Starting phenix.real_space_refine on Wed Feb 4 07:41:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kfi_62297/02_2026/9kfi_62297.map" } resolution = 2.91 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5912 2.51 5 N 1594 2.21 5 O 1715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9293 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2435 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1757 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 174 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 131 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9293 At special positions: 0 Unit cell: (95.319, 117.81, 137.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1715 8.00 N 1594 7.00 C 5912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS A 24 " distance=2.04 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 370.3 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 79 through 107 Processing helix chain 'C' and resid 115 through 134 removed outlier: 3.714A pdb=" N LEU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 144 removed outlier: 3.854A pdb=" N TRP C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 186 Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.850A pdb=" N ALA C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 297 removed outlier: 3.698A pdb=" N LYS C 271 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Proline residue: C 279 - end of helix Processing helix chain 'C' and resid 317 through 353 removed outlier: 3.626A pdb=" N LYS C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 363 through 390 removed outlier: 4.792A pdb=" N PHE C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Proline residue: C 372 - end of helix removed outlier: 4.253A pdb=" N SER C 382 " --> pdb=" O ALA C 378 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS C 383 " --> pdb=" O HIS C 379 " (cutoff:3.500A) Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 393 through 408 removed outlier: 4.130A pdb=" N ALA C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.938A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'I' and resid 6 through 32 removed outlier: 4.169A pdb=" N ARG I 32 " --> pdb=" O GLU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.825A pdb=" N MET I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 211 Processing helix chain 'I' and resid 212 through 217 removed outlier: 4.020A pdb=" N PHE I 216 " --> pdb=" O TRP I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 256 Processing helix chain 'I' and resid 271 through 282 removed outlier: 3.913A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 removed outlier: 3.732A pdb=" N ILE I 286 " --> pdb=" O PRO I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 331 through 353 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.856A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'T' and resid 4 through 25 Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 35 through 37 No H-bonds generated for 'chain 'T' and resid 35 through 37' Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'A' and resid 2 through 11 Processing sheet with id=AA1, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.704A pdb=" N VAL C 239 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 186 through 188 removed outlier: 6.517A pdb=" N VAL I 34 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE I 200 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU I 36 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE I 265 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.507A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'T' and resid 46 through 51 removed outlier: 6.464A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 58 through 63 removed outlier: 3.546A pdb=" N ALA T 60 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP T 83 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS T 89 " --> pdb=" O ASP T 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 100 through 105 removed outlier: 6.878A pdb=" N GLY T 115 " --> pdb=" O MET T 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS T 103 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA T 113 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR T 105 " --> pdb=" O TYR T 111 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR T 111 " --> pdb=" O TYR T 105 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG T 134 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 146 through 151 removed outlier: 3.602A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 191 through 192 removed outlier: 3.522A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP T 212 " --> pdb=" O CYS T 218 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS T 218 " --> pdb=" O ASP T 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 231 through 234 removed outlier: 6.454A pdb=" N CYS T 250 " --> pdb=" O THR T 263 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR T 263 " --> pdb=" O CYS T 250 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU T 252 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN T 259 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 273 through 278 removed outlier: 3.614A pdb=" N CYS T 294 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY T 306 " --> pdb=" O VAL T 296 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP T 298 " --> pdb=" O ARG T 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG T 304 " --> pdb=" O ASP T 298 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1218 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: 1.33 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1600 1.32 - 1.45: 2570 1.45 - 1.57: 5212 1.57 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9483 Sorted by residual: bond pdb=" CA GLY T 244 " pdb=" C GLY T 244 " ideal model delta sigma weight residual 1.519 1.502 0.016 7.00e-03 2.04e+04 5.52e+00 bond pdb=" N LEU C 144 " pdb=" CA LEU C 144 " ideal model delta sigma weight residual 1.464 1.441 0.023 1.20e-02 6.94e+03 3.70e+00 bond pdb=" C LEU C 144 " pdb=" O LEU C 144 " ideal model delta sigma weight residual 1.231 1.199 0.032 1.71e-02 3.42e+03 3.46e+00 bond pdb=" CB VAL C 170 " pdb=" CG1 VAL C 170 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CA ALA T 242 " pdb=" C ALA T 242 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.20e-02 6.94e+03 3.10e+00 ... (remaining 9478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 12416 1.73 - 3.47: 340 3.47 - 5.20: 52 5.20 - 6.93: 21 6.93 - 8.67: 4 Bond angle restraints: 12833 Sorted by residual: angle pdb=" N HIS I 245 " pdb=" CA HIS I 245 " pdb=" C HIS I 245 " ideal model delta sigma weight residual 113.55 107.73 5.82 1.26e+00 6.30e-01 2.13e+01 angle pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta sigma weight residual 121.74 114.93 6.81 1.58e+00 4.01e-01 1.86e+01 angle pdb=" N LEU C 144 " pdb=" CA LEU C 144 " pdb=" C LEU C 144 " ideal model delta sigma weight residual 111.55 106.51 5.04 1.37e+00 5.33e-01 1.35e+01 angle pdb=" CA PHE C 354 " pdb=" C PHE C 354 " pdb=" N ASN C 355 " ideal model delta sigma weight residual 115.75 120.16 -4.41 1.34e+00 5.57e-01 1.08e+01 angle pdb=" N ASP T 246 " pdb=" CA ASP T 246 " pdb=" C ASP T 246 " ideal model delta sigma weight residual 113.61 108.76 4.85 1.50e+00 4.44e-01 1.04e+01 ... (remaining 12828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 5032 16.66 - 33.32: 488 33.32 - 49.98: 90 49.98 - 66.65: 13 66.65 - 83.31: 11 Dihedral angle restraints: 5634 sinusoidal: 2176 harmonic: 3458 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS A 24 " pdb=" CB CYS A 24 " ideal model delta sinusoidal sigma weight residual -86.00 -8.50 -77.50 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS C 155 " pdb=" SG CYS C 155 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual 93.00 170.39 -77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS A 11 " pdb=" CB CYS A 11 " ideal model delta sinusoidal sigma weight residual -86.00 -141.99 55.99 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 5631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 998 0.043 - 0.085: 343 0.085 - 0.128: 98 0.128 - 0.170: 17 0.170 - 0.213: 2 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CG LEU C 248 " pdb=" CB LEU C 248 " pdb=" CD1 LEU C 248 " pdb=" CD2 LEU C 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE S 51 " pdb=" CA ILE S 51 " pdb=" CG1 ILE S 51 " pdb=" CG2 ILE S 51 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA PRO S 181 " pdb=" N PRO S 181 " pdb=" C PRO S 181 " pdb=" CB PRO S 181 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1455 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 309 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" CD GLU I 309 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU I 309 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU I 309 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE T 235 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO T 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO T 236 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO T 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 167 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C TYR C 167 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR C 167 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 168 " -0.011 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 121 2.64 - 3.20: 8363 3.20 - 3.77: 14578 3.77 - 4.33: 20446 4.33 - 4.90: 33945 Nonbonded interactions: 77453 Sorted by model distance: nonbonded pdb=" OG SER T 161 " pdb=" OD1 ASP T 163 " model vdw 2.071 3.040 nonbonded pdb=" O CYS I 255 " pdb=" NZ LYS I 318 " model vdw 2.200 3.120 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.207 3.040 nonbonded pdb=" O LEU C 119 " pdb=" OG1 THR C 122 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR T 274 " pdb=" O VAL T 315 " model vdw 2.222 3.040 ... (remaining 77448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 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 : 0.006 0.059 9488 Z= 0.245 Angle : 0.726 8.665 12843 Z= 0.406 Chirality : 0.047 0.213 1458 Planarity : 0.004 0.057 1615 Dihedral : 13.669 83.308 3381 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 0.40 % Allowed : 0.60 % Favored : 99.00 % 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: -0.66 (0.25), residues: 1171 helix: 0.64 (0.26), residues: 399 sheet: -0.11 (0.32), residues: 285 loop : -1.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 32 TYR 0.028 0.002 TYR S 190 PHE 0.020 0.002 PHE C 129 TRP 0.013 0.002 TRP T 211 HIS 0.005 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 9483) covalent geometry : angle 0.72342 (12833) SS BOND : bond 0.00392 ( 5) SS BOND : angle 2.46062 ( 10) hydrogen bonds : bond 0.15103 ( 433) hydrogen bonds : angle 6.44458 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8295 (mm) cc_final: 0.8045 (mm) REVERT: C 406 ARG cc_start: -0.1004 (OUTLIER) cc_final: -0.2054 (mmm160) REVERT: T 47 THR cc_start: 0.7691 (t) cc_final: 0.7424 (m) outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 0.5151 time to fit residues: 94.4483 Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 406 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN T 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.149865 restraints weight = 12618.464| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.15 r_work: 0.3698 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9488 Z= 0.143 Angle : 0.596 7.407 12843 Z= 0.310 Chirality : 0.043 0.198 1458 Planarity : 0.004 0.055 1615 Dihedral : 4.688 30.132 1292 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.90 % Allowed : 9.35 % Favored : 89.75 % 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: -0.31 (0.25), residues: 1171 helix: 1.11 (0.26), residues: 399 sheet: 0.00 (0.32), residues: 275 loop : -1.42 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 32 TYR 0.024 0.001 TYR S 190 PHE 0.022 0.002 PHE C 293 TRP 0.017 0.001 TRP T 82 HIS 0.003 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9483) covalent geometry : angle 0.59515 (12833) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.47370 ( 10) hydrogen bonds : bond 0.04214 ( 433) hydrogen bonds : angle 4.97451 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 MET cc_start: 0.7486 (tpt) cc_final: 0.7243 (tpp) REVERT: C 224 LEU cc_start: 0.8433 (mm) cc_final: 0.8167 (mt) REVERT: I 309 GLU cc_start: 0.7967 (mp0) cc_final: 0.7726 (mp0) REVERT: T 87 THR cc_start: 0.8274 (p) cc_final: 0.8045 (m) REVERT: T 273 ILE cc_start: 0.8409 (mp) cc_final: 0.8153 (mt) REVERT: T 303 ASP cc_start: 0.7553 (m-30) cc_final: 0.7279 (m-30) outliers start: 9 outliers final: 6 residues processed: 167 average time/residue: 0.4764 time to fit residues: 85.7924 Evaluate side-chains 169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 243 THR Chi-restraints excluded: chain T residue 304 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 1.9990 chunk 103 optimal weight: 0.0030 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.178266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.150321 restraints weight = 12620.850| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.17 r_work: 0.3703 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9488 Z= 0.133 Angle : 0.551 6.443 12843 Z= 0.288 Chirality : 0.042 0.150 1458 Planarity : 0.004 0.052 1615 Dihedral : 4.369 17.764 1288 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.69 % Allowed : 12.04 % Favored : 86.27 % 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: -0.15 (0.25), residues: 1171 helix: 1.37 (0.26), residues: 398 sheet: 0.03 (0.32), residues: 265 loop : -1.37 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 219 TYR 0.023 0.001 TYR S 190 PHE 0.018 0.001 PHE C 171 TRP 0.017 0.001 TRP T 82 HIS 0.002 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9483) covalent geometry : angle 0.55041 (12833) SS BOND : bond 0.00213 ( 5) SS BOND : angle 1.06678 ( 10) hydrogen bonds : bond 0.03922 ( 433) hydrogen bonds : angle 4.69937 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8397 (mm) cc_final: 0.8107 (mt) REVERT: C 285 LEU cc_start: 0.7567 (tt) cc_final: 0.7312 (tp) REVERT: I 354 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7769 (mt) REVERT: T 87 THR cc_start: 0.8227 (p) cc_final: 0.7949 (m) REVERT: T 273 ILE cc_start: 0.8388 (mp) cc_final: 0.8138 (mt) REVERT: T 303 ASP cc_start: 0.7483 (m-30) cc_final: 0.7208 (m-30) outliers start: 17 outliers final: 9 residues processed: 162 average time/residue: 0.5074 time to fit residues: 88.8300 Evaluate side-chains 165 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 217 GLU Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 102 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN ** T 119 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 = 0.4196 r_free = 0.4196 target = 0.177668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149635 restraints weight = 12581.786| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.18 r_work: 0.3697 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9488 Z= 0.148 Angle : 0.549 6.300 12843 Z= 0.289 Chirality : 0.042 0.153 1458 Planarity : 0.004 0.052 1615 Dihedral : 4.320 16.376 1288 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.89 % Allowed : 14.53 % Favored : 83.58 % 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: -0.12 (0.25), residues: 1171 helix: 1.39 (0.26), residues: 394 sheet: 0.00 (0.31), residues: 273 loop : -1.31 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 219 TYR 0.023 0.001 TYR S 190 PHE 0.023 0.002 PHE C 293 TRP 0.016 0.001 TRP T 82 HIS 0.004 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9483) covalent geometry : angle 0.54890 (12833) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.91154 ( 10) hydrogen bonds : bond 0.03884 ( 433) hydrogen bonds : angle 4.62613 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8382 (mm) cc_final: 0.8088 (mt) REVERT: C 285 LEU cc_start: 0.7527 (tt) cc_final: 0.7272 (tp) REVERT: I 309 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: S 140 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6851 (mmm) REVERT: T 217 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7428 (pmm) REVERT: T 223 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8107 (m) REVERT: T 273 ILE cc_start: 0.8452 (mp) cc_final: 0.8236 (mt) REVERT: T 303 ASP cc_start: 0.7475 (m-30) cc_final: 0.7194 (m-30) outliers start: 19 outliers final: 12 residues processed: 167 average time/residue: 0.4688 time to fit residues: 84.8241 Evaluate side-chains 172 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 13 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149748 restraints weight = 12607.958| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.14 r_work: 0.3704 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9488 Z= 0.131 Angle : 0.532 6.944 12843 Z= 0.280 Chirality : 0.042 0.152 1458 Planarity : 0.004 0.051 1615 Dihedral : 4.224 17.097 1288 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.09 % Allowed : 16.42 % Favored : 81.49 % 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: -0.02 (0.25), residues: 1171 helix: 1.46 (0.26), residues: 394 sheet: 0.07 (0.32), residues: 273 loop : -1.25 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 219 TYR 0.021 0.001 TYR S 190 PHE 0.012 0.001 PHE T 199 TRP 0.015 0.001 TRP T 82 HIS 0.003 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9483) covalent geometry : angle 0.53126 (12833) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.84106 ( 10) hydrogen bonds : bond 0.03671 ( 433) hydrogen bonds : angle 4.54970 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8345 (mm) cc_final: 0.8050 (mt) REVERT: C 241 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7611 (p) REVERT: C 285 LEU cc_start: 0.7535 (tt) cc_final: 0.7300 (tp) REVERT: I 35 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8095 (mtmm) REVERT: I 309 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: S 140 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.6797 (mmm) REVERT: T 155 ASN cc_start: 0.8217 (t0) cc_final: 0.7935 (t0) REVERT: T 217 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7386 (pmm) REVERT: T 273 ILE cc_start: 0.8431 (mp) cc_final: 0.8214 (mt) REVERT: T 303 ASP cc_start: 0.7532 (m-30) cc_final: 0.7214 (m-30) REVERT: T 336 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7941 (mt) outliers start: 21 outliers final: 14 residues processed: 170 average time/residue: 0.4421 time to fit residues: 81.8208 Evaluate side-chains 179 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.175123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146779 restraints weight = 12686.713| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.17 r_work: 0.3653 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9488 Z= 0.278 Angle : 0.644 10.457 12843 Z= 0.339 Chirality : 0.047 0.174 1458 Planarity : 0.005 0.053 1615 Dihedral : 4.583 17.561 1288 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.18 % Allowed : 16.22 % Favored : 80.60 % 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: -0.29 (0.25), residues: 1171 helix: 0.99 (0.26), residues: 401 sheet: -0.10 (0.31), residues: 276 loop : -1.20 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 219 TYR 0.028 0.002 TYR S 190 PHE 0.023 0.002 PHE C 293 TRP 0.017 0.002 TRP T 211 HIS 0.009 0.002 HIS T 54 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 9483) covalent geometry : angle 0.64301 (12833) SS BOND : bond 0.00727 ( 5) SS BOND : angle 1.26912 ( 10) hydrogen bonds : bond 0.04579 ( 433) hydrogen bonds : angle 4.86397 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.352 Fit side-chains REVERT: C 224 LEU cc_start: 0.8429 (mm) cc_final: 0.8120 (mt) REVERT: C 241 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7764 (p) REVERT: C 259 ASP cc_start: 0.5261 (OUTLIER) cc_final: 0.4617 (m-30) REVERT: C 285 LEU cc_start: 0.7327 (tt) cc_final: 0.7086 (tp) REVERT: I 35 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8030 (mtmm) REVERT: I 309 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: S 140 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.6834 (mmm) REVERT: T 18 ILE cc_start: 0.7420 (mm) cc_final: 0.7138 (mt) REVERT: T 155 ASN cc_start: 0.8316 (t0) cc_final: 0.7994 (t0) REVERT: T 217 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7436 (pmm) REVERT: T 223 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (m) REVERT: T 277 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7974 (t) REVERT: T 303 ASP cc_start: 0.7549 (m-30) cc_final: 0.7267 (m-30) REVERT: T 336 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8017 (mt) outliers start: 32 outliers final: 16 residues processed: 177 average time/residue: 0.4509 time to fit residues: 86.7640 Evaluate side-chains 183 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 277 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 0.0000 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 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 = 0.4187 r_free = 0.4187 target = 0.177058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149059 restraints weight = 12709.154| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.16 r_work: 0.3682 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9488 Z= 0.148 Angle : 0.558 9.598 12843 Z= 0.293 Chirality : 0.042 0.156 1458 Planarity : 0.004 0.053 1615 Dihedral : 4.341 17.223 1288 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.58 % Allowed : 17.41 % Favored : 79.00 % 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: -0.16 (0.25), residues: 1171 helix: 1.30 (0.26), residues: 394 sheet: 0.01 (0.32), residues: 271 loop : -1.31 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 219 TYR 0.023 0.001 TYR S 190 PHE 0.014 0.001 PHE T 199 TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS T 62 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9483) covalent geometry : angle 0.55763 (12833) SS BOND : bond 0.00344 ( 5) SS BOND : angle 1.23682 ( 10) hydrogen bonds : bond 0.03830 ( 433) hydrogen bonds : angle 4.62360 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8351 (mm) cc_final: 0.8050 (mt) REVERT: C 241 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 259 ASP cc_start: 0.4974 (OUTLIER) cc_final: 0.4319 (m-30) REVERT: C 285 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7104 (tp) REVERT: I 35 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8106 (mtmm) REVERT: I 309 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: S 140 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6830 (mmm) REVERT: T 217 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7436 (pmm) REVERT: T 223 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8194 (m) REVERT: T 277 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (t) REVERT: T 303 ASP cc_start: 0.7528 (m-30) cc_final: 0.7237 (m-30) REVERT: T 336 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 36 outliers final: 18 residues processed: 180 average time/residue: 0.4472 time to fit residues: 87.8844 Evaluate side-chains 186 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 277 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain A residue 24 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.176299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148418 restraints weight = 12584.926| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.16 r_work: 0.3674 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9488 Z= 0.183 Angle : 0.588 8.847 12843 Z= 0.307 Chirality : 0.043 0.151 1458 Planarity : 0.004 0.053 1615 Dihedral : 4.401 17.956 1288 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.78 % Allowed : 17.71 % Favored : 78.51 % 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: -0.20 (0.25), residues: 1171 helix: 1.18 (0.26), residues: 401 sheet: -0.07 (0.31), residues: 273 loop : -1.24 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 219 TYR 0.025 0.002 TYR S 190 PHE 0.026 0.002 PHE C 293 TRP 0.015 0.002 TRP T 82 HIS 0.005 0.001 HIS T 54 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9483) covalent geometry : angle 0.58712 (12833) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.38533 ( 10) hydrogen bonds : bond 0.04022 ( 433) hydrogen bonds : angle 4.65236 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8366 (mm) cc_final: 0.8059 (mt) REVERT: C 259 ASP cc_start: 0.5060 (OUTLIER) cc_final: 0.4437 (m-30) REVERT: C 285 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7204 (tp) REVERT: I 35 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8156 (mtmm) REVERT: I 309 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: S 140 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.6826 (mmm) REVERT: T 155 ASN cc_start: 0.8253 (t0) cc_final: 0.7983 (t0) REVERT: T 217 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7411 (pmm) REVERT: T 223 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8229 (m) REVERT: T 277 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7992 (t) REVERT: T 303 ASP cc_start: 0.7523 (m-30) cc_final: 0.7229 (m-30) REVERT: T 336 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8000 (mt) outliers start: 38 outliers final: 24 residues processed: 181 average time/residue: 0.4423 time to fit residues: 87.2983 Evaluate side-chains 187 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 274 THR Chi-restraints excluded: chain T residue 277 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain A residue 24 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 98 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.177528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.149501 restraints weight = 12639.010| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.17 r_work: 0.3689 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9488 Z= 0.141 Angle : 0.554 8.516 12843 Z= 0.290 Chirality : 0.042 0.154 1458 Planarity : 0.004 0.052 1615 Dihedral : 4.276 18.315 1288 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.38 % Allowed : 18.21 % Favored : 78.41 % 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: -0.10 (0.25), residues: 1171 helix: 1.37 (0.26), residues: 395 sheet: 0.01 (0.32), residues: 271 loop : -1.26 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 219 TYR 0.022 0.001 TYR S 190 PHE 0.014 0.001 PHE T 199 TRP 0.016 0.001 TRP T 82 HIS 0.003 0.001 HIS T 54 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9483) covalent geometry : angle 0.55314 (12833) SS BOND : bond 0.00270 ( 5) SS BOND : angle 1.30515 ( 10) hydrogen bonds : bond 0.03742 ( 433) hydrogen bonds : angle 4.54359 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8332 (mm) cc_final: 0.8029 (mt) REVERT: C 259 ASP cc_start: 0.4939 (OUTLIER) cc_final: 0.4314 (m-30) REVERT: C 285 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7186 (tp) REVERT: I 35 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8131 (mtmm) REVERT: I 309 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: I 318 LYS cc_start: 0.7170 (ttpt) cc_final: 0.6115 (ttpp) REVERT: T 155 ASN cc_start: 0.8231 (t0) cc_final: 0.7989 (t0) REVERT: T 217 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7398 (pmm) REVERT: T 223 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8223 (m) REVERT: T 277 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7966 (t) REVERT: T 336 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7978 (mt) outliers start: 34 outliers final: 21 residues processed: 177 average time/residue: 0.4672 time to fit residues: 90.0162 Evaluate side-chains 183 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 277 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain A residue 24 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148523 restraints weight = 12641.886| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.18 r_work: 0.3678 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9488 Z= 0.185 Angle : 0.588 8.478 12843 Z= 0.308 Chirality : 0.044 0.152 1458 Planarity : 0.004 0.054 1615 Dihedral : 4.373 18.971 1288 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 18.71 % Favored : 78.51 % 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: -0.21 (0.25), residues: 1171 helix: 1.13 (0.26), residues: 406 sheet: -0.08 (0.32), residues: 272 loop : -1.23 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 219 TYR 0.025 0.002 TYR S 190 PHE 0.026 0.002 PHE C 293 TRP 0.021 0.002 TRP C 148 HIS 0.006 0.001 HIS T 54 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9483) covalent geometry : angle 0.58712 (12833) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.37493 ( 10) hydrogen bonds : bond 0.04010 ( 433) hydrogen bonds : angle 4.63783 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: C 224 LEU cc_start: 0.8356 (mm) cc_final: 0.8047 (mt) REVERT: C 259 ASP cc_start: 0.5026 (OUTLIER) cc_final: 0.4396 (m-30) REVERT: C 285 LEU cc_start: 0.7440 (tt) cc_final: 0.7208 (tp) REVERT: I 35 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8132 (mtmm) REVERT: I 309 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: T 155 ASN cc_start: 0.8246 (t0) cc_final: 0.7973 (t0) REVERT: T 217 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7400 (pmm) REVERT: T 223 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8242 (m) REVERT: T 277 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7992 (t) REVERT: T 336 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7994 (mt) outliers start: 28 outliers final: 22 residues processed: 174 average time/residue: 0.4810 time to fit residues: 91.2702 Evaluate side-chains 184 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 188 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 47 THR Chi-restraints excluded: chain T residue 61 MET Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain T residue 217 MET Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 277 SER Chi-restraints excluded: chain T residue 304 ARG Chi-restraints excluded: chain T residue 327 VAL Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain A residue 24 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 GLN ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149571 restraints weight = 12482.239| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.14 r_work: 0.3682 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9488 Z= 0.144 Angle : 0.565 8.114 12843 Z= 0.295 Chirality : 0.042 0.154 1458 Planarity : 0.004 0.055 1615 Dihedral : 4.279 19.717 1288 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 18.71 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.25), residues: 1171 helix: 1.31 (0.26), residues: 400 sheet: -0.00 (0.32), residues: 271 loop : -1.24 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 219 TYR 0.022 0.001 TYR S 190 PHE 0.014 0.001 PHE T 199 TRP 0.018 0.001 TRP C 148 HIS 0.004 0.001 HIS I 189 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9483) covalent geometry : angle 0.56435 (12833) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.31405 ( 10) hydrogen bonds : bond 0.03725 ( 433) hydrogen bonds : angle 4.55124 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.04 seconds wall clock time: 63 minutes 24.12 seconds (3804.12 seconds total)