Starting phenix.real_space_refine on Wed Aug 5 11:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7v_52663/08_2026/9i7v_52663.map" } resolution = 3.84 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= 0.003 sd= 0.031 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 Rb 3 11.75 5 P 3 5.49 5 S 54 5.16 5 C 6324 2.51 5 N 1491 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9525 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3098 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {' RB': 1, '6Z6': 1, 'PX6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C Time building chain proxies: 2.72, per 1000 atoms: 0.29 Number of scatterers: 9525 At special positions: 0 Unit cell: (109.685, 113.63, 71.8081, 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) Rb 3 36.98 S 54 16.00 P 3 15.00 O 1650 8.00 N 1491 7.00 C 6324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 342.0 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 81.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 Processing helix chain 'A' and resid 49 through 69 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.793A pdb=" N GLU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.661A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 146 removed outlier: 4.101A pdb=" N ARG A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.693A pdb=" N PHE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 246 through 283 removed outlier: 3.749A pdb=" N ILE A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.856A pdb=" N PHE A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.684A pdb=" N LEU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 359 removed outlier: 3.848A pdb=" N GLU A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 379 through 397 removed outlier: 3.920A pdb=" N ASN A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.557A pdb=" N THR A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 438 removed outlier: 4.015A pdb=" N VAL A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 451 through 477 removed outlier: 3.654A pdb=" N MET A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.678A pdb=" N GLU A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 49 through 69 Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.793A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.661A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 146 removed outlier: 4.101A pdb=" N ARG B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.693A pdb=" N PHE B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 246 through 283 removed outlier: 3.749A pdb=" N ILE B 264 " --> pdb=" O LYS B 260 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 292 through 311 Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.856A pdb=" N PHE B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.684A pdb=" N LEU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.848A pdb=" N GLU B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 379 through 397 removed outlier: 3.920A pdb=" N ASN B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 removed outlier: 3.557A pdb=" N THR B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 438 removed outlier: 4.015A pdb=" N VAL B 434 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 437 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 451 through 477 removed outlier: 3.654A pdb=" N MET B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.678A pdb=" N GLU B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 484' Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 49 through 69 Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.793A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.661A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 146 removed outlier: 4.101A pdb=" N ARG C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.693A pdb=" N PHE C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 241 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 246 through 283 removed outlier: 3.749A pdb=" N ILE C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 292 through 311 Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 324 through 331 removed outlier: 3.856A pdb=" N PHE C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.684A pdb=" N LEU C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 359 removed outlier: 3.848A pdb=" N GLU C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 379 through 397 removed outlier: 3.920A pdb=" N ASN C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 removed outlier: 3.556A pdb=" N THR C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 418 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 438 removed outlier: 4.014A pdb=" N VAL C 434 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 451 through 477 removed outlier: 3.654A pdb=" N MET C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.678A pdb=" N GLU C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS C 484 " --> pdb=" O LYS C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 484' Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 3.787A pdb=" N VAL A 214 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 194 through 200 removed outlier: 3.787A pdb=" N VAL B 214 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 194 through 200 removed outlier: 3.787A pdb=" N VAL C 214 " --> pdb=" O THR C 199 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2046 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: 1.53 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1464 1.28 - 1.42: 2216 1.42 - 1.55: 5899 1.55 - 1.69: 3 1.69 - 1.82: 102 Bond restraints: 9684 Sorted by residual: bond pdb=" O4 PX6 A1000 " pdb=" P1 PX6 A1000 " ideal model delta sigma weight residual 1.705 1.611 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O4 PX6 C1000 " pdb=" P1 PX6 C1000 " ideal model delta sigma weight residual 1.705 1.611 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O4 PX6 B1000 " pdb=" P1 PX6 B1000 " ideal model delta sigma weight residual 1.705 1.611 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 PX6 A1000 " pdb=" O4 PX6 A1000 " ideal model delta sigma weight residual 1.387 1.463 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 PX6 B1000 " pdb=" O4 PX6 B1000 " ideal model delta sigma weight residual 1.387 1.463 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 9679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11832 1.94 - 3.89: 1122 3.89 - 5.83: 171 5.83 - 7.78: 30 7.78 - 9.72: 12 Bond angle restraints: 13167 Sorted by residual: angle pdb=" N VAL B 299 " pdb=" CA VAL B 299 " pdb=" CB VAL B 299 " ideal model delta sigma weight residual 110.55 118.70 -8.15 1.17e+00 7.31e-01 4.86e+01 angle pdb=" N VAL A 299 " pdb=" CA VAL A 299 " pdb=" CB VAL A 299 " ideal model delta sigma weight residual 110.55 118.69 -8.14 1.17e+00 7.31e-01 4.85e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" CB VAL C 299 " ideal model delta sigma weight residual 110.55 118.68 -8.13 1.17e+00 7.31e-01 4.83e+01 angle pdb=" N GLY B 427 " pdb=" CA GLY B 427 " pdb=" C GLY B 427 " ideal model delta sigma weight residual 114.95 105.26 9.69 1.41e+00 5.03e-01 4.72e+01 angle pdb=" N GLY A 427 " pdb=" CA GLY A 427 " pdb=" C GLY A 427 " ideal model delta sigma weight residual 114.95 105.29 9.66 1.41e+00 5.03e-01 4.69e+01 ... (remaining 13162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.77: 4988 11.77 - 23.54: 517 23.54 - 35.31: 174 35.31 - 47.08: 63 47.08 - 58.86: 39 Dihedral angle restraints: 5781 sinusoidal: 2205 harmonic: 3576 Sorted by residual: dihedral pdb=" C HIS A 476 " pdb=" N HIS A 476 " pdb=" CA HIS A 476 " pdb=" CB HIS A 476 " ideal model delta harmonic sigma weight residual -122.60 -132.78 10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C HIS C 476 " pdb=" N HIS C 476 " pdb=" CA HIS C 476 " pdb=" CB HIS C 476 " ideal model delta harmonic sigma weight residual -122.60 -132.77 10.17 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C HIS B 476 " pdb=" N HIS B 476 " pdb=" CA HIS B 476 " pdb=" CB HIS B 476 " ideal model delta harmonic sigma weight residual -122.60 -132.75 10.15 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 832 0.050 - 0.100: 573 0.100 - 0.150: 190 0.150 - 0.200: 58 0.200 - 0.250: 9 Chirality restraints: 1662 Sorted by residual: chirality pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" C PRO B 270 " pdb=" CB PRO B 270 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO C 270 " pdb=" N PRO C 270 " pdb=" C PRO C 270 " pdb=" CB PRO C 270 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO A 270 " pdb=" N PRO A 270 " pdb=" C PRO A 270 " pdb=" CB PRO A 270 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1659 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 PX6 C1000 " -0.053 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C21 PX6 C1000 " 0.016 2.00e-02 2.50e+03 pdb=" O7 PX6 C1000 " 0.016 2.00e-02 2.50e+03 pdb=" O8 PX6 C1000 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PX6 A1000 " -0.053 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C21 PX6 A1000 " 0.016 2.00e-02 2.50e+03 pdb=" O7 PX6 A1000 " 0.016 2.00e-02 2.50e+03 pdb=" O8 PX6 A1000 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 PX6 B1000 " -0.053 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C21 PX6 B1000 " 0.016 2.00e-02 2.50e+03 pdb=" O7 PX6 B1000 " 0.016 2.00e-02 2.50e+03 pdb=" O8 PX6 B1000 " 0.020 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.86: 3445 2.86 - 3.50: 13101 3.50 - 4.15: 19787 4.15 - 4.79: 34214 4.79 - 5.44: 44917 Nonbonded interactions: 115464 Sorted by model distance: nonbonded pdb=" ND2 ASN C 182 " pdb=" OG SER C 195 " model vdw 2.214 3.120 nonbonded pdb=" ND2 ASN A 182 " pdb=" OG SER A 195 " model vdw 2.215 3.120 nonbonded pdb=" ND2 ASN B 182 " pdb=" OG SER B 195 " model vdw 2.215 3.120 nonbonded pdb=" NH2 ARG A 76 " pdb=" OH TYR B 200 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 200 " pdb=" NH2 ARG C 76 " model vdw 2.305 3.120 ... (remaining 115459 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.510 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.008 0.094 9684 Z= 0.499 Angle : 1.275 9.724 13167 Z= 0.869 Chirality : 0.071 0.250 1662 Planarity : 0.008 0.090 1584 Dihedral : 12.791 58.855 3483 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Cbeta Deviations : 0.26 % 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: -2.84 (0.20), residues: 1236 helix: -1.44 (0.14), residues: 960 sheet: -2.01 (1.07), residues: 36 loop : -2.92 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 69 TYR 0.018 0.004 TYR C 268 PHE 0.023 0.004 PHE C 250 TRP 0.013 0.003 TRP B 267 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.50 ( 9684) covalent geometry : angle 1.27498 / 0.87 (13167) hydrogen bonds : bond 0.17177 / 11.98 ( 694) hydrogen bonds : angle 7.64262 / 5.44 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8284 (tt0) cc_final: 0.8019 (tp30) REVERT: A 114 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8779 (mmtt) REVERT: A 121 MET cc_start: 0.8203 (ttp) cc_final: 0.7344 (tpt) REVERT: A 196 TYR cc_start: 0.9095 (t80) cc_final: 0.8758 (t80) REVERT: A 327 VAL cc_start: 0.8976 (t) cc_final: 0.8761 (t) REVERT: A 359 ASN cc_start: 0.9146 (m-40) cc_final: 0.8926 (m-40) REVERT: B 67 LEU cc_start: 0.8095 (mp) cc_final: 0.7883 (tt) REVERT: B 77 GLU cc_start: 0.8379 (tt0) cc_final: 0.8071 (tp30) REVERT: B 114 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8773 (mmtt) REVERT: B 121 MET cc_start: 0.8194 (ttp) cc_final: 0.7259 (tpt) REVERT: B 196 TYR cc_start: 0.9095 (t80) cc_final: 0.8781 (t80) REVERT: B 359 ASN cc_start: 0.9187 (m-40) cc_final: 0.8689 (m-40) REVERT: C 67 LEU cc_start: 0.8070 (mp) cc_final: 0.7862 (tt) REVERT: C 77 GLU cc_start: 0.8359 (tt0) cc_final: 0.8060 (tp30) REVERT: C 114 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8804 (mmtt) REVERT: C 121 MET cc_start: 0.8199 (ttp) cc_final: 0.7268 (tpt) REVERT: C 196 TYR cc_start: 0.9106 (t80) cc_final: 0.8796 (t80) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.0776 time to fit residues: 42.4425 Evaluate side-chains 277 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN B 243 GLN C 243 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.152548 restraints weight = 11985.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.157588 restraints weight = 6244.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.160901 restraints weight = 4169.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.162796 restraints weight = 3263.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.164221 restraints weight = 2832.568| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9684 Z= 0.160 Angle : 0.692 9.046 13167 Z= 0.340 Chirality : 0.042 0.175 1662 Planarity : 0.005 0.042 1584 Dihedral : 7.823 55.297 1506 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.42 % Allowed : 21.81 % Favored : 73.77 % 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: -0.05 (0.24), residues: 1236 helix: 0.57 (0.16), residues: 969 sheet: -1.43 (0.86), residues: 48 loop : -2.06 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 459 TYR 0.025 0.002 TYR B 297 PHE 0.018 0.002 PHE C 184 TRP 0.016 0.003 TRP A 453 HIS 0.012 0.003 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 9684) covalent geometry : angle 0.69245 / 0.34 (13167) hydrogen bonds : bond 0.05194 / 3.69 ( 694) hydrogen bonds : angle 4.74021 / 3.40 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8634 (tttm) REVERT: A 121 MET cc_start: 0.7797 (ttp) cc_final: 0.6871 (tpt) REVERT: A 276 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 359 ASN cc_start: 0.8812 (m-40) cc_final: 0.8509 (m-40) REVERT: A 403 PHE cc_start: 0.7577 (t80) cc_final: 0.7206 (t80) REVERT: A 461 MET cc_start: 0.7403 (ttp) cc_final: 0.7135 (ttm) REVERT: B 114 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8325 (mmtt) REVERT: B 121 MET cc_start: 0.7829 (ttp) cc_final: 0.6885 (tpt) REVERT: B 196 TYR cc_start: 0.8915 (t80) cc_final: 0.8631 (t80) REVERT: B 217 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 245 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 319 LEU cc_start: 0.8802 (mt) cc_final: 0.8223 (tp) REVERT: B 359 ASN cc_start: 0.8841 (m-40) cc_final: 0.8352 (m-40) REVERT: C 77 GLU cc_start: 0.7079 (tt0) cc_final: 0.6878 (tp30) REVERT: C 89 MET cc_start: 0.8389 (tpp) cc_final: 0.7977 (mmm) REVERT: C 114 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8353 (mmtt) REVERT: C 121 MET cc_start: 0.7853 (ttp) cc_final: 0.6970 (tpt) REVERT: C 217 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7795 (mm-30) REVERT: C 245 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 276 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7868 (mt) REVERT: C 359 ASN cc_start: 0.8907 (m-40) cc_final: 0.8536 (m-40) REVERT: C 452 ASP cc_start: 0.8073 (t0) cc_final: 0.7120 (t0) outliers start: 43 outliers final: 22 residues processed: 327 average time/residue: 0.0787 time to fit residues: 38.1896 Evaluate side-chains 285 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 360 ASN B 360 ASN B 378 ASN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 378 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124390 restraints weight = 11380.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128868 restraints weight = 6079.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131954 restraints weight = 4150.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133724 restraints weight = 3286.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134929 restraints weight = 2860.034| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9684 Z= 0.196 Angle : 0.671 8.212 13167 Z= 0.329 Chirality : 0.042 0.161 1662 Planarity : 0.004 0.039 1584 Dihedral : 8.168 59.109 1506 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 5.66 % Allowed : 22.12 % Favored : 72.22 % 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: 0.58 (0.24), residues: 1236 helix: 0.99 (0.17), residues: 966 sheet: 0.01 (1.07), residues: 30 loop : -1.90 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 459 TYR 0.020 0.002 TYR C 127 PHE 0.015 0.002 PHE C 318 TRP 0.012 0.002 TRP A 453 HIS 0.010 0.002 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 9684) covalent geometry : angle 0.67058 / 0.33 (13167) hydrogen bonds : bond 0.04716 / 3.27 ( 694) hydrogen bonds : angle 4.48348 / 3.24 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8373 (mmtt) REVERT: A 121 MET cc_start: 0.7802 (ttp) cc_final: 0.6797 (tpt) REVERT: A 276 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7809 (mt) REVERT: A 319 LEU cc_start: 0.8689 (mt) cc_final: 0.8172 (tp) REVERT: A 359 ASN cc_start: 0.8883 (m-40) cc_final: 0.8662 (m-40) REVERT: A 403 PHE cc_start: 0.7562 (t80) cc_final: 0.7167 (t80) REVERT: A 461 MET cc_start: 0.7472 (ttp) cc_final: 0.7131 (ttm) REVERT: B 66 PHE cc_start: 0.8122 (m-10) cc_final: 0.7353 (t80) REVERT: B 114 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8329 (mmtt) REVERT: B 121 MET cc_start: 0.7909 (ttp) cc_final: 0.6858 (tpt) REVERT: B 245 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 359 ASN cc_start: 0.8836 (m-40) cc_final: 0.8271 (m-40) REVERT: C 66 PHE cc_start: 0.8162 (m-10) cc_final: 0.7373 (t80) REVERT: C 77 GLU cc_start: 0.7251 (tt0) cc_final: 0.6872 (tp30) REVERT: C 89 MET cc_start: 0.8448 (tpp) cc_final: 0.7926 (mmm) REVERT: C 114 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8374 (mmtt) REVERT: C 121 MET cc_start: 0.7906 (ttp) cc_final: 0.6883 (tpt) REVERT: C 245 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 276 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7795 (mt) REVERT: C 296 MET cc_start: 0.8630 (tpp) cc_final: 0.7718 (tpp) REVERT: C 359 ASN cc_start: 0.8939 (m-40) cc_final: 0.8311 (m-40) outliers start: 55 outliers final: 37 residues processed: 307 average time/residue: 0.0656 time to fit residues: 29.9832 Evaluate side-chains 284 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 360 ASN B 243 GLN B 378 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 378 ASN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.163401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126968 restraints weight = 11471.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131760 restraints weight = 6096.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134724 restraints weight = 4122.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136985 restraints weight = 3264.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138163 restraints weight = 2801.107| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9684 Z= 0.138 Angle : 0.617 7.122 13167 Z= 0.300 Chirality : 0.040 0.158 1662 Planarity : 0.004 0.036 1584 Dihedral : 7.821 57.875 1506 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.81 % Allowed : 26.03 % Favored : 70.16 % 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: 0.87 (0.24), residues: 1236 helix: 1.12 (0.17), residues: 987 sheet: 0.03 (1.07), residues: 30 loop : -1.66 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.025 0.002 TYR B 297 PHE 0.015 0.001 PHE A 184 TRP 0.011 0.002 TRP A 453 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9684) covalent geometry : angle 0.61690 / 0.30 (13167) hydrogen bonds : bond 0.04181 / 2.92 ( 694) hydrogen bonds : angle 4.27628 / 3.11 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8111 (m-10) cc_final: 0.7353 (t80) REVERT: A 114 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8348 (mmtt) REVERT: A 121 MET cc_start: 0.7741 (ttp) cc_final: 0.6706 (tpt) REVERT: A 296 MET cc_start: 0.8507 (tpp) cc_final: 0.7729 (tpp) REVERT: A 319 LEU cc_start: 0.8689 (mt) cc_final: 0.8172 (tp) REVERT: A 359 ASN cc_start: 0.8850 (m-40) cc_final: 0.8620 (m-40) REVERT: A 378 ASN cc_start: 0.8658 (t0) cc_final: 0.8422 (t0) REVERT: A 461 MET cc_start: 0.7531 (ttp) cc_final: 0.7308 (ttm) REVERT: B 66 PHE cc_start: 0.8202 (m-10) cc_final: 0.7377 (t80) REVERT: B 114 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8297 (mmtt) REVERT: B 121 MET cc_start: 0.7844 (ttp) cc_final: 0.6731 (tpt) REVERT: B 245 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 296 MET cc_start: 0.8493 (tpp) cc_final: 0.7616 (tpp) REVERT: B 319 LEU cc_start: 0.8888 (mt) cc_final: 0.8253 (tp) REVERT: B 359 ASN cc_start: 0.8835 (m-40) cc_final: 0.8262 (m-40) REVERT: C 66 PHE cc_start: 0.8181 (m-10) cc_final: 0.7380 (t80) REVERT: C 77 GLU cc_start: 0.7183 (tt0) cc_final: 0.6790 (tp30) REVERT: C 114 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8320 (mmtt) REVERT: C 121 MET cc_start: 0.7800 (ttp) cc_final: 0.6767 (tpt) REVERT: C 296 MET cc_start: 0.8599 (tpp) cc_final: 0.7794 (tpp) REVERT: C 319 LEU cc_start: 0.8699 (mt) cc_final: 0.8137 (tp) REVERT: C 359 ASN cc_start: 0.8905 (m-40) cc_final: 0.8265 (m-40) outliers start: 37 outliers final: 25 residues processed: 292 average time/residue: 0.0728 time to fit residues: 31.7985 Evaluate side-chains 288 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 395 GLN B 243 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS C 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.160684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124155 restraints weight = 11677.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128836 restraints weight = 6240.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131866 restraints weight = 4260.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133918 restraints weight = 3390.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135093 restraints weight = 2936.330| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9684 Z= 0.160 Angle : 0.626 7.002 13167 Z= 0.304 Chirality : 0.040 0.150 1662 Planarity : 0.004 0.037 1584 Dihedral : 7.736 57.881 1506 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 5.14 % Allowed : 26.34 % Favored : 68.52 % 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: 0.96 (0.24), residues: 1236 helix: 1.17 (0.17), residues: 984 sheet: 0.02 (1.07), residues: 30 loop : -1.50 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 368 TYR 0.024 0.002 TYR C 127 PHE 0.015 0.001 PHE C 318 TRP 0.009 0.002 TRP B 453 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9684) covalent geometry : angle 0.62648 / 0.30 (13167) hydrogen bonds : bond 0.04086 / 2.83 ( 694) hydrogen bonds : angle 4.22308 / 3.07 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8346 (mmtt) REVERT: A 121 MET cc_start: 0.7814 (ttp) cc_final: 0.6741 (tpt) REVERT: A 245 GLN cc_start: 0.8493 (tp40) cc_final: 0.7530 (tm-30) REVERT: A 296 MET cc_start: 0.8521 (tpp) cc_final: 0.7782 (tpp) REVERT: A 319 LEU cc_start: 0.8685 (mt) cc_final: 0.8186 (tp) REVERT: A 431 MET cc_start: 0.8493 (ttt) cc_final: 0.8149 (ttm) REVERT: A 461 MET cc_start: 0.7530 (ttp) cc_final: 0.7244 (ttm) REVERT: A 479 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8169 (mmt-90) REVERT: B 66 PHE cc_start: 0.8252 (m-10) cc_final: 0.7456 (t80) REVERT: B 114 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8332 (mmtt) REVERT: B 121 MET cc_start: 0.7786 (ttp) cc_final: 0.6726 (tpt) REVERT: B 296 MET cc_start: 0.8545 (tpp) cc_final: 0.7762 (tpp) REVERT: B 319 LEU cc_start: 0.8902 (mt) cc_final: 0.8283 (tp) REVERT: B 359 ASN cc_start: 0.8805 (m-40) cc_final: 0.8360 (m-40) REVERT: B 431 MET cc_start: 0.8852 (tpp) cc_final: 0.8500 (mmm) REVERT: C 66 PHE cc_start: 0.8172 (m-10) cc_final: 0.7372 (t80) REVERT: C 77 GLU cc_start: 0.7125 (tt0) cc_final: 0.6763 (tp30) REVERT: C 114 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8312 (mmtt) REVERT: C 121 MET cc_start: 0.7828 (ttp) cc_final: 0.6804 (tpt) REVERT: C 245 GLN cc_start: 0.8512 (tp40) cc_final: 0.7639 (tm-30) REVERT: C 259 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7706 (mmp) REVERT: C 276 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7385 (mt) REVERT: C 296 MET cc_start: 0.8608 (tpp) cc_final: 0.7929 (tpp) REVERT: C 319 LEU cc_start: 0.8733 (mt) cc_final: 0.8163 (tp) outliers start: 50 outliers final: 32 residues processed: 290 average time/residue: 0.0676 time to fit residues: 29.5075 Evaluate side-chains 280 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.162321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126750 restraints weight = 11573.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131496 restraints weight = 6177.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134661 restraints weight = 4183.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136485 restraints weight = 3288.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137988 restraints weight = 2846.772| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9684 Z= 0.137 Angle : 0.613 8.257 13167 Z= 0.294 Chirality : 0.040 0.147 1662 Planarity : 0.004 0.034 1584 Dihedral : 7.634 57.311 1506 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.63 % Allowed : 27.57 % Favored : 67.80 % 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: 1.07 (0.24), residues: 1236 helix: 1.22 (0.17), residues: 987 sheet: -0.16 (1.04), residues: 30 loop : -1.30 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.022 0.002 TYR A 127 PHE 0.031 0.002 PHE C 369 TRP 0.024 0.002 TRP C 267 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9684) covalent geometry : angle 0.61287 / 0.29 (13167) hydrogen bonds : bond 0.03861 / 2.71 ( 694) hydrogen bonds : angle 4.12535 / 3.01 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8362 (mmtt) REVERT: A 121 MET cc_start: 0.7763 (ttp) cc_final: 0.6685 (tpt) REVERT: A 276 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7511 (mt) REVERT: A 296 MET cc_start: 0.8526 (tpp) cc_final: 0.7839 (tpp) REVERT: A 319 LEU cc_start: 0.8722 (mt) cc_final: 0.8255 (tp) REVERT: A 461 MET cc_start: 0.7522 (ttp) cc_final: 0.7201 (ttm) REVERT: B 114 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8295 (mmtt) REVERT: B 121 MET cc_start: 0.7794 (ttp) cc_final: 0.6589 (tpt) REVERT: B 296 MET cc_start: 0.8558 (tpp) cc_final: 0.7844 (tpp) REVERT: B 319 LEU cc_start: 0.8938 (mt) cc_final: 0.8336 (tp) REVERT: B 359 ASN cc_start: 0.8819 (m-40) cc_final: 0.8326 (m-40) REVERT: C 77 GLU cc_start: 0.7086 (tt0) cc_final: 0.6779 (tp30) REVERT: C 114 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8311 (mmtt) REVERT: C 121 MET cc_start: 0.7785 (ttp) cc_final: 0.6722 (tpt) REVERT: C 296 MET cc_start: 0.8538 (tpp) cc_final: 0.7912 (tpp) REVERT: C 319 LEU cc_start: 0.8823 (mt) cc_final: 0.8253 (tp) REVERT: C 405 GLN cc_start: 0.8420 (mm110) cc_final: 0.8077 (mm110) REVERT: C 475 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7967 (tm-30) outliers start: 45 outliers final: 33 residues processed: 283 average time/residue: 0.0722 time to fit residues: 31.0673 Evaluate side-chains 283 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127160 restraints weight = 11730.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132019 restraints weight = 6283.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135284 restraints weight = 4255.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137242 restraints weight = 3348.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138626 restraints weight = 2896.615| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9684 Z= 0.134 Angle : 0.617 10.471 13167 Z= 0.295 Chirality : 0.039 0.164 1662 Planarity : 0.004 0.032 1584 Dihedral : 7.605 57.388 1506 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.42 % Allowed : 28.40 % Favored : 67.18 % 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: 1.11 (0.25), residues: 1236 helix: 1.23 (0.17), residues: 996 sheet: -0.26 (1.02), residues: 30 loop : -1.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.028 0.002 TYR C 127 PHE 0.036 0.001 PHE B 369 TRP 0.008 0.001 TRP C 267 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9684) covalent geometry : angle 0.61672 / 0.29 (13167) hydrogen bonds : bond 0.03786 / 2.65 ( 694) hydrogen bonds : angle 4.08253 / 2.98 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 114 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8368 (mmtt) REVERT: A 121 MET cc_start: 0.7748 (ttp) cc_final: 0.6675 (tpt) REVERT: A 296 MET cc_start: 0.8479 (tpp) cc_final: 0.7841 (tpp) REVERT: A 319 LEU cc_start: 0.8738 (mt) cc_final: 0.8250 (tp) REVERT: A 461 MET cc_start: 0.7516 (ttp) cc_final: 0.7175 (ttm) REVERT: B 66 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7458 (t80) REVERT: B 114 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8289 (mmtt) REVERT: B 121 MET cc_start: 0.7769 (ttp) cc_final: 0.6523 (tpt) REVERT: B 296 MET cc_start: 0.8533 (tpp) cc_final: 0.7916 (tpp) REVERT: B 359 ASN cc_start: 0.8825 (m-40) cc_final: 0.8337 (m-40) REVERT: C 66 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 77 GLU cc_start: 0.7106 (tt0) cc_final: 0.6719 (tp30) REVERT: C 114 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8311 (mmtt) REVERT: C 121 MET cc_start: 0.7761 (ttp) cc_final: 0.6679 (tpt) REVERT: C 276 LEU cc_start: 0.7711 (mt) cc_final: 0.7182 (mt) REVERT: C 296 MET cc_start: 0.8526 (tpp) cc_final: 0.7923 (tpp) REVERT: C 319 LEU cc_start: 0.8866 (mt) cc_final: 0.8273 (tp) REVERT: C 405 GLN cc_start: 0.8426 (mm110) cc_final: 0.8082 (mm110) REVERT: C 475 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7968 (tm-30) outliers start: 43 outliers final: 33 residues processed: 276 average time/residue: 0.0765 time to fit residues: 31.6394 Evaluate side-chains 280 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN B 243 GLN C 243 GLN C 308 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.162948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127253 restraints weight = 11619.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132058 restraints weight = 6210.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135294 restraints weight = 4202.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137174 restraints weight = 3297.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138615 restraints weight = 2855.026| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 9684 Z= 0.152 Angle : 0.620 10.471 13167 Z= 0.296 Chirality : 0.039 0.163 1662 Planarity : 0.005 0.102 1584 Dihedral : 7.606 57.388 1506 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.70 % Allowed : 29.01 % Favored : 67.28 % 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: 1.11 (0.25), residues: 1236 helix: 1.23 (0.17), residues: 996 sheet: -0.26 (1.02), residues: 30 loop : -1.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.028 0.002 TYR C 127 PHE 0.036 0.001 PHE B 369 TRP 0.008 0.001 TRP C 267 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 9684) covalent geometry : angle 0.61986 / 0.30 (13167) hydrogen bonds : bond 0.03786 / 2.65 ( 694) hydrogen bonds : angle 4.08252 / 2.98 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 114 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8364 (mmtt) REVERT: A 121 MET cc_start: 0.7745 (ttp) cc_final: 0.6672 (tpt) REVERT: A 296 MET cc_start: 0.8480 (tpp) cc_final: 0.7840 (tpp) REVERT: A 319 LEU cc_start: 0.8740 (mt) cc_final: 0.8254 (tp) REVERT: A 461 MET cc_start: 0.7515 (ttp) cc_final: 0.7176 (ttm) REVERT: B 66 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 114 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8287 (mmtt) REVERT: B 121 MET cc_start: 0.7767 (ttp) cc_final: 0.6518 (tpt) REVERT: B 296 MET cc_start: 0.8530 (tpp) cc_final: 0.7916 (tpp) REVERT: B 359 ASN cc_start: 0.8821 (m-40) cc_final: 0.8329 (m-40) REVERT: C 66 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 77 GLU cc_start: 0.7108 (tt0) cc_final: 0.6717 (tp30) REVERT: C 114 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8306 (mmtt) REVERT: C 121 MET cc_start: 0.7761 (ttp) cc_final: 0.6664 (tpt) REVERT: C 276 LEU cc_start: 0.7701 (mt) cc_final: 0.7167 (mt) REVERT: C 296 MET cc_start: 0.8521 (tpp) cc_final: 0.7920 (tpp) REVERT: C 319 LEU cc_start: 0.8871 (mt) cc_final: 0.8277 (tp) REVERT: C 405 GLN cc_start: 0.8430 (mm110) cc_final: 0.8085 (mm110) REVERT: C 475 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 36 outliers final: 33 residues processed: 267 average time/residue: 0.0763 time to fit residues: 31.0084 Evaluate side-chains 279 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 chunk 93 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127343 restraints weight = 11559.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132137 restraints weight = 6177.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135236 restraints weight = 4188.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137439 restraints weight = 3305.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138651 restraints weight = 2831.992| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9684 Z= 0.147 Angle : 0.618 10.468 13167 Z= 0.296 Chirality : 0.039 0.162 1662 Planarity : 0.005 0.101 1584 Dihedral : 7.777 57.388 1506 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.70 % Allowed : 29.12 % Favored : 67.18 % 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: 1.11 (0.25), residues: 1236 helix: 1.23 (0.17), residues: 996 sheet: -0.26 (1.02), residues: 30 loop : -1.28 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.027 0.002 TYR C 127 PHE 0.034 0.001 PHE B 369 TRP 0.008 0.001 TRP C 267 HIS 0.002 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9684) covalent geometry : angle 0.61837 / 0.30 (13167) hydrogen bonds : bond 0.03786 / 2.64 ( 694) hydrogen bonds : angle 4.08255 / 2.98 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7269 (t80) REVERT: A 114 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8372 (mmtt) REVERT: A 121 MET cc_start: 0.7752 (ttp) cc_final: 0.6696 (tpt) REVERT: A 296 MET cc_start: 0.8478 (tpp) cc_final: 0.7840 (tpp) REVERT: A 319 LEU cc_start: 0.8737 (mt) cc_final: 0.8250 (tp) REVERT: A 461 MET cc_start: 0.7519 (ttp) cc_final: 0.7180 (ttm) REVERT: B 66 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 114 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8294 (mmtt) REVERT: B 121 MET cc_start: 0.7777 (ttp) cc_final: 0.6544 (tpt) REVERT: B 296 MET cc_start: 0.8528 (tpp) cc_final: 0.7916 (tpp) REVERT: B 359 ASN cc_start: 0.8826 (m-40) cc_final: 0.8340 (m-40) REVERT: C 66 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7416 (t80) REVERT: C 77 GLU cc_start: 0.7094 (tt0) cc_final: 0.6715 (tp30) REVERT: C 114 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8313 (mmtt) REVERT: C 121 MET cc_start: 0.7772 (ttp) cc_final: 0.6692 (tpt) REVERT: C 276 LEU cc_start: 0.7719 (mt) cc_final: 0.7185 (mt) REVERT: C 296 MET cc_start: 0.8522 (tpp) cc_final: 0.7921 (tpp) REVERT: C 319 LEU cc_start: 0.8870 (mt) cc_final: 0.8273 (tp) REVERT: C 405 GLN cc_start: 0.8422 (mm110) cc_final: 0.8082 (mm110) REVERT: C 475 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 36 outliers final: 33 residues processed: 266 average time/residue: 0.0768 time to fit residues: 31.0223 Evaluate side-chains 279 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 0.0770 chunk 14 optimal weight: 6.9990 chunk 112 optimal weight: 0.0570 chunk 63 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 GLN C 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128136 restraints weight = 11697.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133111 restraints weight = 6285.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136470 restraints weight = 4266.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138436 restraints weight = 3359.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.139904 restraints weight = 2904.485| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9684 Z= 0.134 Angle : 0.638 9.359 13167 Z= 0.307 Chirality : 0.040 0.153 1662 Planarity : 0.005 0.074 1584 Dihedral : 7.572 57.609 1506 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.19 % Allowed : 29.73 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1236 helix: 1.24 (0.17), residues: 996 sheet: -0.23 (1.02), residues: 30 loop : -1.35 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.026 0.002 TYR C 127 PHE 0.013 0.001 PHE B 369 TRP 0.034 0.003 TRP A 267 HIS 0.002 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9684) covalent geometry : angle 0.63833 / 0.31 (13167) hydrogen bonds : bond 0.03742 / 2.62 ( 694) hydrogen bonds : angle 4.07434 / 2.98 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 114 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8366 (mmtt) REVERT: A 121 MET cc_start: 0.7729 (ttp) cc_final: 0.6631 (tpt) REVERT: A 296 MET cc_start: 0.8462 (tpp) cc_final: 0.7848 (tpp) REVERT: A 319 LEU cc_start: 0.8736 (mt) cc_final: 0.8259 (tp) REVERT: A 369 PHE cc_start: 0.8655 (t80) cc_final: 0.8368 (t80) REVERT: A 461 MET cc_start: 0.7508 (ttp) cc_final: 0.7194 (ttm) REVERT: B 66 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7474 (t80) REVERT: B 114 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8268 (mmtt) REVERT: B 121 MET cc_start: 0.7752 (ttp) cc_final: 0.6486 (tpt) REVERT: B 296 MET cc_start: 0.8546 (tpp) cc_final: 0.7945 (tpp) REVERT: B 359 ASN cc_start: 0.8823 (m-40) cc_final: 0.8316 (m-40) REVERT: C 66 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7375 (t80) REVERT: C 77 GLU cc_start: 0.7076 (tt0) cc_final: 0.6697 (tp30) REVERT: C 89 MET cc_start: 0.8251 (tpp) cc_final: 0.7877 (mmm) REVERT: C 114 LYS cc_start: 0.8907 (mtpt) cc_final: 0.8308 (mmtt) REVERT: C 121 MET cc_start: 0.7723 (ttp) cc_final: 0.6614 (tpt) REVERT: C 243 GLN cc_start: 0.8353 (tp40) cc_final: 0.8102 (tp-100) REVERT: C 276 LEU cc_start: 0.7707 (mt) cc_final: 0.7233 (mt) REVERT: C 296 MET cc_start: 0.8502 (tpp) cc_final: 0.7916 (tpp) REVERT: C 319 LEU cc_start: 0.8877 (mt) cc_final: 0.8294 (tp) REVERT: C 405 GLN cc_start: 0.8431 (mm110) cc_final: 0.8093 (mm110) REVERT: C 475 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7964 (tm-30) outliers start: 31 outliers final: 27 residues processed: 268 average time/residue: 0.0819 time to fit residues: 32.6896 Evaluate side-chains 275 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 267 TRP Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.162987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.126123 restraints weight = 11825.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.130973 restraints weight = 6390.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134204 restraints weight = 4362.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136160 restraints weight = 3451.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137417 restraints weight = 2989.448| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9684 Z= 0.152 Angle : 0.645 9.519 13167 Z= 0.309 Chirality : 0.040 0.151 1662 Planarity : 0.005 0.064 1584 Dihedral : 7.536 58.792 1506 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.70 % Allowed : 29.53 % Favored : 66.77 % 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: 1.15 (0.24), residues: 1236 helix: 1.26 (0.17), residues: 990 sheet: -0.12 (1.02), residues: 30 loop : -1.22 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.024 0.002 TYR C 127 PHE 0.031 0.001 PHE B 369 TRP 0.021 0.002 TRP A 267 HIS 0.002 0.001 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9684) covalent geometry : angle 0.64537 / 0.31 (13167) hydrogen bonds : bond 0.03787 / 2.65 ( 694) hydrogen bonds : angle 4.10720 / 3.01 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1563.97 seconds wall clock time: 27 minutes 45.09 seconds (1665.09 seconds total)