Starting phenix.real_space_refine on Wed Aug 5 21:18:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hmy_34904/08_2026/8hmy_34904.cif" } resolution = 2.94 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= 0.009 sd= 0.144 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: 6 Type Number sf(0) Gaussians P 90 5.49 5 Mg 6 5.21 5 S 31 5.16 5 C 7001 2.51 5 N 2105 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11675 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2608 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 2 Chain: "B" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2057 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain breaks: 1 Chain: "T" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1888 Classifications: {'RNAv2': 90} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 17, 'rna3p': 72} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {' U%rna2p_pyr:plan': 1, ' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 1, ' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2263 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 18, 'TRANS': 266} Chain breaks: 1 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1869 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 361} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1202 Unresolved non-hydrogen angles: 1543 Unresolved non-hydrogen dihedrals: 992 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'PHE:plan': 21, 'GLU:plan': 28, 'ARG:plan': 30, 'GLN:plan1': 11, 'ASN:plan1': 11, 'ASP:plan': 15, 'TRP:plan': 2, 'HIS:plan': 9, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 664 Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11675 At special positions: 0 Unit cell: (128.266, 119.57, 152.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 90 15.00 Mg 6 11.99 O 2442 8.00 N 2105 7.00 C 7001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 505.8 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 35.3% alpha, 20.2% beta 26 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 100 through 118 removed outlier: 4.383A pdb=" N ALA A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A 114 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.898A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.676A pdb=" N LEU A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.719A pdb=" N THR A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 401 through 414 removed outlier: 3.930A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.922A pdb=" N VAL B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 79 through 112 removed outlier: 3.523A pdb=" N GLN B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 214 through 230 Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'C' and resid 19 through 28 removed outlier: 3.588A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 66 removed outlier: 3.531A pdb=" N LEU C 62 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.615A pdb=" N GLN C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 101 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.531A pdb=" N LEU C 145 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.582A pdb=" N TYR C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.883A pdb=" N VAL C 176 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.642A pdb=" N GLU C 441 " --> pdb=" O ARG C 438 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS C 442 " --> pdb=" O LEU C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.535A pdb=" N ALA C 459 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 496 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 56 through 72 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'E' and resid 89 through 110 Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 192 through 195 Processing helix chain 'E' and resid 196 through 218 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 236 through 249 Processing helix chain 'E' and resid 259 through 270 Processing helix chain 'E' and resid 289 through 307 Processing helix chain 'E' and resid 308 through 311 removed outlier: 3.642A pdb=" N CYS E 311 " --> pdb=" O PHE E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 308 through 311' Processing helix chain 'E' and resid 322 through 324 No H-bonds generated for 'chain 'E' and resid 322 through 324' Processing helix chain 'E' and resid 358 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 4.162A pdb=" N VAL A 49 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.822A pdb=" N VAL A 260 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.486A pdb=" N LEU A 366 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 381 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 368 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 379 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N MET A 419 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER A 381 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 421 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 383 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 423 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A 385 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS A 425 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 387 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 418 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 451 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 512 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE C 515 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU C 500 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 505 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 471 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP C 451 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C 473 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.338A pdb=" N SER B 11 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 5 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 2 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL B 69 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 4 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 184 through 187 removed outlier: 4.176A pdb=" N ARG C 70 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 195 through 197 removed outlier: 3.773A pdb=" N VAL B 195 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 236 removed outlier: 3.765A pdb=" N TYR B 258 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE B 259 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS B 291 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 261 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 288 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 303 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR D 104 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 142 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE D 90 " --> pdb=" O PRO D 107 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 95 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU D 78 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.620A pdb=" N ILE B 269 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 114 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.570A pdb=" N VAL C 78 " --> pdb=" O HIS C 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 17 removed outlier: 6.409A pdb=" N SER E 72 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.576A pdb=" N THR E 21 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 81 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.458A pdb=" N THR E 146 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASN E 229 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 148 " --> pdb=" O ASN E 229 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 117 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG E 116 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL E 255 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 118 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU E 257 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL E 120 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 315 through 320 removed outlier: 3.559A pdb=" N SER E 391 " --> pdb=" O THR E 400 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU E 402 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL E 389 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY E 385 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS E 364 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 365 " --> pdb=" O MET E 417 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS E 325 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE E 416 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR E 327 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASP E 418 " --> pdb=" O TYR E 327 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1749 1.29 - 1.42: 3556 1.42 - 1.55: 6534 1.55 - 1.68: 182 1.68 - 1.81: 50 Bond restraints: 12071 Sorted by residual: bond pdb=" CG ASP C 523 " pdb=" OD1 ASP C 523 " ideal model delta sigma weight residual 1.249 1.166 0.083 1.90e-02 2.77e+03 1.89e+01 bond pdb=" C VAL C 524 " pdb=" O VAL C 524 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.19e-02 7.06e+03 1.76e+01 bond pdb=" N PRO C 411 " pdb=" CD PRO C 411 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N GLU A 17 " pdb=" CA GLU A 17 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" C ASP C 523 " pdb=" O ASP C 523 " ideal model delta sigma weight residual 1.236 1.205 0.031 9.90e-03 1.02e+04 9.62e+00 ... (remaining 12066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 16225 2.48 - 4.96: 580 4.96 - 7.45: 25 7.45 - 9.93: 6 9.93 - 12.41: 2 Bond angle restraints: 16838 Sorted by residual: angle pdb=" CA PRO C 411 " pdb=" N PRO C 411 " pdb=" CD PRO C 411 " ideal model delta sigma weight residual 112.00 99.59 12.41 1.40e+00 5.10e-01 7.86e+01 angle pdb=" CA THR A 18 " pdb=" CB THR A 18 " pdb=" OG1 THR A 18 " ideal model delta sigma weight residual 109.60 99.47 10.13 1.50e+00 4.44e-01 4.56e+01 angle pdb=" N VAL C 426 " pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 113.53 107.57 5.96 9.80e-01 1.04e+00 3.69e+01 angle pdb=" N THR A 18 " pdb=" CA THR A 18 " pdb=" CB THR A 18 " ideal model delta sigma weight residual 110.49 118.96 -8.47 1.69e+00 3.50e-01 2.51e+01 angle pdb=" C VAL C 524 " pdb=" N GLY C 525 " pdb=" CA GLY C 525 " ideal model delta sigma weight residual 121.41 111.67 9.74 1.96e+00 2.60e-01 2.47e+01 ... (remaining 16833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6119 17.79 - 35.59: 575 35.59 - 53.38: 246 53.38 - 71.17: 101 71.17 - 88.97: 26 Dihedral angle restraints: 7067 sinusoidal: 3110 harmonic: 3957 Sorted by residual: dihedral pdb=" C4' C T 32 " pdb=" C3' C T 32 " pdb=" C2' C T 32 " pdb=" C1' C T 32 " ideal model delta sinusoidal sigma weight residual 36.34 -41.31 77.65 1 3.10e+00 1.04e-01 7.85e+02 dihedral pdb=" C4' G T 18 " pdb=" C3' G T 18 " pdb=" C2' G T 18 " pdb=" C1' G T 18 " ideal model delta sinusoidal sigma weight residual 36.34 -36.92 73.27 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' U T 63 " pdb=" C3' U T 63 " pdb=" C2' U T 63 " pdb=" C1' U T 63 " ideal model delta sinusoidal sigma weight residual 36.34 -36.88 73.23 1 3.10e+00 1.04e-01 7.11e+02 ... (remaining 7064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1839 0.128 - 0.256: 127 0.256 - 0.384: 31 0.384 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA THR A 18 " pdb=" N THR A 18 " pdb=" C THR A 18 " pdb=" CB THR A 18 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA GLU E 111 " pdb=" N GLU E 111 " pdb=" C GLU E 111 " pdb=" CB GLU E 111 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA VAL A 15 " pdb=" N VAL A 15 " pdb=" C VAL A 15 " pdb=" CB VAL A 15 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1997 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 522 " 0.024 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLN C 522 " -0.086 2.00e-02 2.50e+03 pdb=" O GLN C 522 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP C 523 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 16 " 0.002 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR A 16 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 16 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 16 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 16 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR A 16 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 16 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 16 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 291 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C ASP E 291 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP E 291 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE E 292 " 0.017 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 348 2.69 - 3.24: 10323 3.24 - 3.79: 18039 3.79 - 4.35: 23406 4.35 - 4.90: 37743 Nonbonded interactions: 89859 Sorted by model distance: nonbonded pdb=" O2' U T 16 " pdb=" OP1 A T 19 " model vdw 2.137 3.040 nonbonded pdb=" OD2 ASP B 226 " pdb=" OH TYR B 301 " model vdw 2.154 3.040 nonbonded pdb=" OG SER B 303 " pdb=" O GLY D 158 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLU C 122 " pdb=" OH TYR C 155 " model vdw 2.175 3.040 nonbonded pdb=" O THR A 18 " pdb=" OG SER A 21 " model vdw 2.204 3.040 ... (remaining 89854 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.060 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 0.083 12071 Z= 0.320 Angle : 0.945 12.412 16838 Z= 0.556 Chirality : 0.080 0.639 2000 Planarity : 0.006 0.049 1872 Dihedral : 18.565 88.968 4505 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.50 % Favored : 94.28 % Rotamer: Outliers : 7.49 % Allowed : 25.06 % Favored : 67.45 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.35 (0.20), residues: 1346 helix: -1.07 (0.21), residues: 447 sheet: -0.97 (0.28), residues: 288 loop : -2.18 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.044 0.002 TYR A 16 PHE 0.015 0.001 PHE A 391 TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.32 (12071) covalent geometry : angle 0.94503 / 0.56 (16838) hydrogen bonds : bond 0.16419 / 10.92 ( 543) hydrogen bonds : angle 6.54714 / 4.51 ( 1420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.6497 (t80) cc_final: 0.6268 (t80) REVERT: A 106 HIS cc_start: 0.4398 (OUTLIER) cc_final: 0.3997 (t-170) REVERT: A 283 ARG cc_start: 0.4324 (OUTLIER) cc_final: 0.2898 (ttp-170) REVERT: A 361 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8117 (mttm) REVERT: A 434 MET cc_start: 0.5913 (ttp) cc_final: 0.5455 (tpt) REVERT: A 435 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7036 (pp20) REVERT: D 47 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7161 (mt) REVERT: D 49 MET cc_start: 0.6114 (mtp) cc_final: 0.5677 (mtp) outliers start: 64 outliers final: 24 residues processed: 173 average time/residue: 0.5674 time to fit residues: 106.6366 Evaluate side-chains 127 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 161 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 1.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 46 ASN A 47 ASN A 106 HIS A 280 GLN A 390 HIS B 205 GLN B 272 GLN C 31 GLN C 64 GLN C 69 GLN C 138 GLN C 413 GLN D 117 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.230395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.174448 restraints weight = 13938.628| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.33 r_work: 0.3659 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12071 Z= 0.189 Angle : 0.908 14.988 16838 Z= 0.396 Chirality : 0.074 1.059 2000 Planarity : 0.005 0.047 1872 Dihedral : 15.271 167.982 2599 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 6.91 % Allowed : 27.63 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.97 (0.22), residues: 1346 helix: 0.59 (0.25), residues: 443 sheet: -0.53 (0.29), residues: 283 loop : -1.61 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 88 TYR 0.013 0.002 TYR C 141 PHE 0.014 0.002 PHE A 391 TRP 0.014 0.002 TRP C 82 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (12071) covalent geometry : angle 0.90847 / 0.40 (16838) hydrogen bonds : bond 0.05141 / 3.23 ( 543) hydrogen bonds : angle 4.66661 / 3.27 ( 1420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5252 (mtt180) cc_final: 0.4893 (mtt-85) REVERT: A 61 TYR cc_start: 0.5839 (t80) cc_final: 0.5584 (t80) REVERT: A 95 ASN cc_start: 0.1587 (OUTLIER) cc_final: 0.1289 (m-40) REVERT: A 115 MET cc_start: 0.3963 (mtm) cc_final: 0.3359 (ptp) REVERT: A 294 PHE cc_start: 0.2949 (OUTLIER) cc_final: 0.2705 (p90) REVERT: A 434 MET cc_start: 0.6491 (ttp) cc_final: 0.5158 (tpt) REVERT: A 435 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6669 (pp20) REVERT: B 223 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8750 (mt) REVERT: C 16 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7271 (ptm-80) REVERT: C 36 ARG cc_start: 0.6092 (ptm-80) cc_final: 0.5725 (ptm-80) REVERT: C 90 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: C 426 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6323 (p) REVERT: D 49 MET cc_start: 0.5669 (mtp) cc_final: 0.5000 (mtp) outliers start: 59 outliers final: 27 residues processed: 153 average time/residue: 0.5309 time to fit residues: 88.7442 Evaluate side-chains 126 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 50.0000 chunk 134 optimal weight: 50.0000 chunk 4 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN B 129 GLN C 64 GLN C 413 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.236203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.185791 restraints weight = 14057.649| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.12 r_work: 0.3774 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12071 Z= 0.151 Angle : 0.753 14.463 16838 Z= 0.334 Chirality : 0.063 0.971 2000 Planarity : 0.004 0.047 1872 Dihedral : 15.106 173.012 2566 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 7.26 % Allowed : 27.75 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.43 (0.22), residues: 1346 helix: 1.14 (0.25), residues: 442 sheet: -0.29 (0.29), residues: 282 loop : -1.33 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 118 TYR 0.016 0.002 TYR A 309 PHE 0.013 0.001 PHE A 391 TRP 0.013 0.001 TRP C 82 HIS 0.013 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12071) covalent geometry : angle 0.75331 / 0.33 (16838) hydrogen bonds : bond 0.04692 / 2.99 ( 543) hydrogen bonds : angle 4.29636 / 3.03 ( 1420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 98 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5846 (t80) cc_final: 0.5554 (t80) REVERT: A 95 ASN cc_start: 0.1619 (OUTLIER) cc_final: 0.1295 (m-40) REVERT: A 99 ILE cc_start: 0.4459 (OUTLIER) cc_final: 0.4139 (mm) REVERT: A 115 MET cc_start: 0.4194 (mtm) cc_final: 0.3577 (ptp) REVERT: A 401 TRP cc_start: 0.7181 (OUTLIER) cc_final: 0.6476 (m-10) REVERT: A 434 MET cc_start: 0.6466 (ttp) cc_final: 0.5407 (tpt) REVERT: A 435 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6704 (pp20) REVERT: A 447 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8081 (mp0) REVERT: B 83 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 123 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6030 (mmpt) REVERT: B 223 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8794 (mt) REVERT: C 90 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: C 426 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.6446 (p) REVERT: C 504 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8178 (mt) outliers start: 62 outliers final: 33 residues processed: 156 average time/residue: 0.5432 time to fit residues: 92.4612 Evaluate side-chains 138 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN B 110 GLN B 294 GLN C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.236246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.185349 restraints weight = 14021.087| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 1.89 r_work: 0.3788 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12071 Z= 0.147 Angle : 0.728 14.585 16838 Z= 0.323 Chirality : 0.063 0.941 2000 Planarity : 0.004 0.048 1872 Dihedral : 15.016 173.674 2566 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 7.03 % Allowed : 28.34 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.17 (0.23), residues: 1346 helix: 1.41 (0.25), residues: 444 sheet: -0.21 (0.30), residues: 282 loop : -1.20 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.012 0.002 TYR C 141 PHE 0.013 0.001 PHE A 391 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12071) covalent geometry : angle 0.72806 / 0.32 (16838) hydrogen bonds : bond 0.04473 / 2.83 ( 543) hydrogen bonds : angle 4.13123 / 2.92 ( 1420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5029 (mtt180) cc_final: 0.4632 (mtt-85) REVERT: A 61 TYR cc_start: 0.5600 (t80) cc_final: 0.5293 (t80) REVERT: A 95 ASN cc_start: 0.1990 (OUTLIER) cc_final: 0.1662 (m-40) REVERT: A 99 ILE cc_start: 0.4212 (OUTLIER) cc_final: 0.3960 (mm) REVERT: A 115 MET cc_start: 0.3798 (mtm) cc_final: 0.3286 (ptp) REVERT: A 401 TRP cc_start: 0.7219 (OUTLIER) cc_final: 0.6479 (m-10) REVERT: A 434 MET cc_start: 0.6462 (ttp) cc_final: 0.5384 (tpt) REVERT: A 435 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6758 (pp20) REVERT: B 123 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5953 (mmpt) REVERT: B 223 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8779 (mt) REVERT: C 51 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.5577 (mm-40) REVERT: C 90 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8157 (tp30) REVERT: C 426 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6377 (p) REVERT: C 504 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 60 outliers final: 39 residues processed: 154 average time/residue: 0.5569 time to fit residues: 93.5706 Evaluate side-chains 142 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 116 optimal weight: 50.0000 chunk 106 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN B 110 GLN C 64 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.227876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171327 restraints weight = 13971.545| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.79 r_work: 0.3602 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12071 Z= 0.239 Angle : 0.837 16.848 16838 Z= 0.370 Chirality : 0.072 1.287 2000 Planarity : 0.005 0.055 1872 Dihedral : 15.260 174.194 2566 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 7.38 % Allowed : 27.63 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.19 (0.23), residues: 1346 helix: 1.27 (0.25), residues: 451 sheet: -0.25 (0.30), residues: 279 loop : -1.11 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.017 0.002 TYR A 369 PHE 0.017 0.002 PHE C 98 TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (12071) covalent geometry : angle 0.83652 / 0.37 (16838) hydrogen bonds : bond 0.04944 / 3.11 ( 543) hydrogen bonds : angle 4.25095 / 3.00 ( 1420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 92 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5734 (t80) cc_final: 0.5420 (t80) REVERT: A 95 ASN cc_start: 0.1957 (OUTLIER) cc_final: 0.1626 (m-40) REVERT: A 99 ILE cc_start: 0.4129 (OUTLIER) cc_final: 0.3890 (mm) REVERT: A 113 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: A 115 MET cc_start: 0.4038 (mtm) cc_final: 0.3418 (ptp) REVERT: A 350 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8226 (ttt-90) REVERT: A 401 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: A 434 MET cc_start: 0.6636 (ttp) cc_final: 0.5492 (tpt) REVERT: B 38 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.6658 (ptm160) REVERT: B 123 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5978 (mmpt) REVERT: B 223 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8773 (mt) REVERT: C 53 GLU cc_start: 0.7760 (tp30) cc_final: 0.7478 (tp30) REVERT: C 90 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8366 (tp30) REVERT: C 480 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: C 504 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8206 (mt) REVERT: D 40 MET cc_start: 0.3827 (mmp) cc_final: 0.3335 (mmt) outliers start: 63 outliers final: 42 residues processed: 151 average time/residue: 0.5462 time to fit residues: 90.3043 Evaluate side-chains 143 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 50.0000 chunk 100 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN C 64 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.227392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.171510 restraints weight = 13982.853| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.45 r_work: 0.3612 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12071 Z= 0.249 Angle : 0.837 16.132 16838 Z= 0.371 Chirality : 0.073 1.300 2000 Planarity : 0.005 0.055 1872 Dihedral : 15.323 174.303 2565 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 8.55 % Allowed : 26.11 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.23 (0.23), residues: 1346 helix: 1.27 (0.25), residues: 446 sheet: -0.25 (0.30), residues: 279 loop : -1.15 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 198 TYR 0.021 0.002 TYR A 296 PHE 0.016 0.002 PHE C 98 TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (12071) covalent geometry : angle 0.83721 / 0.37 (16838) hydrogen bonds : bond 0.04908 / 3.07 ( 543) hydrogen bonds : angle 4.24357 / 2.99 ( 1420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 88 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5598 (t80) cc_final: 0.5240 (t80) REVERT: A 99 ILE cc_start: 0.3862 (OUTLIER) cc_final: 0.3654 (mm) REVERT: A 113 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: A 115 MET cc_start: 0.4078 (mtm) cc_final: 0.3189 (ptt) REVERT: A 350 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8241 (ttt-90) REVERT: A 401 TRP cc_start: 0.7406 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: A 434 MET cc_start: 0.6647 (ttp) cc_final: 0.5503 (tpt) REVERT: B 123 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5989 (mmpt) REVERT: B 223 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 16 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7208 (ptm-80) REVERT: C 53 GLU cc_start: 0.7824 (tp30) cc_final: 0.7479 (tp30) REVERT: C 90 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: C 472 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7940 (mtt90) REVERT: C 480 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: C 504 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 40 MET cc_start: 0.3576 (mmp) cc_final: 0.3177 (mmt) REVERT: D 49 MET cc_start: 0.6466 (mmt) cc_final: 0.5724 (mmt) outliers start: 73 outliers final: 47 residues processed: 155 average time/residue: 0.5279 time to fit residues: 89.4513 Evaluate side-chains 143 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN C 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.234061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.181294 restraints weight = 13890.683| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 1.97 r_work: 0.3737 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12071 Z= 0.179 Angle : 0.773 14.432 16838 Z= 0.342 Chirality : 0.067 1.050 2000 Planarity : 0.004 0.049 1872 Dihedral : 15.254 173.150 2565 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 7.73 % Allowed : 26.93 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.01 (0.23), residues: 1346 helix: 1.44 (0.25), residues: 446 sheet: -0.08 (0.29), residues: 288 loop : -1.05 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 516 TYR 0.014 0.002 TYR B 247 PHE 0.014 0.002 PHE C 518 TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (12071) covalent geometry : angle 0.77285 / 0.34 (16838) hydrogen bonds : bond 0.04485 / 2.80 ( 543) hydrogen bonds : angle 4.11472 / 2.90 ( 1420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 92 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5682 (t80) cc_final: 0.5368 (t80) REVERT: A 90 LYS cc_start: 0.4361 (OUTLIER) cc_final: 0.3895 (mmtp) REVERT: A 95 ASN cc_start: 0.2379 (OUTLIER) cc_final: 0.1995 (m-40) REVERT: A 99 ILE cc_start: 0.3944 (OUTLIER) cc_final: 0.3707 (mm) REVERT: A 113 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5225 (mt-10) REVERT: A 115 MET cc_start: 0.4082 (mtm) cc_final: 0.3198 (ptt) REVERT: A 401 TRP cc_start: 0.7345 (OUTLIER) cc_final: 0.6461 (m-10) REVERT: A 434 MET cc_start: 0.6570 (ttp) cc_final: 0.5550 (tpt) REVERT: A 435 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: B 38 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6711 (ptm160) REVERT: B 123 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5988 (mmpt) REVERT: B 223 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8759 (mt) REVERT: C 53 GLU cc_start: 0.7785 (tp30) cc_final: 0.7475 (tp30) REVERT: C 90 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: C 480 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: C 504 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8214 (mt) REVERT: D 40 MET cc_start: 0.3667 (mmp) cc_final: 0.3446 (mmm) REVERT: D 49 MET cc_start: 0.6455 (mmt) cc_final: 0.5708 (mmt) REVERT: D 75 SER cc_start: 0.9222 (m) cc_final: 0.8954 (m) outliers start: 66 outliers final: 46 residues processed: 152 average time/residue: 0.5645 time to fit residues: 93.3728 Evaluate side-chains 148 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 90 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 124 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN C 64 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.226881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.171053 restraints weight = 13896.614| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.24 r_work: 0.3612 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12071 Z= 0.263 Angle : 0.868 16.528 16838 Z= 0.383 Chirality : 0.076 1.443 2000 Planarity : 0.005 0.048 1872 Dihedral : 15.337 175.074 2565 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 8.20 % Allowed : 26.81 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.23), residues: 1346 helix: 1.24 (0.25), residues: 452 sheet: -0.08 (0.30), residues: 285 loop : -1.06 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 198 TYR 0.021 0.002 TYR A 369 PHE 0.017 0.002 PHE C 98 TRP 0.019 0.002 TRP C 82 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.26 (12071) covalent geometry : angle 0.86833 / 0.38 (16838) hydrogen bonds : bond 0.05018 / 3.14 ( 543) hydrogen bonds : angle 4.23625 / 2.98 ( 1420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 89 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5529 (mtt180) REVERT: A 61 TYR cc_start: 0.5609 (t80) cc_final: 0.5295 (t80) REVERT: A 95 ASN cc_start: 0.2354 (OUTLIER) cc_final: 0.2069 (m-40) REVERT: A 99 ILE cc_start: 0.4085 (OUTLIER) cc_final: 0.3868 (mm) REVERT: A 113 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5200 (mt-10) REVERT: A 115 MET cc_start: 0.3977 (mtm) cc_final: 0.3387 (ptp) REVERT: A 401 TRP cc_start: 0.7415 (OUTLIER) cc_final: 0.6475 (m-10) REVERT: A 434 MET cc_start: 0.6631 (ttp) cc_final: 0.5514 (tpt) REVERT: B 38 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.6833 (ptm160) REVERT: B 123 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5952 (mmpt) REVERT: B 223 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8776 (mt) REVERT: C 16 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7078 (ptm-80) REVERT: C 53 GLU cc_start: 0.7762 (tp30) cc_final: 0.7463 (tp30) REVERT: C 57 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7180 (mtp85) REVERT: C 90 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8346 (tp30) REVERT: C 480 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 504 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8155 (mt) REVERT: D 40 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.3361 (mmm) REVERT: D 49 MET cc_start: 0.6352 (mmt) cc_final: 0.5807 (mmt) outliers start: 70 outliers final: 45 residues processed: 151 average time/residue: 0.5743 time to fit residues: 93.9207 Evaluate side-chains 143 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 86 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 516 ARG Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 50.0000 chunk 97 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN C 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.233990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.182294 restraints weight = 13806.172| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 1.85 r_work: 0.3797 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12071 Z= 0.167 Angle : 0.771 14.475 16838 Z= 0.341 Chirality : 0.067 1.037 2000 Planarity : 0.004 0.046 1872 Dihedral : 15.232 173.390 2565 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 7.14 % Allowed : 27.99 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.23), residues: 1346 helix: 1.50 (0.25), residues: 446 sheet: 0.03 (0.30), residues: 288 loop : -0.97 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 350 TYR 0.016 0.002 TYR B 247 PHE 0.017 0.002 PHE C 518 TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12071) covalent geometry : angle 0.77081 / 0.34 (16838) hydrogen bonds : bond 0.04392 / 2.74 ( 543) hydrogen bonds : angle 4.06850 / 2.86 ( 1420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 88 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5772 (t80) cc_final: 0.5467 (t80) REVERT: A 95 ASN cc_start: 0.2358 (OUTLIER) cc_final: 0.2004 (m-40) REVERT: A 99 ILE cc_start: 0.4064 (OUTLIER) cc_final: 0.3859 (mm) REVERT: A 113 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5286 (mt-10) REVERT: A 115 MET cc_start: 0.4218 (mtm) cc_final: 0.3575 (ptp) REVERT: A 401 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 434 MET cc_start: 0.6503 (ttp) cc_final: 0.5593 (tpt) REVERT: A 435 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6789 (pp20) REVERT: A 438 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: B 38 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6779 (ptm160) REVERT: B 123 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.6009 (mmpt) REVERT: B 223 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8758 (mt) REVERT: C 16 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7210 (ptm-80) REVERT: C 53 GLU cc_start: 0.7708 (tp30) cc_final: 0.7418 (tp30) REVERT: C 90 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: C 504 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8153 (mt) REVERT: D 40 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.3475 (mmm) REVERT: D 75 SER cc_start: 0.9277 (m) cc_final: 0.9004 (m) outliers start: 61 outliers final: 42 residues processed: 141 average time/residue: 0.5353 time to fit residues: 82.4174 Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 87 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN C 51 GLN C 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.236040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.183621 restraints weight = 14061.903| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.09 r_work: 0.3765 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12071 Z= 0.122 Angle : 0.721 14.379 16838 Z= 0.319 Chirality : 0.062 0.885 2000 Planarity : 0.004 0.046 1872 Dihedral : 15.069 172.554 2562 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 6.09 % Allowed : 29.16 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.30 (0.23), residues: 1346 helix: 1.68 (0.25), residues: 447 sheet: 0.17 (0.30), residues: 288 loop : -0.90 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 350 TYR 0.014 0.001 TYR A 309 PHE 0.011 0.001 PHE A 391 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS D 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12071) covalent geometry : angle 0.72127 / 0.32 (16838) hydrogen bonds : bond 0.04095 / 2.56 ( 543) hydrogen bonds : angle 3.94897 / 2.77 ( 1420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 87 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.5720 (t80) cc_final: 0.5430 (t80) REVERT: A 113 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: A 115 MET cc_start: 0.4039 (mtm) cc_final: 0.3509 (ptp) REVERT: A 401 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.6440 (m-10) REVERT: A 434 MET cc_start: 0.6504 (ttp) cc_final: 0.5564 (tpt) REVERT: A 435 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6745 (pp20) REVERT: A 447 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8139 (mp0) REVERT: B 123 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.5974 (mmpt) REVERT: B 223 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8730 (mt) REVERT: C 90 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8221 (tp30) REVERT: C 504 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8136 (mt) REVERT: C 526 HIS cc_start: 0.2423 (OUTLIER) cc_final: 0.2177 (t-90) REVERT: D 40 MET cc_start: 0.3504 (OUTLIER) cc_final: 0.2836 (mtt) REVERT: D 49 MET cc_start: 0.6558 (mmt) cc_final: 0.5813 (mmp) REVERT: D 75 SER cc_start: 0.9230 (m) cc_final: 0.8953 (m) outliers start: 52 outliers final: 32 residues processed: 133 average time/residue: 0.5332 time to fit residues: 77.5768 Evaluate side-chains 127 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 401 TRP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 148 HIS Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 526 HIS Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 108 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 47 ASN A 282 ASN B 110 GLN C 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.224604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169838 restraints weight = 13919.699| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.38 r_work: 0.3613 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 12071 Z= 0.380 Angle : 0.985 17.881 16838 Z= 0.434 Chirality : 0.084 1.720 2000 Planarity : 0.006 0.060 1872 Dihedral : 15.221 176.542 2559 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 6.21 % Allowed : 28.45 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 (0.23), residues: 1346 helix: 1.16 (0.25), residues: 452 sheet: -0.11 (0.29), residues: 297 loop : -1.06 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 36 TYR 0.021 0.003 TYR C 513 PHE 0.027 0.003 PHE C 518 TRP 0.022 0.003 TRP C 82 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.38 (12071) covalent geometry : angle 0.98473 / 0.43 (16838) hydrogen bonds : bond 0.05666 / 3.53 ( 543) hydrogen bonds : angle 4.35328 / 3.05 ( 1420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.67 seconds wall clock time: 93 minutes 50.51 seconds (5630.51 seconds total)