Starting phenix.real_space_refine on Sat Sep 12 13:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uqg_20847/09_2026/6uqg_20847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uqg_20847/09_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_20847/09_2026/6uqg_20847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uqg_20847/09_2026/6uqg_20847.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uqg_20847/09_2026/6uqg_20847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uqg_20847/09_2026/6uqg_20847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uqg_20847/09_2026/6uqg_20847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uqg_20847/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.15, per 1000 atoms: 0.26 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: 1.47 Conformation dependent library (CDL) restraints added in 707.9 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: 0.56 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: 3.06 Time building geometry restraints manager: 1.92 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: 21184 2.12 - 4.24: 897 4.24 - 6.36: 95 6.36 - 8.48: 33 8.48 - 10.60: 19 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 - 21.23: 8868 21.23 - 42.47: 708 42.47 - 63.70: 40 63.70 - 84.94: 8 84.94 - 106.17: 12 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: 1831 0.055 - 0.110: 594 0.110 - 0.166: 89 0.166 - 0.221: 22 0.221 - 0.276: 12 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: 0.05 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: 2.150 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.420 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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= 0.383 Angle : 1.007 10.600 22228 Z= 0.575 Chirality : 0.057 0.276 2548 Planarity : 0.008 0.083 2788 Dihedral : 14.771 106.172 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/Z covalent geometry : bond 0.00876 / 0.38 (16348) covalent geometry : angle 1.00664 / 0.57 (22228) hydrogen bonds : bond 0.12927 / 8.54 ( 1185) hydrogen bonds : angle 5.87351 / 4.23 ( 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 : 0.682 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: 0.1297 time to fit residues: 56.7166 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 : 0.610 ------------------------------------------------------------------------------- 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... B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094658 restraints weight = 31098.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098344 restraints weight = 14282.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100848 restraints weight = 8916.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102378 restraints weight = 6753.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103237 restraints weight = 5763.533| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16348 Z= 0.138 Angle : 0.603 8.508 22228 Z= 0.300 Chirality : 0.040 0.198 2548 Planarity : 0.005 0.053 2788 Dihedral : 4.963 33.285 2336 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.24 % Allowed : 12.13 % 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: -0.90 (0.17), residues: 2096 helix: 0.19 (0.12), residues: 1528 sheet: -0.83 (0.46), residues: 88 loop : -2.92 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.012 0.001 TYR D 347 PHE 0.018 0.001 PHE A 109 TRP 0.010 0.001 TRP A 330 HIS 0.003 0.001 HIS D 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (16348) covalent geometry : angle 0.60328 / 0.30 (22228) hydrogen bonds : bond 0.04171 / 2.78 ( 1185) hydrogen bonds : angle 4.42501 / 3.18 ( 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 285 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8159 (mmm) cc_final: 0.7547 (mtt) REVERT: A 281 TRP cc_start: 0.7479 (t60) cc_final: 0.7213 (t60) REVERT: A 305 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7261 (tpp) REVERT: A 401 ASP cc_start: 0.8151 (t0) cc_final: 0.7062 (t70) REVERT: A 410 LYS cc_start: 0.8567 (tttt) cc_final: 0.8324 (ttpt) REVERT: A 624 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 628 HIS cc_start: 0.8030 (t-90) cc_final: 0.7527 (t-170) REVERT: B 156 ASN cc_start: 0.7878 (t0) cc_final: 0.7644 (t0) REVERT: B 281 TRP cc_start: 0.7550 (t60) cc_final: 0.7332 (t60) REVERT: B 305 MET cc_start: 0.7677 (ttm) cc_final: 0.7132 (tpt) REVERT: B 385 CYS cc_start: 0.8726 (m) cc_final: 0.8410 (t) REVERT: B 388 MET cc_start: 0.8245 (mmt) cc_final: 0.8043 (mmt) REVERT: B 530 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7509 (mtp) REVERT: B 628 HIS cc_start: 0.7635 (t-90) cc_final: 0.6899 (t-170) REVERT: C 101 MET cc_start: 0.8202 (mtm) cc_final: 0.7787 (mtp) REVERT: C 305 MET cc_start: 0.7738 (ttm) cc_final: 0.7511 (tpt) REVERT: C 347 TYR cc_start: 0.8701 (t80) cc_final: 0.8409 (t80) REVERT: C 386 TYR cc_start: 0.8316 (t80) cc_final: 0.8097 (t80) REVERT: C 401 ASP cc_start: 0.7936 (t0) cc_final: 0.6769 (t70) REVERT: C 487 MET cc_start: 0.8258 (ttm) cc_final: 0.8000 (ttm) REVERT: C 628 HIS cc_start: 0.7462 (t-90) cc_final: 0.7158 (t-170) REVERT: D 156 ASN cc_start: 0.7860 (t0) cc_final: 0.7631 (t0) REVERT: D 305 MET cc_start: 0.7667 (ttm) cc_final: 0.7456 (tpt) REVERT: D 386 TYR cc_start: 0.8447 (t80) cc_final: 0.8238 (t80) REVERT: D 530 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: D 628 HIS cc_start: 0.7503 (t-90) cc_final: 0.6849 (t-170) outliers start: 33 outliers final: 17 residues processed: 268 average time/residue: 0.1158 time to fit residues: 48.0657 Evaluate side-chains 245 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL 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 C residue 394 THR 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: 0.8980 chunk 34 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 64 optimal weight: 0.0270 chunk 147 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3765 r_free = 0.3765 target = 0.127217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095418 restraints weight = 31405.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099185 restraints weight = 14280.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101706 restraints weight = 8903.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103236 restraints weight = 6745.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104138 restraints weight = 5759.059| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16348 Z= 0.116 Angle : 0.566 8.855 22228 Z= 0.275 Chirality : 0.039 0.153 2548 Planarity : 0.004 0.046 2788 Dihedral : 4.435 31.807 2336 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.76 % Allowed : 15.38 % Favored : 82.86 % 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: 0.38 (0.18), residues: 2096 helix: 1.14 (0.13), residues: 1532 sheet: -0.02 (0.55), residues: 88 loop : -2.65 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.009 0.001 TYR A 347 PHE 0.008 0.001 PHE A 538 TRP 0.010 0.001 TRP C 281 HIS 0.002 0.000 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (16348) covalent geometry : angle 0.56631 / 0.27 (22228) hydrogen bonds : bond 0.03670 / 2.44 ( 1185) hydrogen bonds : angle 4.10728 / 2.94 ( 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 259 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.8146 (mmm) cc_final: 0.7560 (mtt) REVERT: A 305 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7243 (tpp) REVERT: A 401 ASP cc_start: 0.8034 (t0) cc_final: 0.6873 (t70) REVERT: A 410 LYS cc_start: 0.8567 (tttt) cc_final: 0.8335 (ttpt) REVERT: A 624 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 388 MET cc_start: 0.8350 (mmt) cc_final: 0.7993 (mmt) REVERT: B 404 ARG cc_start: 0.7608 (tmt170) cc_final: 0.7348 (tmm160) REVERT: B 530 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7352 (mtp) REVERT: B 628 HIS cc_start: 0.7795 (t-90) cc_final: 0.7315 (t-170) REVERT: C 101 MET cc_start: 0.8210 (mtm) cc_final: 0.7835 (mtp) REVERT: C 192 MET cc_start: 0.7608 (mpp) cc_final: 0.7279 (mpp) REVERT: C 305 MET cc_start: 0.7699 (ttm) cc_final: 0.7414 (tpt) REVERT: C 398 GLN cc_start: 0.8596 (mt0) cc_final: 0.8366 (mt0) REVERT: C 401 ASP cc_start: 0.7787 (t0) cc_final: 0.6599 (t70) REVERT: C 628 HIS cc_start: 0.7485 (t-90) cc_final: 0.7185 (t-170) REVERT: D 376 MET cc_start: 0.9138 (mmm) cc_final: 0.8396 (mmm) REVERT: D 530 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7319 (mtp) REVERT: D 628 HIS cc_start: 0.7779 (t-90) cc_final: 0.7353 (t-170) outliers start: 26 outliers final: 14 residues processed: 246 average time/residue: 0.1121 time to fit residues: 42.4368 Evaluate side-chains 226 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 149 MET 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: 0.4980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 162 optimal weight: 0.3980 chunk 138 optimal weight: 0.6980 chunk 195 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096139 restraints weight = 30676.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099431 restraints weight = 15568.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101669 restraints weight = 10259.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102992 restraints weight = 8011.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103594 restraints weight = 6981.653| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16348 Z= 0.129 Angle : 0.575 9.082 22228 Z= 0.279 Chirality : 0.040 0.156 2548 Planarity : 0.004 0.043 2788 Dihedral : 4.296 32.419 2336 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 16.19 % Favored : 81.78 % 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: 0.97 (0.18), residues: 2096 helix: 1.58 (0.13), residues: 1532 sheet: 0.19 (0.57), residues: 88 loop : -2.45 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.013 0.001 TYR B 347 PHE 0.011 0.001 PHE A 538 TRP 0.012 0.001 TRP A 281 HIS 0.003 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16348) covalent geometry : angle 0.57525 / 0.28 (22228) hydrogen bonds : bond 0.03690 / 2.46 ( 1185) hydrogen bonds : angle 4.04331 / 2.89 ( 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 264 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.624 Fit side-chains REVERT: A 101 MET cc_start: 0.8123 (mmm) cc_final: 0.7599 (mtt) REVERT: A 305 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7241 (tpp) REVERT: A 401 ASP cc_start: 0.8030 (t0) cc_final: 0.6941 (t70) REVERT: A 404 ARG cc_start: 0.7686 (tmt170) cc_final: 0.7032 (tmm-80) REVERT: A 410 LYS cc_start: 0.8625 (tttt) cc_final: 0.8357 (ttpt) REVERT: A 624 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 628 HIS cc_start: 0.8228 (t-170) cc_final: 0.7999 (t-170) REVERT: B 361 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: B 404 ARG cc_start: 0.7685 (tmt170) cc_final: 0.7397 (tmm160) REVERT: B 530 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7432 (mtp) REVERT: B 628 HIS cc_start: 0.7830 (t-90) cc_final: 0.7500 (t-170) REVERT: C 101 MET cc_start: 0.8227 (mtm) cc_final: 0.7844 (mtp) REVERT: C 149 MET cc_start: 0.6882 (mmp) cc_final: 0.6631 (mmp) REVERT: C 192 MET cc_start: 0.7652 (mpp) cc_final: 0.7197 (mmt) REVERT: C 305 MET cc_start: 0.7747 (ttm) cc_final: 0.7130 (tmm) REVERT: C 401 ASP cc_start: 0.7817 (t0) cc_final: 0.6639 (t70) REVERT: C 628 HIS cc_start: 0.7446 (t-90) cc_final: 0.7233 (t-170) REVERT: D 305 MET cc_start: 0.7636 (ttm) cc_final: 0.7307 (tpt) REVERT: D 376 MET cc_start: 0.9159 (mmm) cc_final: 0.8401 (mmm) REVERT: D 404 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7421 (tmm160) REVERT: D 530 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7396 (mtp) outliers start: 30 outliers final: 12 residues processed: 244 average time/residue: 0.1168 time to fit residues: 43.9286 Evaluate side-chains 220 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 259 PHE 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 194 PHE Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 308 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 210 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3759 r_free = 0.3759 target = 0.126673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095914 restraints weight = 30707.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099261 restraints weight = 15352.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.101480 restraints weight = 10062.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102816 restraints weight = 7845.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103617 restraints weight = 6828.871| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16348 Z= 0.131 Angle : 0.579 9.094 22228 Z= 0.280 Chirality : 0.040 0.157 2548 Planarity : 0.004 0.043 2788 Dihedral : 4.211 32.986 2336 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.24 % Allowed : 17.14 % Favored : 80.62 % 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: 1.33 (0.19), residues: 2096 helix: 1.80 (0.13), residues: 1536 sheet: 0.78 (0.60), residues: 84 loop : -2.28 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.013 0.001 TYR D 347 PHE 0.011 0.001 PHE A 538 TRP 0.012 0.001 TRP D 281 HIS 0.002 0.001 HIS B 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16348) covalent geometry : angle 0.57872 / 0.28 (22228) hydrogen bonds : bond 0.03616 / 2.41 ( 1185) hydrogen bonds : angle 4.01645 / 2.87 ( 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 260 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.664 Fit side-chains REVERT: A 101 MET cc_start: 0.8120 (mmm) cc_final: 0.7609 (mtt) REVERT: A 305 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7184 (tpp) REVERT: A 361 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: A 401 ASP cc_start: 0.8039 (t0) cc_final: 0.6854 (t70) REVERT: A 404 ARG cc_start: 0.7753 (tmt170) cc_final: 0.7033 (tmm-80) REVERT: A 410 LYS cc_start: 0.8635 (tttt) cc_final: 0.8375 (ttpt) REVERT: A 624 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 628 HIS cc_start: 0.8164 (t-170) cc_final: 0.7850 (t-170) REVERT: B 259 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: B 305 MET cc_start: 0.7895 (tpp) cc_final: 0.7674 (tpt) REVERT: B 361 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: B 388 MET cc_start: 0.8444 (mmt) cc_final: 0.8226 (mmt) REVERT: B 404 ARG cc_start: 0.7780 (tmt170) cc_final: 0.7357 (tmm160) REVERT: B 530 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (mtp) REVERT: B 628 HIS cc_start: 0.7836 (t-90) cc_final: 0.7521 (t-170) REVERT: C 101 MET cc_start: 0.8274 (mtm) cc_final: 0.7768 (mtp) REVERT: C 149 MET cc_start: 0.6899 (mmp) cc_final: 0.6678 (mmp) REVERT: C 192 MET cc_start: 0.7664 (mpp) cc_final: 0.7237 (mmt) REVERT: C 305 MET cc_start: 0.7748 (ttm) cc_final: 0.7143 (tmm) REVERT: C 401 ASP cc_start: 0.7927 (t0) cc_final: 0.6812 (t70) REVERT: C 628 HIS cc_start: 0.7551 (t-90) cc_final: 0.7252 (t-170) REVERT: D 259 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: D 305 MET cc_start: 0.7667 (ttm) cc_final: 0.7297 (tpt) REVERT: D 361 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: D 404 ARG cc_start: 0.7769 (ttt180) cc_final: 0.7437 (tmm160) REVERT: D 530 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7414 (mtp) REVERT: D 628 HIS cc_start: 0.7564 (t-170) cc_final: 0.7154 (t-170) REVERT: D 632 MET cc_start: 0.6765 (mmp) cc_final: 0.6229 (mtm) outliers start: 33 outliers final: 16 residues processed: 239 average time/residue: 0.1209 time to fit residues: 44.2131 Evaluate side-chains 229 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain A residue 305 MET 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 154 VAL 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 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain B residue 530 MET 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 259 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 10 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099304 restraints weight = 30459.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102640 restraints weight = 15743.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104759 restraints weight = 10612.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105992 restraints weight = 8440.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106748 restraints weight = 7434.684| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16348 Z= 0.114 Angle : 0.563 8.866 22228 Z= 0.271 Chirality : 0.039 0.151 2548 Planarity : 0.004 0.043 2788 Dihedral : 4.131 32.812 2336 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.83 % Allowed : 18.09 % Favored : 80.08 % 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: 0.91 (0.60), residues: 84 loop : -2.06 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.009 0.001 TYR B 347 PHE 0.011 0.001 PHE B 186 TRP 0.013 0.001 TRP D 281 HIS 0.002 0.000 HIS B 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16348) covalent geometry : angle 0.56331 / 0.27 (22228) hydrogen bonds : bond 0.03377 / 2.25 ( 1185) hydrogen bonds : angle 3.93969 / 2.81 ( 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 262 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.596 Fit side-chains REVERT: A 101 MET cc_start: 0.8120 (mmm) cc_final: 0.7733 (mtt) REVERT: A 401 ASP cc_start: 0.7821 (t0) cc_final: 0.6737 (t70) REVERT: A 404 ARG cc_start: 0.7694 (tmt170) cc_final: 0.7476 (ttt180) REVERT: A 624 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 305 MET cc_start: 0.7979 (tpp) cc_final: 0.7742 (tpt) REVERT: B 361 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 398 GLN cc_start: 0.8476 (mt0) cc_final: 0.8206 (mt0) REVERT: C 101 MET cc_start: 0.8152 (mtm) cc_final: 0.7678 (mtp) REVERT: C 305 MET cc_start: 0.7599 (ttm) cc_final: 0.7293 (tmm) REVERT: C 376 MET cc_start: 0.8945 (mmm) cc_final: 0.8362 (mmm) REVERT: C 401 ASP cc_start: 0.7814 (t0) cc_final: 0.6739 (t70) REVERT: D 361 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: D 376 MET cc_start: 0.8911 (mmm) cc_final: 0.8361 (mmm) REVERT: D 401 ASP cc_start: 0.7853 (t0) cc_final: 0.6702 (t70) REVERT: D 404 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7299 (tmm160) REVERT: D 632 MET cc_start: 0.6828 (mmp) cc_final: 0.6132 (tmm) outliers start: 27 outliers final: 17 residues processed: 243 average time/residue: 0.1126 time to fit residues: 42.1090 Evaluate side-chains 228 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 427 MET 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 308 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 361 TYR 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: 0.9980 chunk 164 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 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 = 0.3793 r_free = 0.3793 target = 0.129553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099178 restraints weight = 30530.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102494 restraints weight = 15881.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.104611 restraints weight = 10715.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105847 restraints weight = 8545.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106407 restraints weight = 7540.587| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16348 Z= 0.122 Angle : 0.575 8.968 22228 Z= 0.277 Chirality : 0.040 0.149 2548 Planarity : 0.004 0.041 2788 Dihedral : 4.108 33.035 2336 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.03 % Allowed : 19.31 % Favored : 78.66 % 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: 1.70 (0.19), residues: 2096 helix: 2.02 (0.13), residues: 1536 sheet: 0.95 (0.60), residues: 84 loop : -1.92 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 270 TYR 0.011 0.001 TYR D 347 PHE 0.014 0.001 PHE A 186 TRP 0.011 0.001 TRP D 281 HIS 0.007 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16348) covalent geometry : angle 0.57517 / 0.28 (22228) hydrogen bonds : bond 0.03436 / 2.29 ( 1185) hydrogen bonds : angle 3.95060 / 2.82 ( 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 252 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.603 Fit side-chains REVERT: A 101 MET cc_start: 0.8114 (mmm) cc_final: 0.7708 (mtt) REVERT: A 361 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: A 401 ASP cc_start: 0.7797 (t0) cc_final: 0.6699 (t70) REVERT: A 624 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 305 MET cc_start: 0.7970 (tpp) cc_final: 0.7750 (tpt) REVERT: B 361 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: B 401 ASP cc_start: 0.7873 (t0) cc_final: 0.6843 (t70) REVERT: C 101 MET cc_start: 0.8122 (mtm) cc_final: 0.7661 (mtp) REVERT: C 305 MET cc_start: 0.7609 (ttm) cc_final: 0.7281 (tmm) REVERT: C 336 MET cc_start: 0.7841 (ptp) cc_final: 0.7525 (ptm) REVERT: C 376 MET cc_start: 0.8960 (mmm) cc_final: 0.8379 (mmm) REVERT: C 401 ASP cc_start: 0.7828 (t0) cc_final: 0.6778 (t70) REVERT: C 628 HIS cc_start: 0.7423 (t-170) cc_final: 0.7130 (t-170) REVERT: D 361 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: D 376 MET cc_start: 0.8926 (mmm) cc_final: 0.8390 (mmm) REVERT: D 401 ASP cc_start: 0.7774 (t0) cc_final: 0.6635 (t70) REVERT: D 404 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7334 (tmm160) REVERT: D 632 MET cc_start: 0.7150 (mmp) cc_final: 0.6049 (tmm) outliers start: 30 outliers final: 19 residues processed: 234 average time/residue: 0.1145 time to fit residues: 41.6426 Evaluate side-chains 233 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 427 MET 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 308 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 268 LEU 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: 6.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3799 r_free = 0.3799 target = 0.129895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099638 restraints weight = 30482.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102956 restraints weight = 15812.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105077 restraints weight = 10622.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106360 restraints weight = 8434.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106761 restraints weight = 7407.309| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16348 Z= 0.114 Angle : 0.572 8.889 22228 Z= 0.274 Chirality : 0.039 0.148 2548 Planarity : 0.004 0.042 2788 Dihedral : 4.071 32.885 2336 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.63 % Allowed : 19.24 % Favored : 79.13 % 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: 1.89 (0.19), residues: 2096 helix: 2.18 (0.13), residues: 1528 sheet: 0.95 (0.59), residues: 84 loop : -1.86 (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 D 347 PHE 0.011 0.001 PHE C 186 TRP 0.010 0.001 TRP A 330 HIS 0.010 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16348) covalent geometry : angle 0.57225 / 0.27 (22228) hydrogen bonds : bond 0.03322 / 2.22 ( 1185) hydrogen bonds : angle 3.91466 / 2.79 ( 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 246 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.639 Fit side-chains REVERT: A 101 MET cc_start: 0.8117 (mmm) cc_final: 0.7731 (mtt) REVERT: A 274 LEU cc_start: 0.9285 (tp) cc_final: 0.9060 (tp) REVERT: A 401 ASP cc_start: 0.7775 (t0) cc_final: 0.6732 (t70) REVERT: A 404 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7539 (ttt180) REVERT: A 624 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 305 MET cc_start: 0.7953 (tpp) cc_final: 0.7751 (tpt) REVERT: B 361 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 401 ASP cc_start: 0.7858 (t0) cc_final: 0.6860 (t70) REVERT: C 101 MET cc_start: 0.8111 (mtm) cc_final: 0.7643 (mtp) REVERT: C 149 MET cc_start: 0.7391 (mmp) cc_final: 0.7032 (mmp) REVERT: C 305 MET cc_start: 0.7650 (ttm) cc_final: 0.7335 (tmm) REVERT: C 336 MET cc_start: 0.7822 (ptp) cc_final: 0.7517 (ptm) REVERT: C 376 MET cc_start: 0.8916 (mmm) cc_final: 0.8361 (mmm) REVERT: C 401 ASP cc_start: 0.7881 (t0) cc_final: 0.6786 (t70) REVERT: C 628 HIS cc_start: 0.7412 (t-170) cc_final: 0.7090 (t-170) REVERT: D 361 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: D 401 ASP cc_start: 0.7798 (t0) cc_final: 0.6644 (t70) REVERT: D 404 ARG cc_start: 0.7728 (ttt180) cc_final: 0.7374 (tmm160) REVERT: D 632 MET cc_start: 0.7201 (mmp) cc_final: 0.5869 (tmm) outliers start: 24 outliers final: 20 residues processed: 232 average time/residue: 0.1196 time to fit residues: 42.7596 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 : 0.623 ------------------------------------------------------------------------------- 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 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 106 VAL 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 427 MET Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 259 PHE 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 268 LEU 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: 2.9990 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 HIS B 398 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096698 restraints weight = 30808.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099945 restraints weight = 15949.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102099 restraints weight = 10721.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103355 restraints weight = 8518.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103851 restraints weight = 7492.987| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16348 Z= 0.201 Angle : 0.650 9.644 22228 Z= 0.318 Chirality : 0.043 0.182 2548 Planarity : 0.004 0.039 2788 Dihedral : 4.296 35.664 2336 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 19.51 % 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: 1.77 (0.19), residues: 2096 helix: 2.09 (0.13), residues: 1524 sheet: 0.99 (0.59), residues: 84 loop : -1.90 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.020 0.001 TYR B 347 PHE 0.015 0.001 PHE A 538 TRP 0.016 0.002 TRP B 373 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (16348) covalent geometry : angle 0.64980 / 0.32 (22228) hydrogen bonds : bond 0.04101 / 2.74 ( 1185) hydrogen bonds : angle 4.14055 / 2.95 ( 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 242 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.615 Fit side-chains REVERT: A 152 MET cc_start: 0.7052 (tpt) cc_final: 0.6660 (tpp) REVERT: A 274 LEU cc_start: 0.9368 (tp) cc_final: 0.8994 (tp) REVERT: A 306 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8815 (mm) REVERT: A 361 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: A 401 ASP cc_start: 0.7894 (t0) cc_final: 0.6884 (t70) REVERT: B 305 MET cc_start: 0.8016 (tpp) cc_final: 0.7816 (tpt) REVERT: B 361 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: C 101 MET cc_start: 0.8149 (mtm) cc_final: 0.7679 (mtp) REVERT: C 376 MET cc_start: 0.9061 (mmm) cc_final: 0.8411 (mmm) REVERT: C 401 ASP cc_start: 0.7776 (t0) cc_final: 0.6728 (t70) REVERT: C 628 HIS cc_start: 0.7505 (t-170) cc_final: 0.7143 (t-170) REVERT: D 361 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: D 401 ASP cc_start: 0.7764 (t0) cc_final: 0.6630 (t70) REVERT: D 404 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7363 (tmm160) REVERT: D 632 MET cc_start: 0.7226 (mmp) cc_final: 0.5724 (tmm) outliers start: 35 outliers final: 19 residues processed: 223 average time/residue: 0.1174 time to fit residues: 40.5593 Evaluate side-chains 222 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL 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 188 LEU 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 106 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 106 VAL 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 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 205 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A 628 HIS B 628 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099557 restraints weight = 30376.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102673 restraints weight = 16387.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104729 restraints weight = 11240.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105731 restraints weight = 9004.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106578 restraints weight = 8034.433| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16348 Z= 0.116 Angle : 0.594 9.058 22228 Z= 0.284 Chirality : 0.040 0.151 2548 Planarity : 0.004 0.042 2788 Dihedral : 4.122 34.669 2336 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.56 % Allowed : 20.46 % Favored : 77.98 % 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: 1.91 (0.19), residues: 2096 helix: 2.15 (0.13), residues: 1540 sheet: 0.96 (0.60), residues: 84 loop : -1.78 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.008 0.001 TYR B 347 PHE 0.016 0.001 PHE C 186 TRP 0.011 0.001 TRP D 330 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (16348) covalent geometry : angle 0.59392 / 0.28 (22228) hydrogen bonds : bond 0.03396 / 2.26 ( 1185) hydrogen bonds : angle 3.97896 / 2.83 ( 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 236 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.615 Fit side-chains REVERT: A 101 MET cc_start: 0.8467 (mmm) cc_final: 0.7684 (mtt) REVERT: A 152 MET cc_start: 0.6861 (tpt) cc_final: 0.6475 (tpp) REVERT: A 262 ILE cc_start: 0.9062 (tp) cc_final: 0.8804 (tt) REVERT: A 274 LEU cc_start: 0.9278 (tp) cc_final: 0.9043 (tp) REVERT: A 305 MET cc_start: 0.7529 (mmm) cc_final: 0.7122 (tpt) REVERT: A 361 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: A 401 ASP cc_start: 0.7792 (t0) cc_final: 0.6748 (t70) REVERT: B 305 MET cc_start: 0.7963 (tpp) cc_final: 0.7761 (tpt) REVERT: B 361 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: C 101 MET cc_start: 0.8168 (mtm) cc_final: 0.7711 (mtp) REVERT: C 336 MET cc_start: 0.7920 (ptp) cc_final: 0.7619 (ptm) REVERT: C 376 MET cc_start: 0.9030 (mmm) cc_final: 0.8389 (mmm) REVERT: C 401 ASP cc_start: 0.7903 (t0) cc_final: 0.6819 (t70) REVERT: C 628 HIS cc_start: 0.7530 (t-170) cc_final: 0.7178 (t-170) REVERT: D 361 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: D 376 MET cc_start: 0.9007 (mmm) cc_final: 0.8283 (mmm) REVERT: D 401 ASP cc_start: 0.7795 (t0) cc_final: 0.6639 (t70) REVERT: D 404 ARG cc_start: 0.7727 (ttt180) cc_final: 0.7353 (tmm160) REVERT: D 632 MET cc_start: 0.7073 (mmp) cc_final: 0.5663 (tmm) outliers start: 23 outliers final: 17 residues processed: 222 average time/residue: 0.1171 time to fit residues: 40.3731 Evaluate side-chains 224 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL 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 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 308 LEU Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain C residue 106 VAL 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: 3.9990 chunk 93 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 HIS B 398 GLN B 628 HIS ** D 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097746 restraints weight = 30221.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100525 restraints weight = 17233.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102317 restraints weight = 12297.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103174 restraints weight = 10086.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103933 restraints weight = 9117.175| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16348 Z= 0.125 Angle : 0.602 9.055 22228 Z= 0.287 Chirality : 0.040 0.155 2548 Planarity : 0.004 0.041 2788 Dihedral : 4.089 34.389 2336 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.90 % Allowed : 20.19 % Favored : 77.91 % 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: 2.04 (0.19), residues: 2096 helix: 2.25 (0.13), residues: 1540 sheet: 1.03 (0.60), residues: 84 loop : -1.76 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.017 0.001 TYR C 217 PHE 0.011 0.001 PHE A 538 TRP 0.011 0.001 TRP D 330 HIS 0.004 0.001 HIS B 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16348) covalent geometry : angle 0.60185 / 0.29 (22228) hydrogen bonds : bond 0.03434 / 2.28 ( 1185) hydrogen bonds : angle 3.94696 / 2.81 ( 3471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.43 seconds wall clock time: 46 minutes 16.30 seconds (2776.30 seconds total)