5.060 43.777 1144 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.55 % Allowed : 23.67 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.27), residues: 1014 helix: 1.91 (0.26), residues: 409 sheet: 0.50 (0.36), residues: 216 loop : -1.25 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.002 PHE B 151 TYR 0.015 0.002 TYR N 95 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.206 Fit side-chains REVERT: A 27 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6300 (mm-30) REVERT: B 134 ARG cc_start: 0.7176 (mtm180) cc_final: 0.6716 (mtm110) REVERT: B 228 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7640 (m-30) REVERT: B 318 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7985 (mp) REVERT: N 78 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7779 (m) REVERT: R 147 GLN cc_start: 0.8238 (mt0) cc_final: 0.7708 (mt0) REVERT: R 285 GLU cc_start: 0.7137 (mp0) cc_final: 0.6875 (mp0) REVERT: R 293 MET cc_start: 0.6175 (mtp) cc_final: 0.5734 (mtp) outliers start: 30 outliers final: 16 residues processed: 120 average time/residue: 2.4390 time to fit residues: 313.4099 Evaluate side-chains 112 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.188391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148301 restraints weight = 22451.928| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.00 r_work: 0.3632 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8175 Z= 0.186 Angle : 0.495 4.514 11080 Z= 0.268 Chirality : 0.040 0.159 1265 Planarity : 0.004 0.049 1408 Dihedral : 4.828 39.596 1144 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.84 % Allowed : 24.26 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.27), residues: 1014 helix: 2.14 (0.26), residues: 409 sheet: 0.68 (0.37), residues: 211 loop : -1.19 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 134 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.342 Fit side-chains REVERT: A 27 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6258 (mm-30) REVERT: B 134 ARG cc_start: 0.7155 (mtm180) cc_final: 0.6693 (mtm110) REVERT: N 78 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7753 (m) REVERT: R 82 MET cc_start: 0.6613 (mmp) cc_final: 0.5937 (mmt) REVERT: R 147 GLN cc_start: 0.8231 (mt0) cc_final: 0.7743 (mt0) REVERT: R 293 MET cc_start: 0.6154 (mtp) cc_final: 0.5678 (mtp) outliers start: 24 outliers final: 15 residues processed: 116 average time/residue: 2.4207 time to fit residues: 300.4042 Evaluate side-chains 112 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.189607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150058 restraints weight = 22548.867| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.96 r_work: 0.3629 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8175 Z= 0.153 Angle : 0.470 4.390 11080 Z= 0.253 Chirality : 0.039 0.152 1265 Planarity : 0.004 0.052 1408 Dihedral : 4.633 37.957 1144 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 24.85 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.27), residues: 1014 helix: 2.34 (0.26), residues: 409 sheet: 0.72 (0.36), residues: 212 loop : -1.10 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR R 134 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.225 Fit side-chains REVERT: A 27 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6204 (mm-30) REVERT: B 134 ARG cc_start: 0.7142 (mtm180) cc_final: 0.6690 (mtm110) REVERT: B 228 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: N 78 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7736 (m) REVERT: R 82 MET cc_start: 0.6552 (mmp) cc_final: 0.5942 (mmt) REVERT: R 147 GLN cc_start: 0.8225 (mt0) cc_final: 0.7742 (mt0) REVERT: R 293 MET cc_start: 0.6068 (mtp) cc_final: 0.5556 (mtp) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 2.3811 time to fit residues: 290.2810 Evaluate side-chains 108 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 170 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0570 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.190546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150401 restraints weight = 22364.396| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.01 r_work: 0.3632 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8175 Z= 0.142 Angle : 0.461 4.341 11080 Z= 0.248 Chirality : 0.039 0.151 1265 Planarity : 0.004 0.055 1408 Dihedral : 4.528 36.808 1144 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.72 % Allowed : 24.26 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.27), residues: 1014 helix: 2.47 (0.26), residues: 409 sheet: 0.79 (0.36), residues: 212 loop : -1.04 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR R 134 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.261 Fit side-chains REVERT: A 27 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6222 (mm-30) REVERT: B 228 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: N 78 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7736 (m) REVERT: R 82 MET cc_start: 0.6537 (mmp) cc_final: 0.5987 (mmt) REVERT: R 147 GLN cc_start: 0.8218 (mt0) cc_final: 0.7731 (mt0) REVERT: R 293 MET cc_start: 0.6065 (mtp) cc_final: 0.5537 (mtp) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 2.4009 time to fit residues: 290.8933 Evaluate side-chains 112 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 170 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.188252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148073 restraints weight = 22548.691| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.00 r_work: 0.3600 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8175 Z= 0.202 Angle : 0.497 4.519 11080 Z= 0.268 Chirality : 0.040 0.160 1265 Planarity : 0.004 0.057 1408 Dihedral : 4.716 39.294 1144 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.60 % Allowed : 24.62 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.27), residues: 1014 helix: 2.28 (0.26), residues: 409 sheet: 0.61 (0.36), residues: 217 loop : -1.09 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.001 TYR R 134 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.274 Fit side-chains REVERT: A 27 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6285 (mm-30) REVERT: B 134 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6725 (mtm110) REVERT: B 228 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7559 (m-30) REVERT: B 318 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7964 (mp) REVERT: N 78 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7754 (m) REVERT: R 82 MET cc_start: 0.6585 (mmp) cc_final: 0.5973 (mmt) REVERT: R 147 GLN cc_start: 0.8230 (mt0) cc_final: 0.7732 (mt0) REVERT: R 293 MET cc_start: 0.6129 (mtp) cc_final: 0.5609 (mtp) outliers start: 22 outliers final: 16 residues processed: 113 average time/residue: 2.4440 time to fit residues: 295.3270 Evaluate side-chains 113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.188207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148681 restraints weight = 22484.643| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.95 r_work: 0.3568 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8175 Z= 0.195 Angle : 0.495 4.606 11080 Z= 0.267 Chirality : 0.040 0.158 1265 Planarity : 0.004 0.059 1408 Dihedral : 4.723 38.784 1144 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.49 % Allowed : 24.97 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.27), residues: 1014 helix: 2.28 (0.26), residues: 409 sheet: 0.61 (0.36), residues: 216 loop : -1.09 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR R 134 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue LYS 284 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.162 Fit side-chains REVERT: A 27 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6269 (mm-30) REVERT: B 228 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: B 318 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7973 (mp) REVERT: N 78 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7759 (m) REVERT: R 82 MET cc_start: 0.6608 (mmp) cc_final: 0.6062 (mmt) REVERT: R 147 GLN cc_start: 0.8191 (mt0) cc_final: 0.7704 (mt0) REVERT: R 293 MET cc_start: 0.6217 (mtp) cc_final: 0.5689 (mtp) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 2.4002 time to fit residues: 287.8396 Evaluate side-chains 114 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.188151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148634 restraints weight = 22442.366| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.95 r_work: 0.3509 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8175 Z= 0.191 Angle : 0.493 4.639 11080 Z= 0.266 Chirality : 0.040 0.158 1265 Planarity : 0.004 0.060 1408 Dihedral : 4.715 38.660 1144 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.49 % Allowed : 25.21 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.27), residues: 1014 helix: 2.30 (0.26), residues: 408 sheet: 0.62 (0.36), residues: 217 loop : -1.09 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR R 134 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 11481.00 seconds wall clock time: 204 minutes 20.26 seconds (12260.26 seconds total)