Starting phenix.real_space_refine on Thu Jul 2 23:00:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xr6_33408/07_2026/7xr6_33408.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 3 7.06 5 S 75 5.16 5 C 6860 2.51 5 N 1545 2.21 5 O 1710 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 10199 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3179 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3180 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Chain: "C" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3180 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 2 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-1': 10, 'PC1:plan-2': 10} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-1': 10, 'PC1:plan-2': 10} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 220 Unusual residues: {'GJ0': 1, 'PC1': 10, 'XKJ': 1, 'Y01': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PC1:plan-1': 10, 'PC1:plan-2': 10} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 1.99, per 1000 atoms: 0.20 Number of scatterers: 10199 At special positions: 0 Unit cell: (117.52, 117.52, 84.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 3 34.99 S 75 16.00 F 6 9.00 O 1710 8.00 N 1545 7.00 C 6860 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: 0.89 Conformation dependent library (CDL) restraints added in 261.5 milliseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 3 sheets defined 84.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 44 through 66 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 79 through 107 removed outlier: 4.484A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix removed outlier: 4.118A pdb=" N LEU A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.975A pdb=" N SER A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 143 removed outlier: 3.581A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.731A pdb=" N PHE A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.573A pdb=" N GLY A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.818A pdb=" N PHE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 305 through 330 removed outlier: 3.694A pdb=" N VAL A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 363 through 378 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 382 through 397 Proline residue: A 391 - end of helix removed outlier: 4.128A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.825A pdb=" N ALA A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.931A pdb=" N VAL A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.625A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.646A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 496 removed outlier: 4.096A pdb=" N MET A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.576A pdb=" N GLN A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 44 through 66 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.548A pdb=" N LEU B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Proline residue: B 95 - end of helix removed outlier: 4.125A pdb=" N LEU B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 4.015A pdb=" N SER B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 143 removed outlier: 3.718A pdb=" N TYR B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 241 through 260 removed outlier: 3.562A pdb=" N GLY B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 286 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 305 through 330 removed outlier: 3.715A pdb=" N VAL B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.534A pdb=" N PHE B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 Proline residue: B 369 - end of helix Processing helix chain 'B' and resid 382 through 397 Proline residue: B 391 - end of helix removed outlier: 4.140A pdb=" N THR B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.818A pdb=" N ALA B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.999A pdb=" N VAL B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.636A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.813A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 496 removed outlier: 4.193A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 507 removed outlier: 3.580A pdb=" N GLN B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 44 through 66 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 79 through 107 removed outlier: 4.460A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Proline residue: C 95 - end of helix removed outlier: 4.130A pdb=" N LEU C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 143 removed outlier: 3.766A pdb=" N GLY C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 241 through 260 removed outlier: 3.555A pdb=" N GLY C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 286 removed outlier: 3.668A pdb=" N PHE C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.815A pdb=" N ILE C 301 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 330 removed outlier: 3.765A pdb=" N VAL C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.565A pdb=" N PHE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 363 through 378 Proline residue: C 369 - end of helix Processing helix chain 'C' and resid 382 through 397 Proline residue: C 391 - end of helix removed outlier: 4.293A pdb=" N THR C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.740A pdb=" N ALA C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 removed outlier: 4.050A pdb=" N VAL C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 442 removed outlier: 4.183A pdb=" N SER C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 437 through 442' Processing helix chain 'C' and resid 445 through 457 removed outlier: 3.599A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 471 removed outlier: 3.718A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 496 removed outlier: 4.050A pdb=" N MET C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 507 removed outlier: 3.560A pdb=" N GLN C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 191 Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 191 Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 191 732 hydrogen bonds defined for protein. 2184 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: 1.28 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2665 1.33 - 1.49: 2594 1.49 - 1.64: 4934 1.64 - 1.79: 33 1.79 - 1.94: 102 Bond restraints: 10328 Sorted by residual: bond pdb=" CAX Y01 B 602 " pdb=" OAH Y01 B 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 A 602 " pdb=" OAH Y01 A 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAX Y01 C 603 " pdb=" OAH Y01 C 603 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C13 GJ0 C 602 " pdb=" N12 GJ0 C 602 " ideal model delta sigma weight residual 1.363 1.452 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C13 GJ0 A 601 " pdb=" N12 GJ0 A 601 " ideal model delta sigma weight residual 1.363 1.452 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 10323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13126 1.91 - 3.81: 443 3.81 - 5.72: 260 5.72 - 7.63: 14 7.63 - 9.54: 9 Bond angle restraints: 13852 Sorted by residual: angle pdb=" N ILE A 230 " pdb=" CA ILE A 230 " pdb=" C ILE A 230 " ideal model delta sigma weight residual 113.53 109.14 4.39 9.80e-01 1.04e+00 2.01e+01 angle pdb=" C11 GJ0 C 602 " pdb=" N12 GJ0 C 602 " pdb=" C13 GJ0 C 602 " ideal model delta sigma weight residual 129.20 119.66 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C11 GJ0 A 601 " pdb=" N12 GJ0 A 601 " pdb=" C13 GJ0 A 601 " ideal model delta sigma weight residual 129.20 119.73 9.47 3.00e+00 1.11e-01 9.97e+00 angle pdb=" N VAL A 308 " pdb=" CA VAL A 308 " pdb=" C VAL A 308 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.78e+00 angle pdb=" C11 GJ0 B 601 " pdb=" N12 GJ0 B 601 " pdb=" C13 GJ0 B 601 " ideal model delta sigma weight residual 129.20 120.10 9.10 3.00e+00 1.11e-01 9.19e+00 ... (remaining 13847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.10: 5823 25.10 - 50.20: 316 50.20 - 75.30: 30 75.30 - 100.41: 17 100.41 - 125.51: 6 Dihedral angle restraints: 6192 sinusoidal: 2604 harmonic: 3588 Sorted by residual: dihedral pdb=" CBC Y01 B 602 " pdb=" CAR Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CBH Y01 B 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.38 -125.51 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CBC Y01 C 603 " pdb=" CAR Y01 C 603 " pdb=" CAT Y01 C 603 " pdb=" CBH Y01 C 603 " ideal model delta sinusoidal sigma weight residual -57.13 68.25 -125.38 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 A 602 " pdb=" CAR Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CBH Y01 A 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.04 -125.17 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1633 0.095 - 0.190: 67 0.190 - 0.284: 3 0.284 - 0.379: 3 0.379 - 0.474: 3 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CBG Y01 B 602 " pdb=" CAQ Y01 B 602 " pdb=" CBD Y01 B 602 " pdb=" CBI Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 1706 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 135 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY C 135 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY C 135 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL C 136 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 135 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" C GLY B 135 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY B 135 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL B 136 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 135 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLY A 135 " -0.022 2.00e-02 2.50e+03 pdb=" O GLY A 135 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 136 " 0.007 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1576 2.76 - 3.29: 10203 3.29 - 3.83: 16811 3.83 - 4.36: 19845 4.36 - 4.90: 34593 Nonbonded interactions: 83028 Sorted by model distance: nonbonded pdb=" O HIS B 143 " pdb=" ND1 HIS B 143 " model vdw 2.220 3.120 nonbonded pdb=" NZ LYS B 90 " pdb=" OG1 THR B 461 " model vdw 2.311 3.120 nonbonded pdb=" O ASN A 343 " pdb=" OG SER A 346 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 190 " model vdw 2.325 3.040 nonbonded pdb=" NZ LYS A 90 " pdb=" OG1 THR A 461 " model vdw 2.327 3.120 ... (remaining 83023 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 507 or resid 604 or (resid 607 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E)) or r \ esid 608 through 609 or (resid 610 and (name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or \ name C2B or name C2C or name C2D)) or resid 611)) selection = (chain 'B' and (resid 36 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 128 through 507 or resid 604 or \ (resid 607 and (name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E)) or resid 608 through 609 or (resid 610 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D)) or resid 611)) selection = (chain 'C' and (resid 36 through 126 or (resid 127 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 128 through 507 or (resid 604 an \ d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29)) or resid 607 or (resid 608 and (name C21 or name C \ 22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or na \ me C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F o \ r name C2G)) or (resid 609 through 610 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A \ or name C2B or name C2C or name C2D)) or (resid 611 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 10328 Z= 0.246 Angle : 0.974 9.535 13852 Z= 0.405 Chirality : 0.050 0.474 1709 Planarity : 0.004 0.029 1617 Dihedral : 15.979 125.508 3888 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.44 (0.25), residues: 1254 helix: 0.79 (0.17), residues: 987 sheet: -1.71 (0.81), residues: 48 loop : -1.16 (0.50), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.008 0.001 TYR B 316 PHE 0.020 0.002 PHE C 249 TRP 0.012 0.001 TRP C 472 HIS 0.005 0.002 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (10328) covalent geometry : angle 0.97405 / 0.40 (13852) hydrogen bonds : bond 0.13025 / 8.77 ( 732) hydrogen bonds : angle 6.58280 / 4.82 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0810 time to fit residues: 21.3268 Evaluate side-chains 152 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 143 HIS A 416 ASN A 507 GLN B 507 GLN C 44 ASN C 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111473 restraints weight = 10242.488| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.26 r_work: 0.2991 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10328 Z= 0.144 Angle : 0.599 9.193 13852 Z= 0.294 Chirality : 0.040 0.155 1709 Planarity : 0.004 0.035 1617 Dihedral : 12.528 117.636 1746 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.96 % Allowed : 9.48 % Favored : 89.56 % 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: 1.22 (0.25), residues: 1254 helix: 1.38 (0.17), residues: 999 sheet: -2.18 (0.73), residues: 48 loop : -1.04 (0.52), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 478 TYR 0.011 0.002 TYR A 287 PHE 0.020 0.002 PHE C 249 TRP 0.006 0.001 TRP C 472 HIS 0.017 0.003 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (10328) covalent geometry : angle 0.59931 / 0.29 (13852) hydrogen bonds : bond 0.04093 / 2.79 ( 732) hydrogen bonds : angle 4.50611 / 3.35 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.353 Fit side-chains REVERT: C 304 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7763 (tptt) outliers start: 10 outliers final: 3 residues processed: 171 average time/residue: 0.0743 time to fit residues: 19.1842 Evaluate side-chains 158 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS B 143 HIS B 416 ASN C 143 HIS C 507 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.114401 restraints weight = 10093.159| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.19 r_work: 0.3035 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 0.026 10328 Z= 0.128 Angle : 0.558 9.189 13852 Z= 0.277 Chirality : 0.039 0.154 1709 Planarity : 0.004 0.036 1617 Dihedral : 10.754 115.446 1746 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.86 % Allowed : 12.36 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.25), residues: 1254 helix: 1.58 (0.17), residues: 1008 sheet: -2.36 (0.72), residues: 48 loop : -1.00 (0.53), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.009 0.002 TYR A 404 PHE 0.017 0.002 PHE B 249 TRP 0.007 0.001 TRP C 472 HIS 0.017 0.003 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10328) covalent geometry : angle 0.55831 / 0.28 (13852) hydrogen bonds : bond 0.03703 / 2.51 ( 732) hydrogen bonds : angle 4.21428 / 3.14 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.235 Fit side-chains REVERT: C 304 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7906 (tptt) outliers start: 9 outliers final: 6 residues processed: 165 average time/residue: 0.0717 time to fit residues: 17.5783 Evaluate side-chains 162 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS C 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.108356 restraints weight = 10198.359| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.30 r_work: 0.2961 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10328 Z= 0.171 Angle : 0.582 7.600 13852 Z= 0.289 Chirality : 0.040 0.146 1709 Planarity : 0.004 0.037 1617 Dihedral : 10.575 115.446 1746 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.25 % Allowed : 14.08 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1254 helix: 1.50 (0.17), residues: 1011 sheet: -2.64 (0.70), residues: 48 loop : -1.11 (0.52), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.010 0.002 TYR A 404 PHE 0.019 0.002 PHE B 411 TRP 0.006 0.001 TRP B 286 HIS 0.019 0.003 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (10328) covalent geometry : angle 0.58213 / 0.29 (13852) hydrogen bonds : bond 0.03964 / 2.68 ( 732) hydrogen bonds : angle 4.24785 / 3.17 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.323 Fit side-chains REVERT: A 304 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7598 (tptt) REVERT: C 188 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9010 (tt) REVERT: C 259 MET cc_start: 0.8951 (mtp) cc_final: 0.8550 (mtp) REVERT: C 304 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7890 (tptt) outliers start: 13 outliers final: 10 residues processed: 171 average time/residue: 0.0702 time to fit residues: 18.1169 Evaluate side-chains 166 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS B 143 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.145524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112343 restraints weight = 10054.446| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.27 r_work: 0.3012 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10328 Z= 0.126 Angle : 0.548 7.966 13852 Z= 0.271 Chirality : 0.039 0.152 1709 Planarity : 0.004 0.037 1617 Dihedral : 10.112 116.012 1746 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.82 % Allowed : 14.85 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1254 helix: 1.68 (0.17), residues: 1008 sheet: -2.68 (0.70), residues: 48 loop : -1.10 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.009 0.002 TYR A 404 PHE 0.016 0.002 PHE A 249 TRP 0.006 0.001 TRP B 286 HIS 0.021 0.003 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10328) covalent geometry : angle 0.54777 / 0.27 (13852) hydrogen bonds : bond 0.03571 / 2.42 ( 732) hydrogen bonds : angle 4.07783 / 3.04 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.351 Fit side-chains REVERT: A 387 ARG cc_start: 0.8412 (tmm-80) cc_final: 0.8177 (ttm-80) REVERT: C 259 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: C 304 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7930 (tptt) REVERT: C 315 MET cc_start: 0.7395 (tpp) cc_final: 0.7151 (mmm) REVERT: C 372 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: C 470 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8824 (t) outliers start: 19 outliers final: 13 residues processed: 169 average time/residue: 0.0690 time to fit residues: 17.5804 Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112561 restraints weight = 10113.642| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.29 r_work: 0.3016 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10328 Z= 0.117 Angle : 0.534 7.591 13852 Z= 0.264 Chirality : 0.038 0.151 1709 Planarity : 0.003 0.034 1617 Dihedral : 9.819 116.520 1746 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 16.28 % Favored : 81.80 % 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: 1.88 (0.25), residues: 1254 helix: 1.95 (0.17), residues: 990 sheet: -2.65 (0.70), residues: 48 loop : -1.07 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.008 0.002 TYR A 404 PHE 0.016 0.002 PHE A 249 TRP 0.007 0.001 TRP B 286 HIS 0.011 0.002 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10328) covalent geometry : angle 0.53380 / 0.26 (13852) hydrogen bonds : bond 0.03414 / 2.31 ( 732) hydrogen bonds : angle 3.96150 / 2.96 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.221 Fit side-chains REVERT: A 387 ARG cc_start: 0.8426 (tmm-80) cc_final: 0.8203 (ttp-110) REVERT: C 304 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7840 (tptt) REVERT: C 470 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8867 (t) outliers start: 20 outliers final: 16 residues processed: 166 average time/residue: 0.0742 time to fit residues: 18.5826 Evaluate side-chains 168 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 90 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.0570 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN B 312 GLN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115491 restraints weight = 9972.990| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.28 r_work: 0.3058 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10328 Z= 0.103 Angle : 0.518 7.282 13852 Z= 0.255 Chirality : 0.038 0.156 1709 Planarity : 0.003 0.034 1617 Dihedral : 9.541 118.647 1746 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.63 % Allowed : 16.86 % Favored : 81.51 % 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: 2.12 (0.25), residues: 1254 helix: 2.13 (0.17), residues: 984 sheet: -2.41 (0.73), residues: 48 loop : -1.03 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.007 0.001 TYR A 404 PHE 0.016 0.001 PHE A 249 TRP 0.007 0.001 TRP B 286 HIS 0.011 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (10328) covalent geometry : angle 0.51759 / 0.25 (13852) hydrogen bonds : bond 0.03176 / 2.15 ( 732) hydrogen bonds : angle 3.82482 / 2.85 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.227 Fit side-chains REVERT: A 261 ASP cc_start: 0.8302 (t70) cc_final: 0.8065 (t0) REVERT: A 387 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.8208 (ttp-110) REVERT: B 304 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7759 (tptp) REVERT: C 304 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7863 (tptt) REVERT: C 387 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8135 (ttp80) REVERT: C 470 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (t) outliers start: 17 outliers final: 14 residues processed: 168 average time/residue: 0.0661 time to fit residues: 16.8361 Evaluate side-chains 169 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 84 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.148107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115698 restraints weight = 9894.230| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.24 r_work: 0.3070 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10328 Z= 0.108 Angle : 0.529 7.371 13852 Z= 0.258 Chirality : 0.038 0.150 1709 Planarity : 0.003 0.033 1617 Dihedral : 9.436 116.920 1746 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.30 % Allowed : 16.86 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.25), residues: 1254 helix: 2.14 (0.17), residues: 993 sheet: -2.35 (0.75), residues: 48 loop : -1.01 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.009 0.001 TYR B 494 PHE 0.016 0.001 PHE C 249 TRP 0.007 0.001 TRP C 286 HIS 0.011 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10328) covalent geometry : angle 0.52881 / 0.26 (13852) hydrogen bonds : bond 0.03243 / 2.20 ( 732) hydrogen bonds : angle 3.82811 / 2.86 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.339 Fit side-chains REVERT: A 261 ASP cc_start: 0.8286 (t70) cc_final: 0.8075 (t0) REVERT: C 304 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7845 (tptt) REVERT: C 470 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8809 (t) outliers start: 24 outliers final: 16 residues processed: 173 average time/residue: 0.0643 time to fit residues: 16.9501 Evaluate side-chains 173 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111320 restraints weight = 10232.183| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.21 r_work: 0.2995 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10328 Z= 0.167 Angle : 0.581 7.070 13852 Z= 0.284 Chirality : 0.040 0.155 1709 Planarity : 0.004 0.032 1617 Dihedral : 9.747 116.121 1746 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.72 % Allowed : 17.34 % Favored : 80.94 % 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: 1254 helix: 1.90 (0.17), residues: 990 sheet: -2.60 (0.72), residues: 48 loop : -1.13 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.011 0.002 TYR A 404 PHE 0.018 0.002 PHE A 249 TRP 0.006 0.001 TRP B 286 HIS 0.010 0.002 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (10328) covalent geometry : angle 0.58051 / 0.28 (13852) hydrogen bonds : bond 0.03834 / 2.58 ( 732) hydrogen bonds : angle 4.06146 / 3.03 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.315 Fit side-chains REVERT: A 261 ASP cc_start: 0.8232 (t70) cc_final: 0.8014 (t0) REVERT: C 304 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7781 (tptt) REVERT: C 470 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8847 (t) outliers start: 18 outliers final: 14 residues processed: 168 average time/residue: 0.0623 time to fit residues: 16.1242 Evaluate side-chains 170 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS B 44 ASN B 143 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114156 restraints weight = 10024.006| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.22 r_work: 0.3030 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10328 Z= 0.121 Angle : 0.549 7.467 13852 Z= 0.270 Chirality : 0.039 0.159 1709 Planarity : 0.004 0.033 1617 Dihedral : 9.352 116.771 1746 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.72 % Allowed : 17.72 % Favored : 80.56 % 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: 2.00 (0.25), residues: 1254 helix: 2.03 (0.17), residues: 993 sheet: -2.53 (0.73), residues: 48 loop : -1.09 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.009 0.002 TYR A 404 PHE 0.016 0.001 PHE A 249 TRP 0.006 0.001 TRP B 286 HIS 0.012 0.002 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10328) covalent geometry : angle 0.54947 / 0.27 (13852) hydrogen bonds : bond 0.03414 / 2.31 ( 732) hydrogen bonds : angle 3.90691 / 2.92 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.278 Fit side-chains REVERT: C 304 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7823 (tptt) REVERT: C 470 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8820 (t) outliers start: 18 outliers final: 17 residues processed: 168 average time/residue: 0.0657 time to fit residues: 16.8486 Evaluate side-chains 174 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 188 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 470 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.145400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115262 restraints weight = 10217.608| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.20 r_work: 0.3037 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10328 Z= 0.134 Angle : 0.559 7.514 13852 Z= 0.275 Chirality : 0.039 0.175 1709 Planarity : 0.004 0.033 1617 Dihedral : 9.337 116.700 1746 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 17.72 % Favored : 80.36 % 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: 1.95 (0.25), residues: 1254 helix: 1.99 (0.17), residues: 993 sheet: -2.53 (0.73), residues: 48 loop : -1.12 (0.47), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.010 0.002 TYR A 404 PHE 0.016 0.002 PHE A 249 TRP 0.006 0.001 TRP B 286 HIS 0.009 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (10328) covalent geometry : angle 0.55939 / 0.27 (13852) hydrogen bonds : bond 0.03553 / 2.40 ( 732) hydrogen bonds : angle 3.92890 / 2.93 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.12 seconds wall clock time: 36 minutes 17.34 seconds (2177.34 seconds total)