Starting phenix.real_space_refine on Thu Jul 2 22:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2d_32965/07_2026/7x2d_32965.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic. 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 55 5.16 5 C 5215 2.51 5 N 1428 2.21 5 O 1502 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8203 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2241 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 bond proxies already assigned to first conformer: 2274 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1883 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2619 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Conformer: "B" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} bond proxies already assigned to first conformer: 2640 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'86W': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 2.49, per 1000 atoms: 0.30 Number of scatterers: 8203 At special positions: 0 Unit cell: (78.264, 97.83, 128.266, 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 55 16.00 F 3 9.00 O 1502 8.00 N 1428 7.00 C 5215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 509.0 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 4.205A pdb=" N ILE F 24 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 57 removed outlier: 3.980A pdb=" N ARG F 55 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS F 57 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 77 removed outlier: 4.340A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.241A pdb=" N ILE F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 101 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 127 " --> pdb=" O TRP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.625A pdb=" N MET F 135 " --> pdb=" O TYR F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 161 removed outlier: 3.875A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 203 through 238 Processing helix chain 'F' and resid 265 through 298 removed outlier: 4.092A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL F 282 " --> pdb=" O MET F 278 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 removed outlier: 4.798A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.714A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.562A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.575A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.023A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.554A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 214 removed outlier: 9.237A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.685A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.756A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.969A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.694A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A 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: 6.839A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A 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: 6.441A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.883A 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: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.764A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1321 1.30 - 1.43: 2323 1.43 - 1.57: 4663 1.57 - 1.70: 0 1.70 - 1.83: 74 Bond restraints: 8381 Sorted by residual: bond pdb=" C19 86W F 502 " pdb=" C20 86W F 502 " ideal model delta sigma weight residual 1.359 1.479 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C24 86W F 502 " pdb=" N23 86W F 502 " ideal model delta sigma weight residual 1.372 1.465 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C24 86W F 502 " pdb=" N26 86W F 502 " ideal model delta sigma weight residual 1.380 1.467 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA SER F 191 " pdb=" C SER F 191 " ideal model delta sigma weight residual 1.524 1.478 0.045 1.26e-02 6.30e+03 1.28e+01 bond pdb=" CA CYS F 186 " pdb=" C CYS F 186 " ideal model delta sigma weight residual 1.530 1.493 0.036 1.10e-02 8.26e+03 1.10e+01 ... (remaining 8376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 11169 2.82 - 5.64: 170 5.64 - 8.46: 25 8.46 - 11.28: 2 11.28 - 14.10: 1 Bond angle restraints: 11367 Sorted by residual: angle pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta sigma weight residual 110.39 117.99 -7.60 1.66e+00 3.63e-01 2.09e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.94 112.86 9.08 2.00e+00 2.50e-01 2.06e+01 angle pdb=" N ILE F 125 " pdb=" CA ILE F 125 " pdb=" C ILE F 125 " ideal model delta sigma weight residual 113.53 109.20 4.33 9.80e-01 1.04e+00 1.95e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.07 128.37 -6.30 1.43e+00 4.89e-01 1.94e+01 angle pdb=" N ASN F 185 " pdb=" CA ASN F 185 " pdb=" C ASN F 185 " ideal model delta sigma weight residual 110.28 103.95 6.33 1.48e+00 4.57e-01 1.83e+01 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4461 17.96 - 35.91: 416 35.91 - 53.87: 90 53.87 - 71.82: 11 71.82 - 89.78: 9 Dihedral angle restraints: 4987 sinusoidal: 1969 harmonic: 3018 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CA PHE F 333 " pdb=" C PHE F 333 " pdb=" N ASN F 334 " pdb=" CA ASN F 334 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 974 0.055 - 0.111: 245 0.111 - 0.166: 40 0.166 - 0.221: 11 0.221 - 0.277: 5 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLU D 42 " pdb=" N GLU D 42 " pdb=" C GLU D 42 " pdb=" CB GLU D 42 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG B 8 " pdb=" N ARG B 8 " pdb=" C ARG B 8 " pdb=" CB ARG B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1272 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 157 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO F 158 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 169 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C TRP B 169 " 0.056 2.00e-02 2.50e+03 pdb=" O TRP B 169 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 170 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS A 28 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 28 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 29 " -0.015 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 42 2.47 - 3.08: 5614 3.08 - 3.68: 12517 3.68 - 4.29: 18628 4.29 - 4.90: 31003 Nonbonded interactions: 67804 Sorted by model distance: nonbonded pdb=" F16 86W F 502 " pdb=" O08 86W F 502 " model vdw 1.860 2.990 nonbonded pdb=" OG1 THR F 37 " pdb=" OG SER F 325 " model vdw 2.078 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.079 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.148 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.164 3.120 ... (remaining 67799 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=0.50 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 0.120 8384 Z= 0.272 Angle : 0.854 14.105 11373 Z= 0.475 Chirality : 0.053 0.277 1275 Planarity : 0.006 0.121 1440 Dihedral : 14.499 89.779 3020 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 0.68 % Favored : 98.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1021 helix: 0.60 (0.25), residues: 404 sheet: -0.57 (0.32), residues: 227 loop : -0.97 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 333 TYR 0.021 0.002 TYR A 253 PHE 0.032 0.002 PHE B 234 TRP 0.027 0.002 TRP A 281 HIS 0.010 0.002 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.27 ( 8381) covalent geometry : angle 0.85368 / 0.47 (11367) SS BOND : bond 0.00942 / 0.49 ( 3) SS BOND : angle 1.66133 / 1.09 ( 6) hydrogen bonds : bond 0.12703 / 8.19 ( 430) hydrogen bonds : angle 6.04787 / 4.55 ( 1223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8926 (tp) cc_final: 0.8718 (tp) REVERT: F 157 ILE cc_start: 0.8838 (mm) cc_final: 0.8562 (mt) REVERT: A 386 MET cc_start: 0.7482 (ttp) cc_final: 0.7060 (ttm) REVERT: D 51 LEU cc_start: 0.7813 (tp) cc_final: 0.7432 (tp) REVERT: E 78 THR cc_start: 0.7646 (t) cc_final: 0.7315 (p) REVERT: E 117 TYR cc_start: 0.8412 (m-80) cc_final: 0.8179 (m-80) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.0858 time to fit residues: 22.7709 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 23 ASN A 292 ASN A 294 GLN B 88 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.170094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135280 restraints weight = 33240.116| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 9.28 r_work: 0.3017 rms_B_bonded: 7.39 restraints_weight: 2.0000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8384 Z= 0.142 Angle : 0.578 8.089 11373 Z= 0.313 Chirality : 0.043 0.136 1275 Planarity : 0.005 0.079 1440 Dihedral : 5.120 38.839 1160 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1021 helix: 1.51 (0.25), residues: 409 sheet: 0.04 (0.32), residues: 220 loop : -0.67 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.012 0.001 TYR E 32 PHE 0.029 0.002 PHE F 141 TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8381) covalent geometry : angle 0.57770 / 0.31 (11367) SS BOND : bond 0.00304 / 0.15 ( 3) SS BOND : angle 1.09701 / 0.69 ( 6) hydrogen bonds : bond 0.04454 / 3.00 ( 430) hydrogen bonds : angle 4.66242 / 3.46 ( 1223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8748 (tp) cc_final: 0.8466 (tp) REVERT: A 307 LYS cc_start: 0.7043 (ptpp) cc_final: 0.6349 (pttp) REVERT: A 386 MET cc_start: 0.8684 (ttp) cc_final: 0.8483 (ttm) REVERT: B 44 GLN cc_start: 0.8058 (pm20) cc_final: 0.7825 (tm-30) REVERT: B 197 ARG cc_start: 0.7935 (mmp80) cc_final: 0.7605 (mmp80) REVERT: B 325 MET cc_start: 0.8507 (mmm) cc_final: 0.8236 (tpp) REVERT: B 333 ASP cc_start: 0.8748 (p0) cc_final: 0.8376 (p0) outliers start: 8 outliers final: 6 residues processed: 159 average time/residue: 0.0819 time to fit residues: 18.5276 Evaluate side-chains 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN B 266 HIS E 31 ASN E 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.168205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131925 restraints weight = 27746.273| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 8.06 r_work: 0.2993 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8384 Z= 0.143 Angle : 0.542 7.903 11373 Z= 0.292 Chirality : 0.042 0.132 1275 Planarity : 0.004 0.064 1440 Dihedral : 4.894 48.566 1160 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.50 % Allowed : 11.82 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1021 helix: 1.82 (0.25), residues: 416 sheet: 0.12 (0.31), residues: 225 loop : -0.43 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.013 0.001 TYR B 105 PHE 0.020 0.002 PHE F 29 TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8381) covalent geometry : angle 0.54216 / 0.29 (11367) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 0.96329 / 0.62 ( 6) hydrogen bonds : bond 0.04152 / 2.79 ( 430) hydrogen bonds : angle 4.31911 / 3.17 ( 1223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8713 (tp) cc_final: 0.8434 (tp) REVERT: F 278 MET cc_start: 0.7927 (mmm) cc_final: 0.7534 (tpp) REVERT: A 307 LYS cc_start: 0.7237 (ptpp) cc_final: 0.6555 (pttp) REVERT: A 386 MET cc_start: 0.8657 (ttp) cc_final: 0.8436 (ttm) REVERT: B 197 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7575 (mmp80) REVERT: B 253 PHE cc_start: 0.8837 (m-80) cc_final: 0.8576 (m-80) REVERT: E 123 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7971 (tm-30) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.0842 time to fit residues: 20.1458 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134602 restraints weight = 33803.785| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 8.56 r_work: 0.2987 rms_B_bonded: 7.08 restraints_weight: 2.0000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8384 Z= 0.118 Angle : 0.507 7.093 11373 Z= 0.273 Chirality : 0.041 0.129 1275 Planarity : 0.004 0.058 1440 Dihedral : 4.784 52.295 1160 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.05 % Allowed : 14.20 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1021 helix: 1.98 (0.25), residues: 422 sheet: 0.05 (0.31), residues: 229 loop : -0.33 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.013 0.001 TYR B 105 PHE 0.019 0.001 PHE F 264 TRP 0.014 0.001 TRP B 169 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8381) covalent geometry : angle 0.50721 / 0.27 (11367) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 0.83979 / 0.54 ( 6) hydrogen bonds : bond 0.03900 / 2.63 ( 430) hydrogen bonds : angle 4.19733 / 3.07 ( 1223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8699 (tp) cc_final: 0.8417 (tp) REVERT: F 278 MET cc_start: 0.7989 (mmm) cc_final: 0.7599 (tpp) REVERT: F 333 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: A 307 LYS cc_start: 0.7275 (ptpp) cc_final: 0.6632 (pttp) REVERT: A 386 MET cc_start: 0.8647 (ttp) cc_final: 0.8447 (ttm) REVERT: B 37 ILE cc_start: 0.8210 (tp) cc_final: 0.7468 (pt) REVERT: B 197 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7591 (mmp80) REVERT: B 253 PHE cc_start: 0.8841 (m-80) cc_final: 0.8602 (m-80) REVERT: D 48 ASP cc_start: 0.8634 (t0) cc_final: 0.8430 (t0) REVERT: E 31 ASN cc_start: 0.8253 (m-40) cc_final: 0.7956 (t0) REVERT: E 123 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7948 (tm-30) outliers start: 15 outliers final: 13 residues processed: 154 average time/residue: 0.0861 time to fit residues: 18.8065 Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133628 restraints weight = 24458.138| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 7.17 r_work: 0.3022 rms_B_bonded: 6.41 restraints_weight: 2.0000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8384 Z= 0.115 Angle : 0.495 6.663 11373 Z= 0.266 Chirality : 0.041 0.128 1275 Planarity : 0.004 0.053 1440 Dihedral : 4.700 52.034 1160 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.84 % Allowed : 15.00 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.26), residues: 1021 helix: 2.27 (0.25), residues: 411 sheet: 0.13 (0.31), residues: 229 loop : -0.24 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.011 0.001 TYR B 105 PHE 0.020 0.001 PHE F 29 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8381) covalent geometry : angle 0.49456 / 0.27 (11367) SS BOND : bond 0.00252 / 0.13 ( 3) SS BOND : angle 0.77962 / 0.51 ( 6) hydrogen bonds : bond 0.03788 / 2.55 ( 430) hydrogen bonds : angle 4.12710 / 3.01 ( 1223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8706 (tp) cc_final: 0.8419 (tp) REVERT: F 278 MET cc_start: 0.7965 (mmm) cc_final: 0.7575 (tpp) REVERT: F 333 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: A 307 LYS cc_start: 0.7284 (ptpp) cc_final: 0.6627 (pttp) REVERT: A 386 MET cc_start: 0.8628 (ttp) cc_final: 0.8417 (ttm) REVERT: B 197 ARG cc_start: 0.7877 (mmp80) cc_final: 0.7624 (mmp80) REVERT: B 253 PHE cc_start: 0.8785 (m-80) cc_final: 0.8470 (m-80) REVERT: B 325 MET cc_start: 0.8558 (tpp) cc_final: 0.8346 (tpp) REVERT: E 31 ASN cc_start: 0.8323 (m-40) cc_final: 0.8006 (t0) REVERT: E 60 TYR cc_start: 0.8740 (m-80) cc_final: 0.8426 (m-80) REVERT: E 123 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7893 (tm-30) outliers start: 22 outliers final: 14 residues processed: 159 average time/residue: 0.0838 time to fit residues: 18.8308 Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.169215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120248 restraints weight = 43254.076| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 5.35 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8384 Z= 0.115 Angle : 0.492 6.612 11373 Z= 0.265 Chirality : 0.041 0.154 1275 Planarity : 0.004 0.051 1440 Dihedral : 4.623 50.555 1160 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 16.02 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1021 helix: 2.32 (0.25), residues: 411 sheet: 0.31 (0.31), residues: 233 loop : -0.13 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.011 0.001 TYR F 214 PHE 0.019 0.001 PHE F 264 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8381) covalent geometry : angle 0.49169 / 0.26 (11367) SS BOND : bond 0.00427 / 0.21 ( 3) SS BOND : angle 0.88170 / 0.56 ( 6) hydrogen bonds : bond 0.03730 / 2.51 ( 430) hydrogen bonds : angle 4.07931 / 2.96 ( 1223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8800 (tp) cc_final: 0.8564 (tp) REVERT: F 278 MET cc_start: 0.7751 (mmm) cc_final: 0.7367 (tpp) REVERT: F 333 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: A 307 LYS cc_start: 0.7315 (ptpp) cc_final: 0.6680 (pttp) REVERT: A 386 MET cc_start: 0.7719 (ttp) cc_final: 0.7434 (ttm) REVERT: B 45 MET cc_start: 0.8181 (mtt) cc_final: 0.7815 (mtt) REVERT: B 197 ARG cc_start: 0.7704 (mmp80) cc_final: 0.7434 (mmp80) REVERT: B 325 MET cc_start: 0.8009 (tpp) cc_final: 0.7763 (tpp) REVERT: E 31 ASN cc_start: 0.8111 (m-40) cc_final: 0.7820 (t0) REVERT: E 60 TYR cc_start: 0.8613 (m-80) cc_final: 0.8309 (m-80) REVERT: E 123 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8043 (tm-30) outliers start: 21 outliers final: 19 residues processed: 152 average time/residue: 0.0864 time to fit residues: 18.6267 Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.168246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132852 restraints weight = 31026.791| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 8.74 r_work: 0.2997 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8384 Z= 0.123 Angle : 0.493 6.882 11373 Z= 0.265 Chirality : 0.041 0.144 1275 Planarity : 0.003 0.048 1440 Dihedral : 4.564 46.479 1160 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.30 % Allowed : 15.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.27), residues: 1021 helix: 2.35 (0.25), residues: 411 sheet: 0.34 (0.31), residues: 233 loop : -0.12 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.012 0.001 TYR E 95 PHE 0.021 0.001 PHE F 29 TRP 0.013 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8381) covalent geometry : angle 0.49241 / 0.26 (11367) SS BOND : bond 0.00267 / 0.13 ( 3) SS BOND : angle 0.80105 / 0.51 ( 6) hydrogen bonds : bond 0.03744 / 2.53 ( 430) hydrogen bonds : angle 4.08774 / 2.97 ( 1223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8765 (tp) cc_final: 0.8464 (tp) REVERT: F 278 MET cc_start: 0.7983 (mmm) cc_final: 0.7602 (tpp) REVERT: F 333 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7530 (m-10) REVERT: A 307 LYS cc_start: 0.7308 (ptpp) cc_final: 0.6744 (pttp) REVERT: A 386 MET cc_start: 0.8711 (ttp) cc_final: 0.8504 (ttm) REVERT: B 197 ARG cc_start: 0.7965 (mmp80) cc_final: 0.7621 (mmp80) REVERT: B 220 GLN cc_start: 0.7815 (mt0) cc_final: 0.7203 (mt0) REVERT: B 325 MET cc_start: 0.8705 (tpp) cc_final: 0.8471 (tpp) REVERT: E 31 ASN cc_start: 0.8362 (m-40) cc_final: 0.8134 (t0) REVERT: E 60 TYR cc_start: 0.8783 (m-80) cc_final: 0.8505 (m-80) REVERT: E 123 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7970 (tm-30) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.0921 time to fit residues: 19.3468 Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN A 294 GLN E 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.167240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131007 restraints weight = 26666.227| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 7.81 r_work: 0.3014 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8384 Z= 0.134 Angle : 0.503 6.912 11373 Z= 0.271 Chirality : 0.041 0.138 1275 Planarity : 0.004 0.047 1440 Dihedral : 4.603 43.950 1160 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 16.25 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1021 helix: 2.26 (0.25), residues: 417 sheet: 0.40 (0.32), residues: 223 loop : -0.05 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 67 TYR 0.012 0.001 TYR E 117 PHE 0.019 0.001 PHE F 264 TRP 0.014 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 8381) covalent geometry : angle 0.50288 / 0.27 (11367) SS BOND : bond 0.00293 / 0.15 ( 3) SS BOND : angle 0.86058 / 0.56 ( 6) hydrogen bonds : bond 0.03826 / 2.59 ( 430) hydrogen bonds : angle 4.15926 / 3.03 ( 1223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8710 (tp) cc_final: 0.8409 (tp) REVERT: F 278 MET cc_start: 0.8066 (mmm) cc_final: 0.7717 (tpp) REVERT: F 333 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7522 (m-10) REVERT: A 307 LYS cc_start: 0.7284 (ptpp) cc_final: 0.6686 (pttp) REVERT: A 386 MET cc_start: 0.8686 (ttp) cc_final: 0.8459 (ttm) REVERT: B 197 ARG cc_start: 0.7920 (mmp80) cc_final: 0.7639 (mmp80) REVERT: B 220 GLN cc_start: 0.7784 (mt0) cc_final: 0.7153 (mt0) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7558 (t80) REVERT: B 325 MET cc_start: 0.8678 (tpp) cc_final: 0.8371 (tpp) REVERT: E 31 ASN cc_start: 0.8314 (m-40) cc_final: 0.8070 (t0) REVERT: E 123 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7955 (tm-30) outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 0.0905 time to fit residues: 19.2647 Evaluate side-chains 151 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 0.0030 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117531 restraints weight = 33536.337| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.22 r_work: 0.3092 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8384 Z= 0.110 Angle : 0.489 6.867 11373 Z= 0.262 Chirality : 0.040 0.132 1275 Planarity : 0.003 0.046 1440 Dihedral : 4.486 44.150 1160 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.30 % Allowed : 16.02 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1021 helix: 2.37 (0.25), residues: 417 sheet: 0.41 (0.31), residues: 231 loop : -0.05 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.011 0.001 TYR E 117 PHE 0.028 0.001 PHE A 315 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8381) covalent geometry : angle 0.48917 / 0.26 (11367) SS BOND : bond 0.00244 / 0.12 ( 3) SS BOND : angle 0.82038 / 0.53 ( 6) hydrogen bonds : bond 0.03634 / 2.45 ( 430) hydrogen bonds : angle 4.07469 / 2.97 ( 1223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8716 (tp) cc_final: 0.8422 (tp) REVERT: F 333 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: A 307 LYS cc_start: 0.7326 (ptpp) cc_final: 0.6746 (pttp) REVERT: A 322 GLU cc_start: 0.8357 (mp0) cc_final: 0.8124 (mp0) REVERT: A 386 MET cc_start: 0.8573 (ttp) cc_final: 0.8329 (ttm) REVERT: B 45 MET cc_start: 0.8381 (mtt) cc_final: 0.8017 (mtt) REVERT: B 197 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7574 (mmp80) REVERT: B 220 GLN cc_start: 0.7736 (mt0) cc_final: 0.7067 (mt0) REVERT: B 234 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7554 (t80) REVERT: B 325 MET cc_start: 0.8549 (tpp) cc_final: 0.8237 (tpp) REVERT: E 31 ASN cc_start: 0.8251 (m-40) cc_final: 0.8032 (t0) REVERT: E 60 TYR cc_start: 0.8716 (m-80) cc_final: 0.8427 (m-80) outliers start: 26 outliers final: 18 residues processed: 153 average time/residue: 0.0841 time to fit residues: 18.1944 Evaluate side-chains 154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 99 optimal weight: 0.4980 chunk 60 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 0.0270 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123082 restraints weight = 36974.990| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 5.40 r_work: 0.3102 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8384 Z= 0.108 Angle : 0.494 7.905 11373 Z= 0.263 Chirality : 0.041 0.133 1275 Planarity : 0.003 0.046 1440 Dihedral : 4.433 43.373 1160 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.61 % Allowed : 16.93 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1021 helix: 2.42 (0.25), residues: 411 sheet: 0.45 (0.32), residues: 231 loop : -0.10 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.010 0.001 TYR E 117 PHE 0.028 0.001 PHE A 315 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8381) covalent geometry : angle 0.49417 / 0.26 (11367) SS BOND : bond 0.00240 / 0.12 ( 3) SS BOND : angle 0.79100 / 0.52 ( 6) hydrogen bonds : bond 0.03600 / 2.42 ( 430) hydrogen bonds : angle 4.04073 / 2.95 ( 1223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8742 (tp) cc_final: 0.8442 (tp) REVERT: F 333 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: A 307 LYS cc_start: 0.7399 (ptpp) cc_final: 0.6811 (pttp) REVERT: A 386 MET cc_start: 0.8592 (ttp) cc_final: 0.8352 (ttm) REVERT: B 17 GLN cc_start: 0.5389 (tt0) cc_final: 0.5134 (pt0) REVERT: B 45 MET cc_start: 0.8337 (mtt) cc_final: 0.8007 (mtt) REVERT: B 197 ARG cc_start: 0.7846 (mmp80) cc_final: 0.7592 (mmp80) REVERT: B 220 GLN cc_start: 0.7794 (mt0) cc_final: 0.7153 (mt0) REVERT: B 234 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7568 (t80) REVERT: B 325 MET cc_start: 0.8574 (tpp) cc_final: 0.8278 (tpp) REVERT: E 60 TYR cc_start: 0.8713 (m-80) cc_final: 0.8422 (m-80) REVERT: E 123 GLN cc_start: 0.8275 (tp-100) cc_final: 0.8002 (tm-30) outliers start: 20 outliers final: 18 residues processed: 150 average time/residue: 0.0898 time to fit residues: 18.6670 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131804 restraints weight = 31601.393| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 8.33 r_work: 0.3008 rms_B_bonded: 6.72 restraints_weight: 2.0000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8384 Z= 0.114 Angle : 0.496 7.173 11373 Z= 0.264 Chirality : 0.041 0.128 1275 Planarity : 0.003 0.046 1440 Dihedral : 4.406 40.902 1160 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.84 % Allowed : 16.93 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1021 helix: 2.43 (0.25), residues: 411 sheet: 0.48 (0.32), residues: 231 loop : -0.07 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.010 0.001 TYR E 117 PHE 0.027 0.002 PHE A 315 TRP 0.012 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 8381) covalent geometry : angle 0.49576 / 0.26 (11367) SS BOND : bond 0.00246 / 0.12 ( 3) SS BOND : angle 0.83815 / 0.55 ( 6) hydrogen bonds : bond 0.03619 / 2.44 ( 430) hydrogen bonds : angle 4.02926 / 2.94 ( 1223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.73 seconds wall clock time: 38 minutes 17.28 seconds (2297.28 seconds total)