Starting phenix.real_space_refine on Thu Jul 2 18:35:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7v_52663/07_2026/9i7v_52663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7v_52663/07_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_52663/07_2026/9i7v_52663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7v_52663/07_2026/9i7v_52663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i7v_52663/07_2026/9i7v_52663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7v_52663/07_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-dev-6108/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, 76 Ad-hoc single atom residues: {' RB': 1} Unusual residues: {'6Z6': 1, 'PX6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.05, per 1000 atoms: 0.22 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: 0.98 Conformation dependent library (CDL) restraints added in 317.9 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: 0.27 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: 1.63 Time building geometry restraints manager: 1.21 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.200 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- 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 : 0.232 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: 0.0748 time to fit residues: 40.6057 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 : 0.331 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.187650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.152735 restraints weight = 11912.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.157607 restraints weight = 6188.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160935 restraints weight = 4144.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.162975 restraints weight = 3252.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.164065 restraints weight = 2807.383| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9684 Z= 0.161 Angle : 0.688 9.078 13167 Z= 0.339 Chirality : 0.042 0.186 1662 Planarity : 0.005 0.042 1584 Dihedral : 7.872 55.373 1506 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.32 % Allowed : 21.91 % 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: -0.03 (0.24), residues: 1236 helix: 0.58 (0.16), residues: 969 sheet: -1.43 (0.86), residues: 48 loop : -2.04 (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 0.015 0.003 TRP A 453 HIS 0.013 0.003 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9684) covalent geometry : angle 0.68763 / 0.34 (13167) hydrogen bonds : bond 0.05185 / 3.68 ( 694) hydrogen bonds : angle 4.73803 / 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 338 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8652 (tttm) REVERT: A 121 MET cc_start: 0.7799 (ttp) cc_final: 0.6909 (tpt) REVERT: A 276 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 359 ASN cc_start: 0.8811 (m-40) cc_final: 0.8520 (m-40) REVERT: A 403 PHE cc_start: 0.7603 (t80) cc_final: 0.7231 (t80) REVERT: A 461 MET cc_start: 0.7406 (ttp) cc_final: 0.7127 (ttm) REVERT: B 114 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8341 (mmtt) REVERT: B 121 MET cc_start: 0.7835 (ttp) cc_final: 0.6933 (tpt) REVERT: B 196 TYR cc_start: 0.8912 (t80) cc_final: 0.8637 (t80) REVERT: B 217 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 245 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 319 LEU cc_start: 0.8815 (mt) cc_final: 0.8231 (tp) REVERT: B 359 ASN cc_start: 0.8868 (m-40) cc_final: 0.8400 (m-40) REVERT: C 89 MET cc_start: 0.8414 (tpp) cc_final: 0.8015 (mmm) REVERT: C 91 MET cc_start: 0.8196 (ttm) cc_final: 0.7951 (ttm) REVERT: C 114 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8366 (mmtt) REVERT: C 121 MET cc_start: 0.7849 (ttp) cc_final: 0.7007 (tpt) REVERT: C 217 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 245 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 276 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7895 (mt) REVERT: C 359 ASN cc_start: 0.8921 (m-40) cc_final: 0.8559 (m-40) REVERT: C 452 ASP cc_start: 0.8042 (t0) cc_final: 0.7104 (t0) outliers start: 42 outliers final: 22 residues processed: 326 average time/residue: 0.0736 time to fit residues: 35.4830 Evaluate side-chains 279 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 3.9990 chunk 106 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 360 ASN B 360 ASN B 476 HIS C 243 GLN ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.164731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128642 restraints weight = 11156.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.133392 restraints weight = 5869.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136561 restraints weight = 3948.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138368 restraints weight = 3097.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139766 restraints weight = 2684.906| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3147 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= 0.151 Angle : 0.619 8.452 13167 Z= 0.306 Chirality : 0.040 0.120 1662 Planarity : 0.004 0.038 1584 Dihedral : 7.855 56.190 1506 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.32 % Allowed : 23.56 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1236 helix: 1.04 (0.17), residues: 969 sheet: 0.14 (1.10), residues: 30 loop : -1.87 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.022 0.002 TYR C 127 PHE 0.014 0.002 PHE C 318 TRP 0.013 0.002 TRP A 453 HIS 0.012 0.003 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9684) covalent geometry : angle 0.61932 / 0.31 (13167) hydrogen bonds : bond 0.04544 / 3.16 ( 694) hydrogen bonds : angle 4.36851 / 3.16 ( 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 314 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 272 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.6836 (tp30) cc_final: 0.6587 (tp30) REVERT: A 114 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8362 (mmtt) REVERT: A 121 MET cc_start: 0.7780 (ttp) cc_final: 0.6778 (tpt) REVERT: A 276 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 319 LEU cc_start: 0.8677 (mt) cc_final: 0.8151 (tp) REVERT: A 403 PHE cc_start: 0.7548 (t80) cc_final: 0.7167 (t80) REVERT: A 461 MET cc_start: 0.7471 (ttp) cc_final: 0.7222 (ttm) REVERT: B 114 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8309 (mmtt) REVERT: B 121 MET cc_start: 0.7870 (ttp) cc_final: 0.6783 (tpt) REVERT: B 319 LEU cc_start: 0.8856 (mt) cc_final: 0.8297 (tp) REVERT: B 359 ASN cc_start: 0.8852 (m-40) cc_final: 0.8367 (m-40) REVERT: B 456 ASP cc_start: 0.7842 (t70) cc_final: 0.7256 (t70) REVERT: B 477 LEU cc_start: 0.9181 (mm) cc_final: 0.8921 (mm) REVERT: C 66 PHE cc_start: 0.8186 (m-10) cc_final: 0.7362 (t80) REVERT: C 77 GLU cc_start: 0.6906 (tp30) cc_final: 0.6623 (tp30) REVERT: C 89 MET cc_start: 0.8397 (tpp) cc_final: 0.7999 (mmm) REVERT: C 114 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8348 (mmtt) REVERT: C 121 MET cc_start: 0.7845 (ttp) cc_final: 0.6780 (tpt) REVERT: C 196 TYR cc_start: 0.9050 (t80) cc_final: 0.8805 (t80) REVERT: C 217 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7746 (mm-30) REVERT: C 245 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 276 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7766 (mt) REVERT: C 296 MET cc_start: 0.8595 (tpp) cc_final: 0.7742 (tpp) REVERT: C 319 LEU cc_start: 0.8724 (mt) cc_final: 0.8172 (tp) REVERT: C 359 ASN cc_start: 0.8910 (m-40) cc_final: 0.8360 (m-40) outliers start: 42 outliers final: 23 residues processed: 296 average time/residue: 0.0669 time to fit residues: 29.3444 Evaluate side-chains 263 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 LEU 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 301 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 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 87 LEU Chi-restraints excluded: chain B residue 218 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 276 LEU Chi-restraints excluded: chain C residue 301 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 41 optimal weight: 20.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 334 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 = 0.3809 r_free = 0.3809 target = 0.166089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129836 restraints weight = 11355.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134839 restraints weight = 5951.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137944 restraints weight = 3979.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.140183 restraints weight = 3137.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.141135 restraints weight = 2688.555| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9684 Z= 0.128 Angle : 0.592 7.268 13167 Z= 0.289 Chirality : 0.040 0.118 1662 Planarity : 0.004 0.033 1584 Dihedral : 7.678 55.161 1506 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.70 % Allowed : 25.82 % Favored : 70.47 % 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: 1.04 (0.24), residues: 1236 helix: 1.23 (0.17), residues: 987 sheet: 0.16 (1.08), residues: 30 loop : -1.57 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 368 TYR 0.027 0.002 TYR B 297 PHE 0.022 0.001 PHE A 184 TRP 0.011 0.002 TRP A 453 HIS 0.004 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9684) covalent geometry : angle 0.59237 / 0.29 (13167) hydrogen bonds : bond 0.04007 / 2.80 ( 694) hydrogen bonds : angle 4.17972 / 3.03 ( 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 295 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.7788 (ttp) cc_final: 0.6693 (tpt) REVERT: A 296 MET cc_start: 0.8491 (tpp) cc_final: 0.7698 (tpp) REVERT: A 319 LEU cc_start: 0.8685 (mt) cc_final: 0.8179 (tp) REVERT: A 461 MET cc_start: 0.7500 (ttp) cc_final: 0.7220 (ttm) REVERT: B 89 MET cc_start: 0.8289 (tpp) cc_final: 0.7946 (mmm) REVERT: B 114 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8294 (mmtt) REVERT: B 121 MET cc_start: 0.7798 (ttp) cc_final: 0.6659 (tpt) REVERT: B 296 MET cc_start: 0.8491 (tpp) cc_final: 0.7649 (tpp) REVERT: B 359 ASN cc_start: 0.8825 (m-40) cc_final: 0.8238 (m-40) REVERT: C 66 PHE cc_start: 0.8151 (m-10) cc_final: 0.7364 (t80) REVERT: C 114 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8310 (mmtt) REVERT: C 121 MET cc_start: 0.7768 (ttp) cc_final: 0.6736 (tpt) REVERT: C 296 MET cc_start: 0.8581 (tpp) cc_final: 0.7739 (tpp) REVERT: C 319 LEU cc_start: 0.8773 (mt) cc_final: 0.8313 (tp) REVERT: C 359 ASN cc_start: 0.8860 (m-40) cc_final: 0.8286 (m-40) outliers start: 36 outliers final: 24 residues processed: 279 average time/residue: 0.0652 time to fit residues: 27.3071 Evaluate side-chains 273 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET 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 301 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 A residue 445 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 301 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 C residue 68 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 301 VAL 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: 10.0000 chunk 106 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** C 243 GLN C 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125797 restraints weight = 11658.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130580 restraints weight = 6168.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133645 restraints weight = 4171.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.135817 restraints weight = 3305.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136780 restraints weight = 2837.671| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9684 Z= 0.158 Angle : 0.616 6.888 13167 Z= 0.299 Chirality : 0.040 0.163 1662 Planarity : 0.004 0.035 1584 Dihedral : 7.505 55.369 1506 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.94 % Allowed : 26.95 % Favored : 68.11 % 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: 1.02 (0.24), residues: 1236 helix: 1.20 (0.17), residues: 990 sheet: 0.24 (1.10), residues: 30 loop : -1.49 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 368 TYR 0.024 0.002 TYR C 297 PHE 0.021 0.001 PHE C 66 TRP 0.010 0.002 TRP B 267 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9684) covalent geometry : angle 0.61584 / 0.30 (13167) hydrogen bonds : bond 0.04037 / 2.81 ( 694) hydrogen bonds : angle 4.14400 / 3.02 ( 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 310 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.8094 (m-10) cc_final: 0.7348 (t80) REVERT: A 114 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8351 (mmtt) REVERT: A 121 MET cc_start: 0.7752 (ttp) cc_final: 0.6678 (tpt) REVERT: A 296 MET cc_start: 0.8538 (tpp) cc_final: 0.7788 (tpp) REVERT: A 319 LEU cc_start: 0.8709 (mt) cc_final: 0.8233 (tp) REVERT: A 356 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 461 MET cc_start: 0.7478 (ttp) cc_final: 0.7188 (ttm) REVERT: B 114 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8266 (mmtt) REVERT: B 121 MET cc_start: 0.7784 (ttp) cc_final: 0.6657 (tpt) REVERT: B 296 MET cc_start: 0.8536 (tpp) cc_final: 0.7752 (tpp) REVERT: B 319 LEU cc_start: 0.8926 (mt) cc_final: 0.8329 (tp) REVERT: B 359 ASN cc_start: 0.8788 (m-40) cc_final: 0.8309 (m-40) REVERT: C 66 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7407 (t80) REVERT: C 114 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8304 (mmtt) REVERT: C 121 MET cc_start: 0.7788 (ttp) cc_final: 0.6754 (tpt) REVERT: C 276 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 296 MET cc_start: 0.8571 (tpp) cc_final: 0.7908 (tpp) REVERT: C 359 ASN cc_start: 0.8844 (m-40) cc_final: 0.8193 (m-40) REVERT: C 405 GLN cc_start: 0.8444 (mm110) cc_final: 0.8090 (mm110) outliers start: 48 outliers final: 30 residues processed: 287 average time/residue: 0.0625 time to fit residues: 27.0085 Evaluate side-chains 271 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET 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 301 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 356 LEU 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 445 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 267 TRP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 301 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 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 301 VAL Chi-restraints excluded: chain C residue 417 SER 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: 1.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128488 restraints weight = 11515.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133225 restraints weight = 6078.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.136630 restraints weight = 4112.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138758 restraints weight = 3200.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139939 restraints weight = 2742.181| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9684 Z= 0.131 Angle : 0.596 6.966 13167 Z= 0.287 Chirality : 0.039 0.149 1662 Planarity : 0.004 0.042 1584 Dihedral : 7.330 57.006 1506 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.32 % Allowed : 28.70 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1236 helix: 1.27 (0.17), residues: 990 sheet: 0.10 (1.07), residues: 30 loop : -1.34 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.024 0.002 TYR C 127 PHE 0.047 0.002 PHE B 369 TRP 0.024 0.003 TRP A 267 HIS 0.002 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9684) covalent geometry : angle 0.59559 / 0.29 (13167) hydrogen bonds : bond 0.03788 / 2.66 ( 694) hydrogen bonds : angle 4.06315 / 2.96 ( 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 289 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8353 (mmtt) REVERT: A 121 MET cc_start: 0.7712 (ttp) cc_final: 0.6634 (tpt) REVERT: A 296 MET cc_start: 0.8523 (tpp) cc_final: 0.7817 (tpp) REVERT: A 319 LEU cc_start: 0.8713 (mt) cc_final: 0.8256 (tp) REVERT: A 461 MET cc_start: 0.7506 (ttp) cc_final: 0.7173 (ttm) REVERT: B 114 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8261 (mmtt) REVERT: B 121 MET cc_start: 0.7765 (ttp) cc_final: 0.6551 (tpt) REVERT: B 296 MET cc_start: 0.8518 (tpp) cc_final: 0.7833 (tpp) REVERT: B 319 LEU cc_start: 0.8932 (mt) cc_final: 0.8319 (tp) REVERT: B 359 ASN cc_start: 0.8792 (m-40) cc_final: 0.8326 (m-40) REVERT: B 369 PHE cc_start: 0.8626 (t80) cc_final: 0.8412 (t80) REVERT: B 431 MET cc_start: 0.8814 (tpp) cc_final: 0.8458 (mmm) REVERT: C 114 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8309 (mmtt) REVERT: C 121 MET cc_start: 0.7788 (ttp) cc_final: 0.6689 (tpt) REVERT: C 276 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7376 (mt) REVERT: C 296 MET cc_start: 0.8546 (tpp) cc_final: 0.7915 (tpp) REVERT: C 319 LEU cc_start: 0.8896 (mt) cc_final: 0.8270 (tp) REVERT: C 369 PHE cc_start: 0.8735 (t80) cc_final: 0.8504 (t80) REVERT: C 405 GLN cc_start: 0.8410 (mm110) cc_final: 0.8064 (mm110) REVERT: C 463 ASN cc_start: 0.9097 (t0) cc_final: 0.8742 (t0) outliers start: 42 outliers final: 28 residues processed: 270 average time/residue: 0.0618 time to fit residues: 25.2959 Evaluate side-chains 269 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET 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 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 445 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 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 267 TRP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 301 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 68 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 417 SER 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: 4.9990 chunk 33 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.162191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125744 restraints weight = 11628.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130589 restraints weight = 6250.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133832 restraints weight = 4249.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135803 restraints weight = 3341.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.136702 restraints weight = 2890.033| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9684 Z= 0.148 Angle : 0.613 10.676 13167 Z= 0.295 Chirality : 0.040 0.172 1662 Planarity : 0.005 0.068 1584 Dihedral : 7.355 58.454 1506 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.42 % Allowed : 28.70 % Favored : 66.87 % 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: 1.14 (0.24), residues: 1236 helix: 1.26 (0.17), residues: 999 sheet: -0.07 (1.06), residues: 30 loop : -1.37 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.025 0.002 TYR C 297 PHE 0.034 0.001 PHE B 369 TRP 0.011 0.002 TRP A 267 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9684) covalent geometry : angle 0.61266 / 0.30 (13167) hydrogen bonds : bond 0.03807 / 2.66 ( 694) hydrogen bonds : angle 4.05910 / 2.97 ( 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 283 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8355 (mmtt) REVERT: A 121 MET cc_start: 0.7713 (ttp) cc_final: 0.6626 (tpt) REVERT: A 276 LEU cc_start: 0.7703 (mt) cc_final: 0.7201 (mt) REVERT: A 296 MET cc_start: 0.8524 (tpp) cc_final: 0.7863 (tpp) REVERT: A 319 LEU cc_start: 0.8741 (mt) cc_final: 0.8267 (tp) REVERT: A 461 MET cc_start: 0.7532 (ttp) cc_final: 0.7185 (ttm) REVERT: A 479 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8257 (mmt-90) REVERT: B 114 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8281 (mmtt) REVERT: B 121 MET cc_start: 0.7756 (ttp) cc_final: 0.6537 (tpt) REVERT: B 296 MET cc_start: 0.8568 (tpp) cc_final: 0.7953 (tpp) REVERT: B 359 ASN cc_start: 0.8815 (m-40) cc_final: 0.8329 (m-40) REVERT: C 66 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7345 (t80) REVERT: C 114 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8328 (mmtt) REVERT: C 121 MET cc_start: 0.7795 (ttp) cc_final: 0.6719 (tpt) REVERT: C 276 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7345 (mt) REVERT: C 296 MET cc_start: 0.8517 (tpp) cc_final: 0.7909 (tpp) REVERT: C 319 LEU cc_start: 0.8900 (mt) cc_final: 0.8258 (tp) REVERT: C 405 GLN cc_start: 0.8438 (mm110) cc_final: 0.8092 (mm110) outliers start: 43 outliers final: 29 residues processed: 261 average time/residue: 0.0773 time to fit residues: 30.6210 Evaluate side-chains 270 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 178 ASP 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 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 267 TRP Chi-restraints excluded: chain B residue 281 ILE 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 94 MET Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 417 SER 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: 0.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 115 optimal weight: 0.0050 chunk 103 optimal weight: 3.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125692 restraints weight = 11704.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130565 restraints weight = 6285.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133528 restraints weight = 4268.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.135810 restraints weight = 3390.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136770 restraints weight = 2912.079| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9684 Z= 0.149 Angle : 0.617 9.305 13167 Z= 0.297 Chirality : 0.040 0.156 1662 Planarity : 0.004 0.062 1584 Dihedral : 7.412 58.930 1506 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.53 % Allowed : 28.50 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1236 helix: 1.26 (0.17), residues: 999 sheet: -0.21 (1.01), residues: 30 loop : -1.34 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 69 TYR 0.026 0.002 TYR C 297 PHE 0.033 0.001 PHE A 369 TRP 0.009 0.002 TRP B 267 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9684) covalent geometry : angle 0.61651 / 0.30 (13167) hydrogen bonds : bond 0.03821 / 2.67 ( 694) hydrogen bonds : angle 4.04947 / 2.96 ( 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 286 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8361 (mmtt) REVERT: A 121 MET cc_start: 0.7712 (ttp) cc_final: 0.6630 (tpt) REVERT: A 276 LEU cc_start: 0.7738 (mt) cc_final: 0.7205 (mt) REVERT: A 296 MET cc_start: 0.8528 (tpp) cc_final: 0.7875 (tpp) REVERT: A 319 LEU cc_start: 0.8747 (mt) cc_final: 0.8277 (tp) REVERT: A 461 MET cc_start: 0.7506 (ttp) cc_final: 0.7242 (ttm) REVERT: A 479 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8245 (mmt-90) REVERT: B 114 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8284 (mmtt) REVERT: B 121 MET cc_start: 0.7742 (ttp) cc_final: 0.6519 (tpt) REVERT: B 296 MET cc_start: 0.8543 (tpp) cc_final: 0.7943 (tpp) REVERT: B 359 ASN cc_start: 0.8817 (m-40) cc_final: 0.8324 (m-40) REVERT: C 66 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7371 (t80) REVERT: C 114 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8326 (mmtt) REVERT: C 121 MET cc_start: 0.7775 (ttp) cc_final: 0.6702 (tpt) REVERT: C 276 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7346 (mt) REVERT: C 296 MET cc_start: 0.8531 (tpp) cc_final: 0.7916 (tpp) REVERT: C 319 LEU cc_start: 0.8884 (mt) cc_final: 0.8247 (tp) REVERT: C 405 GLN cc_start: 0.8435 (mm110) cc_final: 0.8084 (mm110) outliers start: 44 outliers final: 34 residues processed: 267 average time/residue: 0.0744 time to fit residues: 30.2623 Evaluate side-chains 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 178 ASP 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 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 267 TRP 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 94 MET 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 301 VAL Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 SER 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: 3.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125473 restraints weight = 11630.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130275 restraints weight = 6266.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133549 restraints weight = 4258.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135520 restraints weight = 3360.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136820 restraints weight = 2909.039| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9684 Z= 0.149 Angle : 0.617 9.305 13167 Z= 0.297 Chirality : 0.040 0.156 1662 Planarity : 0.004 0.070 1584 Dihedral : 7.411 58.930 1506 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.81 % Allowed : 29.32 % Favored : 66.87 % 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: 999 sheet: -0.21 (1.01), residues: 30 loop : -1.34 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 69 TYR 0.026 0.002 TYR C 297 PHE 0.033 0.001 PHE A 369 TRP 0.009 0.002 TRP B 267 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9684) covalent geometry : angle 0.61650 / 0.30 (13167) hydrogen bonds : bond 0.03821 / 2.67 ( 694) hydrogen bonds : angle 4.04947 / 2.96 ( 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 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8977 (mtpt) cc_final: 0.8363 (mmtt) REVERT: A 121 MET cc_start: 0.7713 (ttp) cc_final: 0.6634 (tpt) REVERT: A 276 LEU cc_start: 0.7735 (mt) cc_final: 0.7204 (mt) REVERT: A 296 MET cc_start: 0.8527 (tpp) cc_final: 0.7876 (tpp) REVERT: A 319 LEU cc_start: 0.8750 (mt) cc_final: 0.8277 (tp) REVERT: A 461 MET cc_start: 0.7509 (ttp) cc_final: 0.7243 (ttm) REVERT: A 479 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8236 (mmt-90) REVERT: B 114 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8288 (mmtt) REVERT: B 121 MET cc_start: 0.7748 (ttp) cc_final: 0.6526 (tpt) REVERT: B 296 MET cc_start: 0.8541 (tpp) cc_final: 0.7942 (tpp) REVERT: B 359 ASN cc_start: 0.8814 (m-40) cc_final: 0.8326 (m-40) REVERT: C 66 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7376 (t80) REVERT: C 114 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8330 (mmtt) REVERT: C 121 MET cc_start: 0.7775 (ttp) cc_final: 0.6706 (tpt) REVERT: C 276 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7342 (mt) REVERT: C 296 MET cc_start: 0.8526 (tpp) cc_final: 0.7916 (tpp) REVERT: C 319 LEU cc_start: 0.8888 (mt) cc_final: 0.8246 (tp) REVERT: C 405 GLN cc_start: 0.8426 (mm110) cc_final: 0.8080 (mm110) outliers start: 37 outliers final: 34 residues processed: 255 average time/residue: 0.0770 time to fit residues: 29.9179 Evaluate side-chains 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 178 ASP 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 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 267 TRP 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 94 MET 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 301 VAL Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 SER 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: 0.8980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125458 restraints weight = 11612.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130249 restraints weight = 6272.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133195 restraints weight = 4279.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135466 restraints weight = 3405.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136414 restraints weight = 2927.530| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9684 Z= 0.149 Angle : 0.617 9.305 13167 Z= 0.297 Chirality : 0.040 0.156 1662 Planarity : 0.004 0.070 1584 Dihedral : 7.411 58.930 1506 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.81 % Allowed : 29.32 % Favored : 66.87 % 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: 999 sheet: -0.21 (1.01), residues: 30 loop : -1.34 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 69 TYR 0.026 0.002 TYR C 297 PHE 0.033 0.001 PHE A 369 TRP 0.009 0.002 TRP B 267 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9684) covalent geometry : angle 0.61650 / 0.30 (13167) hydrogen bonds : bond 0.03821 / 2.67 ( 694) hydrogen bonds : angle 4.04947 / 2.96 ( 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 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8360 (mmtt) REVERT: A 121 MET cc_start: 0.7714 (ttp) cc_final: 0.6629 (tpt) REVERT: A 276 LEU cc_start: 0.7732 (mt) cc_final: 0.7203 (mt) REVERT: A 296 MET cc_start: 0.8530 (tpp) cc_final: 0.7875 (tpp) REVERT: A 319 LEU cc_start: 0.8750 (mt) cc_final: 0.8279 (tp) REVERT: A 461 MET cc_start: 0.7509 (ttp) cc_final: 0.7244 (ttm) REVERT: A 479 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8243 (mmt-90) REVERT: B 114 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8283 (mmtt) REVERT: B 121 MET cc_start: 0.7745 (ttp) cc_final: 0.6517 (tpt) REVERT: B 296 MET cc_start: 0.8542 (tpp) cc_final: 0.7941 (tpp) REVERT: B 359 ASN cc_start: 0.8811 (m-40) cc_final: 0.8322 (m-40) REVERT: C 66 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7370 (t80) REVERT: C 114 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8326 (mmtt) REVERT: C 121 MET cc_start: 0.7773 (ttp) cc_final: 0.6695 (tpt) REVERT: C 276 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7341 (mt) REVERT: C 296 MET cc_start: 0.8530 (tpp) cc_final: 0.7918 (tpp) REVERT: C 319 LEU cc_start: 0.8886 (mt) cc_final: 0.8247 (tp) REVERT: C 405 GLN cc_start: 0.8435 (mm110) cc_final: 0.8083 (mm110) outliers start: 37 outliers final: 34 residues processed: 255 average time/residue: 0.0756 time to fit residues: 29.4382 Evaluate side-chains 272 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 178 ASP 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 396 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 267 TRP 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 94 MET 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 301 VAL Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 SER 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: 2.9990 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125461 restraints weight = 11636.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.130189 restraints weight = 6264.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133466 restraints weight = 4290.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135313 restraints weight = 3375.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136812 restraints weight = 2929.759| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9684 Z= 0.149 Angle : 0.617 9.305 13167 Z= 0.297 Chirality : 0.040 0.156 1662 Planarity : 0.004 0.070 1584 Dihedral : 7.411 58.930 1506 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.81 % Allowed : 29.32 % Favored : 66.87 % 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: 999 sheet: -0.21 (1.01), residues: 30 loop : -1.34 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 69 TYR 0.026 0.002 TYR C 297 PHE 0.033 0.001 PHE A 369 TRP 0.009 0.002 TRP B 267 HIS 0.001 0.000 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9684) covalent geometry : angle 0.61650 / 0.30 (13167) hydrogen bonds : bond 0.03821 / 2.67 ( 694) hydrogen bonds : angle 4.04947 / 2.96 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1539.01 seconds wall clock time: 27 minutes 23.72 seconds (1643.72 seconds total)