Starting phenix.real_space_refine on Thu Jul 2 23:05:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.map" model { file = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nsg_12566/07_2026/7nsg_12566.cif" } resolution = 3.34 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= 0.000 sd= 0.008 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 9 5.49 5 S 69 5.16 5 C 6855 2.51 5 N 1575 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10356 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3255 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 197 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR5': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 7, 185 Unusual residues: {'PC1': 5, 'UR8': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 171 Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AUR5 A 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 A 501 " occ=0.50 residue: pdb=" N BUR8 A 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 A 502 " occ=0.50 residue: pdb=" N AUR5 B 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 B 501 " occ=0.50 residue: pdb=" N BUR8 B 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 B 502 " occ=0.50 residue: pdb=" N AUR5 C 501 " occ=0.50 ... (10 atoms not shown) pdb=" O3 AUR5 C 501 " occ=0.50 residue: pdb=" N BUR8 C 502 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BUR8 C 502 " occ=0.50 Time building chain proxies: 2.09, per 1000 atoms: 0.20 Number of scatterers: 10356 At special positions: 0 Unit cell: (116.202, 116.202, 89.052, 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 69 16.00 P 9 15.00 O 1848 8.00 N 1575 7.00 C 6855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 285.4 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 81.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 18 through 40 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.513A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.504A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.865A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.765A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.307A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.653A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.092A pdb=" N ALA A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 409 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.542A pdb=" N LEU A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.843A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.616A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 18 through 40 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.514A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.505A pdb=" N LEU B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.866A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.766A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.306A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.654A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.091A pdb=" N ALA B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 409 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.541A pdb=" N LEU B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 434 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.844A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.616A pdb=" N GLU B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 18 through 40 Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.566A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 3.621A pdb=" N ILE C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.514A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 150 removed outlier: 4.230A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.504A pdb=" N LEU C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.814A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.866A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.766A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.307A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.654A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.627A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.092A pdb=" N ALA C 408 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 409 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.542A pdb=" N LEU C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.801A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 434 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.845A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.615A pdb=" N GLU C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 168 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 168 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 168 708 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1623 1.32 - 1.44: 2352 1.44 - 1.56: 6381 1.56 - 1.68: 18 1.68 - 1.80: 123 Bond restraints: 10497 Sorted by residual: bond pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 1.205 1.340 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C21 PC1 A 506 " pdb=" O22 PC1 A 506 " ideal model delta sigma weight residual 1.205 1.340 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 1.205 1.339 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C21 PC1 A 506 " pdb=" O21 PC1 A 506 " ideal model delta sigma weight residual 1.331 1.200 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C21 PC1 C 506 " pdb=" O21 PC1 C 506 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.25e+01 ... (remaining 10492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 13872 2.83 - 5.66: 247 5.66 - 8.49: 47 8.49 - 11.32: 3 11.32 - 14.15: 6 Bond angle restraints: 14175 Sorted by residual: angle pdb=" N ILE A 391 " pdb=" CA ILE A 391 " pdb=" C ILE A 391 " ideal model delta sigma weight residual 112.90 106.66 6.24 9.60e-01 1.09e+00 4.23e+01 angle pdb=" N ILE B 391 " pdb=" CA ILE B 391 " pdb=" C ILE B 391 " ideal model delta sigma weight residual 112.90 106.67 6.23 9.60e-01 1.09e+00 4.21e+01 angle pdb=" N ILE C 391 " pdb=" CA ILE C 391 " pdb=" C ILE C 391 " ideal model delta sigma weight residual 112.90 106.67 6.23 9.60e-01 1.09e+00 4.20e+01 angle pdb=" C22 PC1 A 506 " pdb=" C21 PC1 A 506 " pdb=" O22 PC1 A 506 " ideal model delta sigma weight residual 125.37 111.22 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 125.37 111.28 14.09 3.00e+00 1.11e-01 2.21e+01 ... (remaining 14170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5688 17.90 - 35.79: 483 35.79 - 53.69: 75 53.69 - 71.58: 18 71.58 - 89.48: 3 Dihedral angle restraints: 6267 sinusoidal: 2562 harmonic: 3705 Sorted by residual: dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLU A 48 " pdb=" C GLU A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1226 0.048 - 0.095: 406 0.095 - 0.143: 104 0.143 - 0.190: 25 0.190 - 0.238: 6 Chirality restraints: 1767 Sorted by residual: chirality pdb=" C1 BUR8 C 502 " pdb=" C2 BUR8 C 502 " pdb=" C4 BUR8 C 502 " pdb=" O1 BUR8 C 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 BUR8 B 502 " pdb=" C2 BUR8 B 502 " pdb=" C4 BUR8 B 502 " pdb=" O1 BUR8 B 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 BUR8 A 502 " pdb=" C2 BUR8 A 502 " pdb=" C4 BUR8 A 502 " pdb=" O1 BUR8 A 502 " both_signs ideal model delta sigma weight residual False 2.69 2.93 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1764 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 302 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.037 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO B 302 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.037 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 302 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.031 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2968 2.83 - 3.34: 9327 3.34 - 3.86: 15903 3.86 - 4.38: 18601 4.38 - 4.90: 33103 Nonbonded interactions: 79902 Sorted by model distance: nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.307 3.040 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.307 3.040 nonbonded pdb=" O SER C 331 " pdb=" OG SER C 331 " model vdw 2.308 3.040 nonbonded pdb=" OD1 ASP A 444 " pdb=" N1 AUR5 A 501 " model vdw 2.405 3.120 nonbonded pdb=" OD1 ASP B 444 " pdb=" N1 AUR5 B 501 " model vdw 2.411 3.120 ... (remaining 79897 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.135 10497 Z= 0.406 Angle : 1.005 14.147 14175 Z= 0.521 Chirality : 0.052 0.238 1767 Planarity : 0.007 0.055 1677 Dihedral : 13.503 89.476 3873 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -3.82 (0.18), residues: 1272 helix: -2.30 (0.12), residues: 963 sheet: -1.29 (0.76), residues: 60 loop : -2.71 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 353 TYR 0.021 0.003 TYR C 373 PHE 0.035 0.003 PHE A 341 TRP 0.008 0.001 TRP A 276 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.41 (10497) covalent geometry : angle 1.00540 / 0.52 (14175) hydrogen bonds : bond 0.15694 / 9.97 ( 708) hydrogen bonds : angle 6.06687 / 4.25 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.314 Fit side-chains REVERT: A 165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7673 (ptmm) REVERT: A 258 MET cc_start: 0.7869 (ttp) cc_final: 0.7593 (ttp) REVERT: A 325 LEU cc_start: 0.8155 (tp) cc_final: 0.7886 (tp) REVERT: A 353 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7518 (ttm110) REVERT: A 449 MET cc_start: 0.7640 (ttp) cc_final: 0.7254 (ttt) REVERT: A 473 MET cc_start: 0.7087 (mtm) cc_final: 0.6473 (tmm) REVERT: B 39 ARG cc_start: 0.7438 (ttt-90) cc_final: 0.7097 (ttt180) REVERT: B 165 LYS cc_start: 0.8204 (pttt) cc_final: 0.7613 (ptmm) REVERT: B 258 MET cc_start: 0.7822 (ttp) cc_final: 0.7547 (ttt) REVERT: B 353 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7532 (ttm110) REVERT: B 419 MET cc_start: 0.8770 (tpt) cc_final: 0.8229 (tpt) REVERT: B 449 MET cc_start: 0.7654 (ttp) cc_final: 0.7317 (ttt) REVERT: C 165 LYS cc_start: 0.8170 (pttt) cc_final: 0.7572 (ptmm) REVERT: C 248 MET cc_start: 0.8461 (mmm) cc_final: 0.8240 (mmm) REVERT: C 258 MET cc_start: 0.7831 (ttp) cc_final: 0.7486 (ttp) REVERT: C 315 ARG cc_start: 0.7274 (mmt90) cc_final: 0.6752 (mmm160) REVERT: C 353 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7258 (ttm110) REVERT: C 419 MET cc_start: 0.8660 (tpt) cc_final: 0.8020 (tpt) REVERT: C 449 MET cc_start: 0.7530 (ttp) cc_final: 0.7198 (ttt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1056 time to fit residues: 22.8270 Evaluate side-chains 134 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 GLN B 413 GLN C 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099695 restraints weight = 11331.653| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.87 r_work: 0.2741 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10497 Z= 0.121 Angle : 0.519 8.563 14175 Z= 0.272 Chirality : 0.037 0.131 1767 Planarity : 0.004 0.036 1677 Dihedral : 8.305 57.299 1677 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.04 % Allowed : 8.40 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1272 helix: 0.04 (0.17), residues: 966 sheet: -1.10 (0.76), residues: 60 loop : -2.54 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.012 0.001 TYR C 257 PHE 0.017 0.001 PHE A 341 TRP 0.006 0.001 TRP B 441 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10497) covalent geometry : angle 0.51895 / 0.27 (14175) hydrogen bonds : bond 0.04761 / 3.15 ( 708) hydrogen bonds : angle 4.04535 / 2.81 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.319 Fit side-chains REVERT: A 60 MET cc_start: 0.8800 (mmt) cc_final: 0.8559 (mmm) REVERT: A 165 LYS cc_start: 0.8135 (pttt) cc_final: 0.7550 (ptmm) REVERT: A 258 MET cc_start: 0.8083 (ttp) cc_final: 0.7716 (ttt) REVERT: A 353 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7482 (ttm110) REVERT: A 449 MET cc_start: 0.7858 (ttp) cc_final: 0.7551 (ttt) REVERT: B 160 GLN cc_start: 0.8952 (pt0) cc_final: 0.8507 (pt0) REVERT: B 165 LYS cc_start: 0.8063 (pttt) cc_final: 0.7403 (ptmm) REVERT: B 258 MET cc_start: 0.8028 (ttp) cc_final: 0.7763 (ttt) REVERT: B 353 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7526 (ttm110) REVERT: B 356 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.7455 (mmt-90) REVERT: B 449 MET cc_start: 0.7808 (ttp) cc_final: 0.7560 (ttp) REVERT: C 165 LYS cc_start: 0.8124 (pttt) cc_final: 0.7501 (ptmm) REVERT: C 258 MET cc_start: 0.8186 (ttp) cc_final: 0.7832 (ttt) REVERT: C 315 ARG cc_start: 0.7392 (mmt90) cc_final: 0.6697 (mmm160) REVERT: C 353 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7251 (ttm110) REVERT: C 356 ARG cc_start: 0.7830 (mmt-90) cc_final: 0.7629 (mmt-90) REVERT: C 449 MET cc_start: 0.7778 (ttp) cc_final: 0.7497 (ttp) outliers start: 11 outliers final: 8 residues processed: 160 average time/residue: 0.1077 time to fit residues: 23.3199 Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.143595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094376 restraints weight = 11442.876| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.85 r_work: 0.2663 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10497 Z= 0.200 Angle : 0.583 8.068 14175 Z= 0.300 Chirality : 0.040 0.162 1767 Planarity : 0.004 0.034 1677 Dihedral : 8.498 59.196 1677 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.79 % Allowed : 10.86 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1272 helix: 0.55 (0.17), residues: 978 sheet: -1.13 (0.75), residues: 60 loop : -2.31 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.011 0.001 TYR B 162 PHE 0.017 0.002 PHE C 240 TRP 0.005 0.001 TRP C 19 HIS 0.000 0.000 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.20 (10497) covalent geometry : angle 0.58345 / 0.30 (14175) hydrogen bonds : bond 0.05528 / 3.67 ( 708) hydrogen bonds : angle 4.04322 / 2.80 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.361 Fit side-chains REVERT: A 165 LYS cc_start: 0.8243 (pttt) cc_final: 0.7638 (ptmm) REVERT: A 258 MET cc_start: 0.8271 (ttp) cc_final: 0.7907 (ttt) REVERT: A 353 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7444 (ttm110) REVERT: A 449 MET cc_start: 0.8161 (ttp) cc_final: 0.7844 (ttt) REVERT: B 165 LYS cc_start: 0.8173 (pttt) cc_final: 0.7532 (ptmm) REVERT: B 206 TYR cc_start: 0.9192 (m-80) cc_final: 0.8833 (m-80) REVERT: B 258 MET cc_start: 0.8227 (ttp) cc_final: 0.7967 (ttt) REVERT: B 353 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7460 (ttm110) REVERT: B 449 MET cc_start: 0.8151 (ttp) cc_final: 0.7877 (ttp) REVERT: C 39 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7321 (mtp180) REVERT: C 165 LYS cc_start: 0.8242 (pttt) cc_final: 0.7622 (ptmm) REVERT: C 258 MET cc_start: 0.8220 (ttp) cc_final: 0.7871 (ttt) REVERT: C 315 ARG cc_start: 0.7564 (mmt90) cc_final: 0.6995 (tpp-160) REVERT: C 353 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7308 (ttm110) REVERT: C 356 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.7651 (mtt-85) REVERT: C 473 MET cc_start: 0.6646 (mtm) cc_final: 0.6380 (mtm) outliers start: 19 outliers final: 10 residues processed: 152 average time/residue: 0.1106 time to fit residues: 22.8060 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.147782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098708 restraints weight = 11516.348| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.87 r_work: 0.2728 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10497 Z= 0.114 Angle : 0.492 8.056 14175 Z= 0.253 Chirality : 0.037 0.128 1767 Planarity : 0.003 0.031 1677 Dihedral : 8.114 59.989 1677 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.51 % Allowed : 11.52 % Favored : 86.97 % 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: 0.74 (0.25), residues: 1272 helix: 1.20 (0.18), residues: 954 sheet: -0.90 (0.75), residues: 60 loop : -1.73 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 356 TYR 0.011 0.001 TYR A 162 PHE 0.009 0.001 PHE C 357 TRP 0.005 0.001 TRP C 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10497) covalent geometry : angle 0.49150 / 0.25 (14175) hydrogen bonds : bond 0.04337 / 2.88 ( 708) hydrogen bonds : angle 3.79563 / 2.63 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.351 Fit side-chains REVERT: A 165 LYS cc_start: 0.8141 (pttt) cc_final: 0.7489 (ptmm) REVERT: A 258 MET cc_start: 0.8201 (ttp) cc_final: 0.7832 (ttt) REVERT: A 449 MET cc_start: 0.8086 (ttp) cc_final: 0.7772 (ttt) REVERT: B 39 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7274 (mtp180) REVERT: B 165 LYS cc_start: 0.8134 (pttt) cc_final: 0.7513 (ptmm) REVERT: B 258 MET cc_start: 0.8117 (ttp) cc_final: 0.7909 (ttt) REVERT: B 449 MET cc_start: 0.8027 (ttp) cc_final: 0.7812 (ttp) REVERT: C 39 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7278 (mtp180) REVERT: C 165 LYS cc_start: 0.8218 (pttt) cc_final: 0.7605 (ptmm) REVERT: C 258 MET cc_start: 0.8211 (ttp) cc_final: 0.7887 (ttt) REVERT: C 315 ARG cc_start: 0.7595 (mmt90) cc_final: 0.7013 (tpp-160) REVERT: C 353 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.7319 (ttm110) REVERT: C 449 MET cc_start: 0.8010 (ttp) cc_final: 0.7636 (ttp) REVERT: C 473 MET cc_start: 0.6503 (mtm) cc_final: 0.6271 (mtm) outliers start: 16 outliers final: 9 residues processed: 157 average time/residue: 0.1029 time to fit residues: 22.1070 Evaluate side-chains 146 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.147526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098525 restraints weight = 11434.642| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.85 r_work: 0.2723 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10497 Z= 0.121 Angle : 0.499 9.218 14175 Z= 0.254 Chirality : 0.038 0.134 1767 Planarity : 0.003 0.029 1677 Dihedral : 8.026 59.420 1677 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.70 % Allowed : 12.37 % Favored : 85.93 % 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: 1.06 (0.25), residues: 1272 helix: 1.41 (0.18), residues: 957 sheet: -0.80 (0.75), residues: 60 loop : -1.56 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 356 TYR 0.009 0.001 TYR A 162 PHE 0.011 0.001 PHE C 159 TRP 0.005 0.001 TRP C 19 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10497) covalent geometry : angle 0.49894 / 0.25 (14175) hydrogen bonds : bond 0.04338 / 2.88 ( 708) hydrogen bonds : angle 3.73375 / 2.60 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.300 Fit side-chains REVERT: A 165 LYS cc_start: 0.8126 (pttt) cc_final: 0.7494 (ptmm) REVERT: A 258 MET cc_start: 0.8167 (ttp) cc_final: 0.7792 (ttt) REVERT: A 449 MET cc_start: 0.8124 (ttp) cc_final: 0.7804 (ttt) REVERT: B 39 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7282 (mtp180) REVERT: B 165 LYS cc_start: 0.8129 (pttt) cc_final: 0.7489 (ptmm) REVERT: B 258 MET cc_start: 0.8111 (ttp) cc_final: 0.7909 (ttt) REVERT: C 39 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7362 (mtp180) REVERT: C 165 LYS cc_start: 0.8212 (pttt) cc_final: 0.7597 (ptmm) REVERT: C 258 MET cc_start: 0.8163 (ttp) cc_final: 0.7842 (ttt) REVERT: C 315 ARG cc_start: 0.7527 (mmt90) cc_final: 0.6953 (tpp-160) REVERT: C 353 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7279 (ttm110) REVERT: C 449 MET cc_start: 0.7916 (ttp) cc_final: 0.7645 (ttt) outliers start: 18 outliers final: 14 residues processed: 154 average time/residue: 0.1004 time to fit residues: 21.2413 Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094558 restraints weight = 11408.921| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.84 r_work: 0.2661 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2475 r_free = 0.2475 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10497 Z= 0.195 Angle : 0.568 8.088 14175 Z= 0.291 Chirality : 0.041 0.163 1767 Planarity : 0.003 0.030 1677 Dihedral : 8.689 59.604 1677 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.70 % Allowed : 13.50 % Favored : 84.80 % 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: 0.75 (0.25), residues: 1272 helix: 1.15 (0.17), residues: 978 sheet: -0.87 (0.75), residues: 60 loop : -1.74 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.010 0.001 TYR B 162 PHE 0.016 0.002 PHE C 240 TRP 0.005 0.001 TRP C 276 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.19 (10497) covalent geometry : angle 0.56756 / 0.29 (14175) hydrogen bonds : bond 0.05306 / 3.52 ( 708) hydrogen bonds : angle 3.92082 / 2.71 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.249 Fit side-chains REVERT: A 165 LYS cc_start: 0.8225 (pttt) cc_final: 0.7607 (ptmm) REVERT: A 258 MET cc_start: 0.8121 (ttp) cc_final: 0.7777 (ttt) REVERT: A 449 MET cc_start: 0.8088 (ttp) cc_final: 0.7748 (ttt) REVERT: B 39 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7339 (mtp180) REVERT: B 165 LYS cc_start: 0.8136 (pttt) cc_final: 0.7493 (ptmm) REVERT: B 255 MET cc_start: 0.8778 (mmm) cc_final: 0.8401 (mmm) REVERT: C 39 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7555 (mtp180) REVERT: C 165 LYS cc_start: 0.8254 (pttt) cc_final: 0.7628 (ptmm) REVERT: C 258 MET cc_start: 0.8199 (ttp) cc_final: 0.7879 (ttt) REVERT: C 315 ARG cc_start: 0.7562 (mmt90) cc_final: 0.6987 (tpp-160) outliers start: 18 outliers final: 16 residues processed: 153 average time/residue: 0.0946 time to fit residues: 19.9201 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.096814 restraints weight = 11222.178| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.84 r_work: 0.2694 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10497 Z= 0.143 Angle : 0.521 8.496 14175 Z= 0.266 Chirality : 0.039 0.144 1767 Planarity : 0.003 0.029 1677 Dihedral : 8.457 58.948 1677 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 13.60 % Favored : 84.42 % 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: 1.03 (0.25), residues: 1272 helix: 1.38 (0.17), residues: 975 sheet: -0.89 (0.76), residues: 60 loop : -1.70 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.022 0.001 TYR A 206 PHE 0.012 0.001 PHE A 159 TRP 0.005 0.001 TRP A 441 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (10497) covalent geometry : angle 0.52064 / 0.27 (14175) hydrogen bonds : bond 0.04699 / 3.12 ( 708) hydrogen bonds : angle 3.84099 / 2.66 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.286 Fit side-chains REVERT: A 165 LYS cc_start: 0.8181 (pttt) cc_final: 0.7512 (ptmm) REVERT: A 258 MET cc_start: 0.8130 (ttp) cc_final: 0.7765 (ttt) REVERT: A 449 MET cc_start: 0.8165 (ttp) cc_final: 0.7845 (ttt) REVERT: B 39 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7312 (mtp180) REVERT: B 165 LYS cc_start: 0.8169 (pttt) cc_final: 0.7537 (ptmm) REVERT: C 39 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7422 (mtp180) REVERT: C 165 LYS cc_start: 0.8235 (pttt) cc_final: 0.7616 (ptmm) REVERT: C 258 MET cc_start: 0.8185 (ttp) cc_final: 0.7860 (ttt) REVERT: C 315 ARG cc_start: 0.7557 (mmt90) cc_final: 0.6981 (tpp-160) outliers start: 21 outliers final: 13 residues processed: 151 average time/residue: 0.0847 time to fit residues: 17.9637 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.149352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.100578 restraints weight = 11231.327| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.84 r_work: 0.2752 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10497 Z= 0.107 Angle : 0.491 8.699 14175 Z= 0.251 Chirality : 0.037 0.125 1767 Planarity : 0.003 0.028 1677 Dihedral : 8.033 57.831 1677 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 14.45 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.25), residues: 1272 helix: 1.75 (0.18), residues: 957 sheet: -0.89 (0.76), residues: 60 loop : -1.11 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.018 0.001 TYR C 206 PHE 0.010 0.001 PHE A 159 TRP 0.006 0.001 TRP A 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10497) covalent geometry : angle 0.49139 / 0.25 (14175) hydrogen bonds : bond 0.03969 / 2.63 ( 708) hydrogen bonds : angle 3.74149 / 2.61 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.266 Fit side-chains REVERT: A 60 MET cc_start: 0.8939 (mmt) cc_final: 0.8613 (mmm) REVERT: A 165 LYS cc_start: 0.8145 (pttt) cc_final: 0.7491 (ptmm) REVERT: A 258 MET cc_start: 0.8155 (ttp) cc_final: 0.7780 (ttt) REVERT: A 449 MET cc_start: 0.8127 (ttp) cc_final: 0.7806 (ttt) REVERT: B 39 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7276 (mtp180) REVERT: B 165 LYS cc_start: 0.8169 (pttt) cc_final: 0.7544 (ptmm) REVERT: C 39 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7381 (mtp180) REVERT: C 165 LYS cc_start: 0.8229 (pttt) cc_final: 0.7614 (ptmm) REVERT: C 258 MET cc_start: 0.8125 (ttp) cc_final: 0.7809 (ttt) REVERT: C 315 ARG cc_start: 0.7562 (mmt90) cc_final: 0.7037 (tpp-160) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.0869 time to fit residues: 18.1872 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.148459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.099399 restraints weight = 11245.874| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.85 r_work: 0.2734 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10497 Z= 0.115 Angle : 0.499 8.564 14175 Z= 0.255 Chirality : 0.038 0.128 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.969 57.580 1677 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.04 % Allowed : 14.45 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1272 helix: 1.91 (0.18), residues: 942 sheet: -0.95 (0.75), residues: 60 loop : -0.81 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.016 0.001 TYR C 206 PHE 0.009 0.001 PHE A 159 TRP 0.006 0.001 TRP B 19 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10497) covalent geometry : angle 0.49937 / 0.25 (14175) hydrogen bonds : bond 0.04126 / 2.74 ( 708) hydrogen bonds : angle 3.75642 / 2.61 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.282 Fit side-chains REVERT: A 165 LYS cc_start: 0.8168 (pttt) cc_final: 0.7520 (ptmm) REVERT: A 258 MET cc_start: 0.8156 (ttp) cc_final: 0.7800 (ttt) REVERT: A 315 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.7296 (tpm170) REVERT: A 449 MET cc_start: 0.8153 (ttp) cc_final: 0.7833 (ttt) REVERT: B 39 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7266 (mtp180) REVERT: B 165 LYS cc_start: 0.8177 (pttt) cc_final: 0.7540 (ptmm) REVERT: C 39 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7394 (mtp180) REVERT: C 165 LYS cc_start: 0.8223 (pttt) cc_final: 0.7619 (ptmm) REVERT: C 258 MET cc_start: 0.8171 (ttp) cc_final: 0.7869 (ttt) REVERT: C 315 ARG cc_start: 0.7557 (mmt90) cc_final: 0.7034 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.0893 time to fit residues: 18.3782 Evaluate side-chains 144 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.147810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098900 restraints weight = 11190.020| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.83 r_work: 0.2729 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10497 Z= 0.126 Angle : 0.512 8.356 14175 Z= 0.263 Chirality : 0.038 0.162 1767 Planarity : 0.003 0.027 1677 Dihedral : 8.012 57.088 1677 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.85 % Allowed : 15.30 % Favored : 83.85 % 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: 1.83 (0.25), residues: 1272 helix: 1.91 (0.18), residues: 945 sheet: -0.95 (0.75), residues: 60 loop : -0.76 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 353 TYR 0.015 0.001 TYR C 206 PHE 0.010 0.001 PHE A 159 TRP 0.005 0.001 TRP B 19 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10497) covalent geometry : angle 0.51225 / 0.26 (14175) hydrogen bonds : bond 0.04307 / 2.86 ( 708) hydrogen bonds : angle 3.80692 / 2.65 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.388 Fit side-chains REVERT: A 165 LYS cc_start: 0.8152 (pttt) cc_final: 0.7495 (ptmm) REVERT: A 258 MET cc_start: 0.8150 (ttp) cc_final: 0.7787 (ttt) REVERT: A 315 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7307 (tpm170) REVERT: A 449 MET cc_start: 0.8140 (ttp) cc_final: 0.7818 (ttt) REVERT: B 39 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7269 (mtp180) REVERT: B 165 LYS cc_start: 0.8171 (pttt) cc_final: 0.7532 (ptmm) REVERT: C 39 ARG cc_start: 0.7698 (ttp80) cc_final: 0.7402 (mtp180) REVERT: C 165 LYS cc_start: 0.8203 (pttt) cc_final: 0.7608 (ptmm) REVERT: C 168 GLU cc_start: 0.8046 (pm20) cc_final: 0.7668 (mp0) REVERT: C 258 MET cc_start: 0.8172 (ttp) cc_final: 0.7863 (ttt) REVERT: C 315 ARG cc_start: 0.7559 (mmt90) cc_final: 0.7030 (tpp-160) outliers start: 9 outliers final: 9 residues processed: 144 average time/residue: 0.1114 time to fit residues: 22.5188 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.148816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.099808 restraints weight = 11436.042| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.84 r_work: 0.2739 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10497 Z= 0.113 Angle : 0.498 8.428 14175 Z= 0.255 Chirality : 0.038 0.184 1767 Planarity : 0.003 0.028 1677 Dihedral : 7.894 56.439 1677 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.85 % Allowed : 15.39 % Favored : 83.76 % 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 (0.25), residues: 1272 helix: 1.91 (0.18), residues: 963 sheet: -0.96 (0.75), residues: 60 loop : -1.15 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.015 0.001 TYR C 206 PHE 0.009 0.001 PHE A 159 TRP 0.006 0.001 TRP B 19 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10497) covalent geometry : angle 0.49811 / 0.26 (14175) hydrogen bonds : bond 0.04077 / 2.71 ( 708) hydrogen bonds : angle 3.76456 / 2.62 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.96 seconds wall clock time: 41 minutes 54.54 seconds (2514.54 seconds total)