Starting phenix.real_space_refine on Wed Mar 4 20:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uqg_20847/03_2026/6uqg_20847.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 10388 2.51 5 N 2756 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3972 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 16, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 371 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 4, 'PHE:plan': 4, 'GLU:plan': 15, 'TRP:plan': 1, 'ASP:plan': 15, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 218 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.48, per 1000 atoms: 0.22 Number of scatterers: 15976 At special positions: 0 Unit cell: (107.12, 108.15, 128.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 2712 8.00 N 2756 7.00 C 10388 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: 1.41 Conformation dependent library (CDL) restraints added in 722.6 milliseconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 76.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.679A pdb=" N VAL A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 195 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 221 through 230 removed outlier: 4.726A pdb=" N SER A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.623A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 270 through 286 removed outlier: 3.743A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 323 removed outlier: 3.790A pdb=" N SER A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.677A pdb=" N GLN A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.710A pdb=" N ARG A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.504A pdb=" N LYS A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.726A pdb=" N ILE A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.662A pdb=" N ALA A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.052A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.565A pdb=" N ASN A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 635 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 removed outlier: 3.678A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 195 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 221 through 230 removed outlier: 4.727A pdb=" N SER B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.624A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 270 through 286 removed outlier: 3.742A pdb=" N LEU B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 323 removed outlier: 3.790A pdb=" N SER B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix removed outlier: 3.678A pdb=" N GLN B 323 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.710A pdb=" N ARG B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 removed outlier: 3.504A pdb=" N LYS B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.725A pdb=" N ILE B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 removed outlier: 3.662A pdb=" N ALA B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.052A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 577 through 595 Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.565A pdb=" N ASN B 610 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 635 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 removed outlier: 3.679A pdb=" N VAL C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 195 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 221 through 230 removed outlier: 4.726A pdb=" N SER C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE C 230 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.623A pdb=" N ILE C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 270 through 286 removed outlier: 3.742A pdb=" N LEU C 274 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 280 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 323 removed outlier: 3.790A pdb=" N SER C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix removed outlier: 3.678A pdb=" N GLN C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.710A pdb=" N ARG C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 removed outlier: 3.505A pdb=" N LYS C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.725A pdb=" N ILE C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 removed outlier: 3.662A pdb=" N ALA C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.052A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 577 through 595 Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.565A pdb=" N ASN C 610 " --> pdb=" O GLN C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 635 Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 removed outlier: 3.679A pdb=" N VAL D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 195 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 221 through 230 removed outlier: 4.726A pdb=" N SER D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE D 230 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.623A pdb=" N ILE D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 263 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 270 through 286 removed outlier: 3.742A pdb=" N LEU D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 280 " --> pdb=" O ARG D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 323 removed outlier: 3.790A pdb=" N SER D 293 " --> pdb=" O ASP D 289 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix removed outlier: 3.677A pdb=" N GLN D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.710A pdb=" N ARG D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 removed outlier: 3.504A pdb=" N LYS D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.726A pdb=" N ILE D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.661A pdb=" N ALA D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.052A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 577 through 595 Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.564A pdb=" N ASN D 610 " --> pdb=" O GLN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 635 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.524A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 536 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.525A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 552 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.524A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 536 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.526A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 552 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.524A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 536 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.524A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 552 " --> pdb=" O ILE C 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.523A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER D 536 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.525A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 552 " --> pdb=" O ILE D 523 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4439 1.34 - 1.45: 2947 1.45 - 1.57: 8750 1.57 - 1.69: 8 1.69 - 1.81: 204 Bond restraints: 16348 Sorted by residual: bond pdb=" CG1 ILE D 374 " pdb=" CD1 ILE D 374 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.82e+00 bond pdb=" CG1 ILE B 374 " pdb=" CD1 ILE B 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.75e+00 bond pdb=" CG1 ILE A 374 " pdb=" CD1 ILE A 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.75e+00 bond pdb=" CG1 ILE C 374 " pdb=" CD1 ILE C 374 " ideal model delta sigma weight residual 1.513 1.412 0.101 3.90e-02 6.57e+02 6.73e+00 bond pdb=" CA ILE B 160 " pdb=" C ILE B 160 " ideal model delta sigma weight residual 1.524 1.550 -0.025 1.05e-02 9.07e+03 5.77e+00 ... (remaining 16343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21196 2.12 - 4.24: 901 4.24 - 6.36: 95 6.36 - 8.48: 25 8.48 - 10.60: 11 Bond angle restraints: 22228 Sorted by residual: angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 110.53 117.62 -7.09 9.40e-01 1.13e+00 5.69e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 110.53 117.62 -7.09 9.40e-01 1.13e+00 5.69e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 110.53 117.61 -7.08 9.40e-01 1.13e+00 5.67e+01 angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 110.53 117.60 -7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N ILE B 164 " pdb=" CA ILE B 164 " pdb=" C ILE B 164 " ideal model delta sigma weight residual 110.42 117.59 -7.17 9.60e-01 1.09e+00 5.58e+01 ... (remaining 22223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.77: 9327 30.77 - 61.54: 289 61.54 - 92.32: 12 92.32 - 123.09: 4 123.09 - 153.86: 4 Dihedral angle restraints: 9636 sinusoidal: 3404 harmonic: 6232 Sorted by residual: dihedral pdb=" C5' CMP D 901 " pdb=" O5' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.17 -106.17 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" C5' CMP A 901 " pdb=" O5' CMP A 901 " pdb=" P CMP A 901 " pdb=" O1P CMP A 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.15 -106.15 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" C5' CMP C 901 " pdb=" O5' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual 60.00 166.15 -106.15 1 2.00e+01 2.50e-03 3.07e+01 ... (remaining 9633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1839 0.055 - 0.110: 590 0.110 - 0.166: 89 0.166 - 0.221: 22 0.221 - 0.276: 8 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA CYS B 358 " pdb=" N CYS B 358 " pdb=" C CYS B 358 " pdb=" CB CYS B 358 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA CYS A 358 " pdb=" N CYS A 358 " pdb=" C CYS A 358 " pdb=" CB CYS A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA CYS D 358 " pdb=" N CYS D 358 " pdb=" C CYS D 358 " pdb=" CB CYS D 358 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2545 not shown) Planarity restraints: 2788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 319 " 0.056 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO C 320 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 320 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 320 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.047 5.00e-02 4.00e+02 ... (remaining 2785 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4729 2.81 - 3.33: 14737 3.33 - 3.85: 25965 3.85 - 4.38: 27203 4.38 - 4.90: 49018 Nonbonded interactions: 121652 Sorted by model distance: nonbonded pdb=" OG SER A 403 " pdb=" NE2 GLN D 416 " model vdw 2.286 3.120 nonbonded pdb=" OG SER C 565 " pdb=" OD1 ASN C 568 " model vdw 2.300 3.040 nonbonded pdb=" OG SER A 565 " pdb=" OD1 ASN A 568 " model vdw 2.300 3.040 nonbonded pdb=" OG SER B 565 " pdb=" OD1 ASN B 568 " model vdw 2.301 3.040 nonbonded pdb=" OG SER D 565 " pdb=" OD1 ASN D 568 " model vdw 2.301 3.040 ... (remaining 121647 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.009 0.102 16348 Z= 0.382 Angle : 0.979 10.600 22228 Z= 0.573 Chirality : 0.055 0.276 2548 Planarity : 0.008 0.083 2788 Dihedral : 15.113 153.860 5596 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.14), residues: 2096 helix: -2.07 (0.10), residues: 1516 sheet: -2.03 (0.39), residues: 124 loop : -2.76 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 593 TYR 0.023 0.002 TYR C 347 PHE 0.029 0.003 PHE C 194 TRP 0.020 0.002 TRP C 330 HIS 0.005 0.002 HIS C 421 Details of bonding type rmsd covalent geometry : bond 0.00873 (16348) covalent geometry : angle 0.97949 (22228) hydrogen bonds : bond 0.12927 ( 1185) hydrogen bonds : angle 5.87351 ( 3471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8178 (mmm) cc_final: 0.7477 (mtt) REVERT: A 152 MET cc_start: 0.7631 (tpp) cc_final: 0.7389 (tpp) REVERT: A 401 ASP cc_start: 0.8492 (t0) cc_final: 0.7311 (t70) REVERT: A 410 LYS cc_start: 0.8663 (tttt) cc_final: 0.8417 (ttpt) REVERT: A 624 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 628 HIS cc_start: 0.8277 (t-90) cc_final: 0.7786 (t-170) REVERT: B 281 TRP cc_start: 0.7768 (t60) cc_final: 0.7477 (t60) REVERT: B 386 TYR cc_start: 0.8735 (t80) cc_final: 0.8364 (t80) REVERT: B 451 ASN cc_start: 0.9140 (t0) cc_final: 0.8937 (t0) REVERT: B 624 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7730 (tp40) REVERT: B 628 HIS cc_start: 0.7496 (t-90) cc_final: 0.6443 (t-170) REVERT: C 149 MET cc_start: 0.7406 (mmp) cc_final: 0.7142 (mmp) REVERT: C 281 TRP cc_start: 0.7766 (t60) cc_final: 0.7476 (t60) REVERT: C 347 TYR cc_start: 0.8697 (t80) cc_final: 0.8405 (t80) REVERT: C 386 TYR cc_start: 0.8587 (t80) cc_final: 0.8265 (t80) REVERT: C 401 ASP cc_start: 0.8126 (t0) cc_final: 0.6860 (t70) REVERT: C 624 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7728 (tp40) REVERT: C 628 HIS cc_start: 0.7558 (t-90) cc_final: 0.7259 (t-170) REVERT: D 281 TRP cc_start: 0.7789 (t60) cc_final: 0.7489 (t60) REVERT: D 386 TYR cc_start: 0.8667 (t80) cc_final: 0.8341 (t80) REVERT: D 409 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 624 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7693 (tp40) REVERT: D 628 HIS cc_start: 0.7496 (t-90) cc_final: 0.6455 (t-170) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1321 time to fit residues: 57.2324 Evaluate side-chains 228 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094207 restraints weight = 31101.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097896 restraints weight = 14328.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100336 restraints weight = 8983.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101902 restraints weight = 6836.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102805 restraints weight = 5830.726| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16348 Z= 0.140 Angle : 0.584 7.960 22228 Z= 0.302 Chirality : 0.040 0.194 2548 Planarity : 0.005 0.054 2788 Dihedral : 8.461 153.134 2336 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 12.20 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2096 helix: 0.14 (0.12), residues: 1528 sheet: -0.89 (0.46), residues: 88 loop : -2.91 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.012 0.001 TYR D 347 PHE 0.017 0.001 PHE A 109 TRP 0.011 0.001 TRP A 330 HIS 0.004 0.001 HIS D 628 Details of bonding type rmsd covalent geometry : bond 0.00299 (16348) covalent geometry : angle 0.58373 (22228) hydrogen bonds : bond 0.04292 ( 1185) hydrogen bonds : angle 4.45650 ( 3471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8160 (mmm) cc_final: 0.7537 (mtt) REVERT: A 281 TRP cc_start: 0.7501 (t60) cc_final: 0.7202 (t60) REVERT: A 305 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7265 (tpp) REVERT: A 401 ASP cc_start: 0.8177 (t0) cc_final: 0.7118 (t70) REVERT: A 409 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 410 LYS cc_start: 0.8536 (tttt) cc_final: 0.8325 (ttpt) REVERT: A 624 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7676 (tm-30) REVERT: A 628 HIS cc_start: 0.8052 (t-90) cc_final: 0.7525 (t-170) REVERT: B 156 ASN cc_start: 0.7888 (t0) cc_final: 0.7658 (t0) REVERT: B 281 TRP cc_start: 0.7518 (t60) cc_final: 0.7285 (t60) REVERT: B 305 MET cc_start: 0.7702 (ttm) cc_final: 0.7122 (tpt) REVERT: B 385 CYS cc_start: 0.8725 (m) cc_final: 0.8406 (t) REVERT: B 530 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: B 628 HIS cc_start: 0.7560 (t-90) cc_final: 0.6801 (t-170) REVERT: C 101 MET cc_start: 0.8071 (mtm) cc_final: 0.7694 (mtp) REVERT: C 281 TRP cc_start: 0.7697 (t60) cc_final: 0.7495 (t60) REVERT: C 305 MET cc_start: 0.7710 (ttm) cc_final: 0.7487 (tpt) REVERT: C 347 TYR cc_start: 0.8698 (t80) cc_final: 0.8407 (t80) REVERT: C 386 TYR cc_start: 0.8339 (t80) cc_final: 0.8132 (t80) REVERT: C 401 ASP cc_start: 0.7963 (t0) cc_final: 0.6800 (t70) REVERT: C 487 MET cc_start: 0.8296 (ttm) cc_final: 0.8022 (ttm) REVERT: C 628 HIS cc_start: 0.7425 (t-90) cc_final: 0.7104 (t-170) REVERT: D 281 TRP cc_start: 0.7604 (t60) cc_final: 0.7393 (t60) REVERT: D 305 MET cc_start: 0.7643 (ttm) cc_final: 0.7411 (tpt) REVERT: D 386 TYR cc_start: 0.8455 (t80) cc_final: 0.8233 (t80) REVERT: D 530 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7526 (mtp) REVERT: D 628 HIS cc_start: 0.7548 (t-90) cc_final: 0.6816 (t-170) outliers start: 32 outliers final: 17 residues processed: 263 average time/residue: 0.1153 time to fit residues: 46.4541 Evaluate side-chains 243 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 chunk 64 optimal weight: 0.0370 chunk 147 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097255 restraints weight = 30968.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101022 restraints weight = 14962.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101396 restraints weight = 9444.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101536 restraints weight = 8752.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101737 restraints weight = 8399.357| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16348 Z= 0.122 Angle : 0.543 7.716 22228 Z= 0.277 Chirality : 0.039 0.125 2548 Planarity : 0.004 0.046 2788 Dihedral : 7.665 141.560 2336 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.76 % Allowed : 15.04 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2096 helix: 1.10 (0.13), residues: 1532 sheet: -0.10 (0.55), residues: 88 loop : -2.70 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 267 TYR 0.010 0.001 TYR A 347 PHE 0.009 0.001 PHE A 538 TRP 0.009 0.001 TRP A 330 HIS 0.005 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00255 (16348) covalent geometry : angle 0.54287 (22228) hydrogen bonds : bond 0.03753 ( 1185) hydrogen bonds : angle 4.15852 ( 3471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8152 (mmm) cc_final: 0.7560 (mtt) REVERT: A 305 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7321 (tpp) REVERT: A 401 ASP cc_start: 0.8061 (t0) cc_final: 0.6908 (t70) REVERT: A 410 LYS cc_start: 0.8583 (tttt) cc_final: 0.8366 (ttpt) REVERT: A 624 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 156 ASN cc_start: 0.7900 (t0) cc_final: 0.7694 (t0) REVERT: B 388 MET cc_start: 0.8338 (mmt) cc_final: 0.8002 (mmt) REVERT: B 404 ARG cc_start: 0.7591 (tmt170) cc_final: 0.7358 (tmm160) REVERT: B 530 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7538 (mtp) REVERT: B 628 HIS cc_start: 0.7853 (t-90) cc_final: 0.7336 (t-170) REVERT: C 101 MET cc_start: 0.8259 (mtm) cc_final: 0.7866 (mtp) REVERT: C 192 MET cc_start: 0.7671 (mpp) cc_final: 0.7362 (mpp) REVERT: C 305 MET cc_start: 0.7706 (ttm) cc_final: 0.7441 (tpt) REVERT: C 398 GLN cc_start: 0.8582 (mt0) cc_final: 0.8340 (mt0) REVERT: C 401 ASP cc_start: 0.7822 (t0) cc_final: 0.6621 (t70) REVERT: C 628 HIS cc_start: 0.7468 (t-90) cc_final: 0.7168 (t-170) REVERT: D 376 MET cc_start: 0.9120 (mmm) cc_final: 0.8473 (mmm) REVERT: D 404 ARG cc_start: 0.7541 (tmt170) cc_final: 0.7264 (tmm160) REVERT: D 530 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: D 628 HIS cc_start: 0.7836 (t-90) cc_final: 0.7326 (t-170) outliers start: 26 outliers final: 17 residues processed: 242 average time/residue: 0.1192 time to fit residues: 44.0500 Evaluate side-chains 226 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 149 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 162 optimal weight: 0.3980 chunk 138 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093797 restraints weight = 30904.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097114 restraints weight = 15382.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099394 restraints weight = 10072.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100784 restraints weight = 7798.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101647 restraints weight = 6720.153| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16348 Z= 0.160 Angle : 0.569 8.284 22228 Z= 0.292 Chirality : 0.040 0.129 2548 Planarity : 0.004 0.042 2788 Dihedral : 7.499 138.903 2336 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.91 % Allowed : 15.85 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2096 helix: 1.49 (0.13), residues: 1532 sheet: 0.07 (0.56), residues: 88 loop : -2.55 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.018 0.001 TYR D 347 PHE 0.013 0.001 PHE A 538 TRP 0.011 0.002 TRP A 281 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00362 (16348) covalent geometry : angle 0.56854 (22228) hydrogen bonds : bond 0.04028 ( 1185) hydrogen bonds : angle 4.18868 ( 3471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8121 (mmm) cc_final: 0.7573 (mtt) REVERT: A 305 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7204 (tpp) REVERT: A 401 ASP cc_start: 0.8098 (t0) cc_final: 0.6959 (t70) REVERT: A 404 ARG cc_start: 0.7750 (tmt170) cc_final: 0.7018 (tmm-80) REVERT: A 410 LYS cc_start: 0.8565 (tttt) cc_final: 0.8328 (ttpt) REVERT: A 624 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 628 HIS cc_start: 0.8163 (t-170) cc_final: 0.7831 (t-170) REVERT: B 361 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: B 404 ARG cc_start: 0.7703 (tmt170) cc_final: 0.7343 (tmm160) REVERT: B 530 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7492 (mtp) REVERT: B 628 HIS cc_start: 0.7851 (t-90) cc_final: 0.7444 (t-170) REVERT: C 101 MET cc_start: 0.8280 (mtm) cc_final: 0.7915 (mtp) REVERT: C 305 MET cc_start: 0.7729 (ttm) cc_final: 0.7094 (tmm) REVERT: C 401 ASP cc_start: 0.7884 (t0) cc_final: 0.6695 (t70) REVERT: C 628 HIS cc_start: 0.7496 (t-90) cc_final: 0.7272 (t-170) REVERT: D 305 MET cc_start: 0.7700 (ttm) cc_final: 0.7295 (tpt) REVERT: D 376 MET cc_start: 0.9163 (mmm) cc_final: 0.8334 (mmm) REVERT: D 404 ARG cc_start: 0.7677 (tmt170) cc_final: 0.7309 (tmm160) REVERT: D 530 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7405 (mtp) REVERT: D 628 HIS cc_start: 0.7915 (t-90) cc_final: 0.7505 (t-170) outliers start: 43 outliers final: 22 residues processed: 241 average time/residue: 0.1203 time to fit residues: 44.2121 Evaluate side-chains 228 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 210 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 209 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093824 restraints weight = 30918.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097116 restraints weight = 15575.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099336 restraints weight = 10251.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100662 restraints weight = 8005.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.101480 restraints weight = 6947.093| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16348 Z= 0.159 Angle : 0.567 7.737 22228 Z= 0.290 Chirality : 0.040 0.127 2548 Planarity : 0.004 0.043 2788 Dihedral : 7.363 137.163 2336 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 16.33 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 2096 helix: 1.69 (0.13), residues: 1532 sheet: 0.49 (0.58), residues: 84 loop : -2.42 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.016 0.001 TYR D 347 PHE 0.013 0.001 PHE A 538 TRP 0.013 0.002 TRP A 281 HIS 0.003 0.001 HIS D 628 Details of bonding type rmsd covalent geometry : bond 0.00362 (16348) covalent geometry : angle 0.56672 (22228) hydrogen bonds : bond 0.03924 ( 1185) hydrogen bonds : angle 4.18701 ( 3471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8145 (mmm) cc_final: 0.7621 (mtt) REVERT: A 361 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: A 401 ASP cc_start: 0.7955 (t0) cc_final: 0.6804 (t70) REVERT: A 404 ARG cc_start: 0.7723 (tmt170) cc_final: 0.7241 (tmm160) REVERT: A 624 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 628 HIS cc_start: 0.8163 (t-170) cc_final: 0.7842 (t-170) REVERT: B 259 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: B 305 MET cc_start: 0.7681 (tpt) cc_final: 0.7081 (tpt) REVERT: B 361 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 530 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: C 101 MET cc_start: 0.8292 (mtm) cc_final: 0.7786 (mtp) REVERT: C 192 MET cc_start: 0.7715 (mpp) cc_final: 0.7208 (mmt) REVERT: C 305 MET cc_start: 0.7760 (ttm) cc_final: 0.7153 (tmm) REVERT: C 401 ASP cc_start: 0.7876 (t0) cc_final: 0.6684 (t70) REVERT: C 628 HIS cc_start: 0.7483 (t-90) cc_final: 0.7192 (t-170) REVERT: D 305 MET cc_start: 0.7706 (ttm) cc_final: 0.7319 (tpt) REVERT: D 361 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: D 401 ASP cc_start: 0.7971 (t0) cc_final: 0.6694 (t70) REVERT: D 404 ARG cc_start: 0.7750 (tmt170) cc_final: 0.7235 (tmm160) REVERT: D 530 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7422 (mtp) REVERT: D 628 HIS cc_start: 0.7863 (t-90) cc_final: 0.7586 (t-170) outliers start: 42 outliers final: 28 residues processed: 243 average time/residue: 0.1252 time to fit residues: 46.0203 Evaluate side-chains 240 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095618 restraints weight = 30639.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099000 restraints weight = 15370.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101253 restraints weight = 10055.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102590 restraints weight = 7836.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103258 restraints weight = 6803.888| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16348 Z= 0.127 Angle : 0.543 7.236 22228 Z= 0.277 Chirality : 0.039 0.127 2548 Planarity : 0.004 0.043 2788 Dihedral : 7.226 136.225 2336 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.17 % Allowed : 18.16 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 2096 helix: 1.84 (0.13), residues: 1532 sheet: 0.62 (0.60), residues: 84 loop : -2.22 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 270 TYR 0.011 0.001 TYR D 347 PHE 0.012 0.001 PHE C 186 TRP 0.013 0.001 TRP B 281 HIS 0.006 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00279 (16348) covalent geometry : angle 0.54252 (22228) hydrogen bonds : bond 0.03589 ( 1185) hydrogen bonds : angle 4.08212 ( 3471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 101 MET cc_start: 0.8141 (mmm) cc_final: 0.7631 (mtt) REVERT: A 312 ASP cc_start: 0.8495 (t70) cc_final: 0.8255 (t70) REVERT: A 401 ASP cc_start: 0.8084 (t0) cc_final: 0.6957 (t70) REVERT: A 624 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 628 HIS cc_start: 0.8006 (t-170) cc_final: 0.7668 (t-170) REVERT: B 305 MET cc_start: 0.7714 (tpt) cc_final: 0.7115 (tpt) REVERT: B 361 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: B 530 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7451 (mtp) REVERT: B 628 HIS cc_start: 0.7485 (t-170) cc_final: 0.6517 (t-170) REVERT: C 101 MET cc_start: 0.8293 (mtm) cc_final: 0.7796 (mtp) REVERT: C 305 MET cc_start: 0.7747 (ttm) cc_final: 0.7180 (tmm) REVERT: C 388 MET cc_start: 0.8387 (mmt) cc_final: 0.8184 (mmt) REVERT: C 401 ASP cc_start: 0.7879 (t0) cc_final: 0.6721 (t70) REVERT: C 628 HIS cc_start: 0.7412 (t-90) cc_final: 0.7159 (t-170) REVERT: D 305 MET cc_start: 0.7695 (ttm) cc_final: 0.7306 (tpt) REVERT: D 361 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: D 376 MET cc_start: 0.9144 (mmm) cc_final: 0.8430 (mmm) REVERT: D 401 ASP cc_start: 0.7974 (t0) cc_final: 0.6876 (t70) REVERT: D 530 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7412 (mtp) outliers start: 32 outliers final: 18 residues processed: 233 average time/residue: 0.1139 time to fit residues: 41.0116 Evaluate side-chains 230 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 0.0050 chunk 164 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 171 optimal weight: 0.4980 chunk 11 optimal weight: 0.0870 chunk 180 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102086 restraints weight = 30198.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105487 restraints weight = 15357.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107674 restraints weight = 10240.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109007 restraints weight = 8085.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109733 restraints weight = 7078.667| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16348 Z= 0.110 Angle : 0.531 7.735 22228 Z= 0.269 Chirality : 0.038 0.125 2548 Planarity : 0.004 0.042 2788 Dihedral : 7.098 135.522 2336 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.90 % Allowed : 19.04 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 2096 helix: 1.96 (0.13), residues: 1536 sheet: 0.70 (0.60), residues: 84 loop : -2.01 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 270 TYR 0.006 0.001 TYR B 347 PHE 0.024 0.001 PHE C 186 TRP 0.014 0.001 TRP C 281 HIS 0.005 0.000 HIS D 628 Details of bonding type rmsd covalent geometry : bond 0.00222 (16348) covalent geometry : angle 0.53075 (22228) hydrogen bonds : bond 0.03239 ( 1185) hydrogen bonds : angle 4.00140 ( 3471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.610 Fit side-chains REVERT: A 101 MET cc_start: 0.8103 (mmm) cc_final: 0.7753 (mtt) REVERT: A 361 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: A 401 ASP cc_start: 0.7729 (t0) cc_final: 0.6686 (t70) REVERT: A 624 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 401 ASP cc_start: 0.7765 (t0) cc_final: 0.6712 (t70) REVERT: C 101 MET cc_start: 0.8070 (mtm) cc_final: 0.7616 (mtp) REVERT: C 305 MET cc_start: 0.7573 (ttm) cc_final: 0.7266 (tmm) REVERT: C 336 MET cc_start: 0.7868 (ptp) cc_final: 0.7603 (ptm) REVERT: C 401 ASP cc_start: 0.7786 (t0) cc_final: 0.6681 (t70) REVERT: D 361 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: D 401 ASP cc_start: 0.7751 (t0) cc_final: 0.6710 (t70) outliers start: 28 outliers final: 16 residues processed: 247 average time/residue: 0.1167 time to fit residues: 44.7550 Evaluate side-chains 232 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098760 restraints weight = 30653.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102038 restraints weight = 15898.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104169 restraints weight = 10696.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105366 restraints weight = 8505.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106117 restraints weight = 7519.260| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16348 Z= 0.127 Angle : 0.554 8.256 22228 Z= 0.280 Chirality : 0.039 0.132 2548 Planarity : 0.004 0.041 2788 Dihedral : 7.067 134.963 2336 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.69 % Allowed : 19.99 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 2096 helix: 2.12 (0.13), residues: 1528 sheet: 0.79 (0.61), residues: 84 loop : -1.94 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.011 0.001 TYR D 347 PHE 0.013 0.001 PHE C 186 TRP 0.010 0.001 TRP D 330 HIS 0.008 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00280 (16348) covalent geometry : angle 0.55442 (22228) hydrogen bonds : bond 0.03428 ( 1185) hydrogen bonds : angle 3.98292 ( 3471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.596 Fit side-chains REVERT: A 101 MET cc_start: 0.8141 (mmm) cc_final: 0.7746 (mtt) REVERT: A 152 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6444 (tpp) REVERT: A 274 LEU cc_start: 0.9301 (tp) cc_final: 0.8939 (tp) REVERT: A 306 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 361 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: A 401 ASP cc_start: 0.7793 (t0) cc_final: 0.6750 (t70) REVERT: A 624 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 361 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 401 ASP cc_start: 0.7793 (t0) cc_final: 0.6784 (t70) REVERT: C 101 MET cc_start: 0.8118 (mtm) cc_final: 0.7674 (mtp) REVERT: C 153 MET cc_start: 0.7435 (mtp) cc_final: 0.6916 (ttm) REVERT: C 186 PHE cc_start: 0.7190 (m-10) cc_final: 0.6985 (m-80) REVERT: C 305 MET cc_start: 0.7556 (ttm) cc_final: 0.7211 (tmm) REVERT: C 336 MET cc_start: 0.7851 (ptp) cc_final: 0.7545 (ptm) REVERT: C 401 ASP cc_start: 0.7825 (t0) cc_final: 0.6791 (t70) REVERT: C 628 HIS cc_start: 0.7342 (t-170) cc_final: 0.7057 (t-170) REVERT: D 361 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 401 ASP cc_start: 0.7814 (t0) cc_final: 0.6813 (t70) outliers start: 25 outliers final: 17 residues processed: 225 average time/residue: 0.1185 time to fit residues: 41.0532 Evaluate side-chains 229 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS B 628 HIS D 628 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099791 restraints weight = 30445.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.102880 restraints weight = 16298.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104891 restraints weight = 11203.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106049 restraints weight = 9004.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106701 restraints weight = 7981.167| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16348 Z= 0.124 Angle : 0.554 7.954 22228 Z= 0.280 Chirality : 0.039 0.146 2548 Planarity : 0.004 0.041 2788 Dihedral : 7.019 134.568 2336 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.83 % Allowed : 20.12 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 2096 helix: 2.21 (0.13), residues: 1528 sheet: 0.82 (0.61), residues: 84 loop : -1.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.009 0.001 TYR B 347 PHE 0.011 0.001 PHE D 538 TRP 0.010 0.001 TRP B 330 HIS 0.004 0.001 HIS D 628 Details of bonding type rmsd covalent geometry : bond 0.00269 (16348) covalent geometry : angle 0.55373 (22228) hydrogen bonds : bond 0.03383 ( 1185) hydrogen bonds : angle 3.96986 ( 3471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.671 Fit side-chains REVERT: A 101 MET cc_start: 0.8137 (mmm) cc_final: 0.7717 (mtt) REVERT: A 152 MET cc_start: 0.6824 (tpt) cc_final: 0.6371 (tpp) REVERT: A 274 LEU cc_start: 0.9268 (tp) cc_final: 0.9027 (tp) REVERT: A 306 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 361 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: A 401 ASP cc_start: 0.7808 (t0) cc_final: 0.6790 (t70) REVERT: A 624 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 305 MET cc_start: 0.7750 (tpt) cc_final: 0.7083 (tpt) REVERT: B 361 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: B 401 ASP cc_start: 0.7887 (t0) cc_final: 0.6834 (t70) REVERT: C 101 MET cc_start: 0.8155 (mtm) cc_final: 0.7663 (mtp) REVERT: C 305 MET cc_start: 0.7732 (ttm) cc_final: 0.7306 (tmm) REVERT: C 336 MET cc_start: 0.7896 (ptp) cc_final: 0.7570 (ptm) REVERT: C 376 MET cc_start: 0.9029 (mmm) cc_final: 0.8290 (mmm) REVERT: C 401 ASP cc_start: 0.7818 (t0) cc_final: 0.6761 (t70) REVERT: C 628 HIS cc_start: 0.7447 (t-170) cc_final: 0.7132 (t-170) REVERT: D 361 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: D 401 ASP cc_start: 0.7803 (t0) cc_final: 0.6800 (t70) outliers start: 27 outliers final: 14 residues processed: 220 average time/residue: 0.1159 time to fit residues: 38.8081 Evaluate side-chains 226 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 205 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS B 628 HIS D 355 HIS D 628 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100234 restraints weight = 30653.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103516 restraints weight = 15855.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105617 restraints weight = 10665.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106886 restraints weight = 8468.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107638 restraints weight = 7437.927| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16348 Z= 0.116 Angle : 0.564 8.462 22228 Z= 0.280 Chirality : 0.039 0.139 2548 Planarity : 0.004 0.042 2788 Dihedral : 6.968 134.181 2336 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.76 % Allowed : 20.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 2096 helix: 2.25 (0.13), residues: 1540 sheet: 0.85 (0.61), residues: 84 loop : -1.74 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 270 TYR 0.012 0.001 TYR C 277 PHE 0.010 0.001 PHE B 538 TRP 0.011 0.001 TRP B 330 HIS 0.004 0.001 HIS D 628 Details of bonding type rmsd covalent geometry : bond 0.00248 (16348) covalent geometry : angle 0.56388 (22228) hydrogen bonds : bond 0.03262 ( 1185) hydrogen bonds : angle 3.93846 ( 3471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.663 Fit side-chains REVERT: A 101 MET cc_start: 0.8108 (mmm) cc_final: 0.7736 (mtt) REVERT: A 152 MET cc_start: 0.6803 (tpt) cc_final: 0.6408 (tpp) REVERT: A 305 MET cc_start: 0.7479 (mmm) cc_final: 0.7105 (tpt) REVERT: A 306 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8787 (mm) REVERT: A 361 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: A 401 ASP cc_start: 0.7791 (t0) cc_final: 0.6721 (t70) REVERT: A 624 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7326 (tm-30) REVERT: B 305 MET cc_start: 0.7728 (tpt) cc_final: 0.7035 (tpt) REVERT: B 361 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 401 ASP cc_start: 0.7761 (t0) cc_final: 0.6720 (t70) REVERT: C 101 MET cc_start: 0.8104 (mtm) cc_final: 0.7635 (mtp) REVERT: C 305 MET cc_start: 0.7684 (ttm) cc_final: 0.7314 (tmm) REVERT: C 336 MET cc_start: 0.7860 (ptp) cc_final: 0.7548 (ptm) REVERT: C 401 ASP cc_start: 0.7863 (t0) cc_final: 0.6787 (t70) REVERT: D 361 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: D 401 ASP cc_start: 0.7695 (t0) cc_final: 0.6716 (t70) outliers start: 26 outliers final: 16 residues processed: 230 average time/residue: 0.1234 time to fit residues: 43.1152 Evaluate side-chains 232 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 137 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS B 628 HIS C 628 HIS D 355 HIS D 628 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096332 restraints weight = 30498.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099484 restraints weight = 16071.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101464 restraints weight = 10927.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.102709 restraints weight = 8764.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103380 restraints weight = 7729.413| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16348 Z= 0.168 Angle : 0.613 8.928 22228 Z= 0.309 Chirality : 0.041 0.163 2548 Planarity : 0.004 0.040 2788 Dihedral : 7.074 134.614 2336 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.90 % Allowed : 20.33 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 2096 helix: 2.20 (0.13), residues: 1536 sheet: 0.78 (0.61), residues: 84 loop : -1.74 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.016 0.001 TYR B 347 PHE 0.015 0.001 PHE A 538 TRP 0.015 0.002 TRP B 373 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00389 (16348) covalent geometry : angle 0.61294 (22228) hydrogen bonds : bond 0.03878 ( 1185) hydrogen bonds : angle 4.08258 ( 3471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.69 seconds wall clock time: 44 minutes 58.75 seconds (2698.75 seconds total)