Starting phenix.real_space_refine on Sun Dec 29 23:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoa_28332/12_2024/8eoa_28332.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.007 sd= 0.728 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 P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7298 2.51 5 N 1939 2.21 5 O 2234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5092 Classifications: {'peptide': 629} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5072 Classifications: {'peptide': 627} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1307 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASP C 7 " occ=0.93 ... (6 atoms not shown) pdb=" OD2 ASP C 7 " occ=0.93 residue: pdb=" N LEU C 10 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 10 " occ=0.93 residue: pdb=" N LEU C 11 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 11 " occ=0.93 residue: pdb=" N LEU C 12 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 12 " occ=0.93 Time building chain proxies: 7.05, per 1000 atoms: 0.61 Number of scatterers: 11535 At special positions: 0 Unit cell: (94.848, 114.816, 131.04, 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) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2234 8.00 N 1939 7.00 C 7298 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: 2.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 43.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 60 removed outlier: 3.810A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.868A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 397 through 420 removed outlier: 4.105A pdb=" N LEU A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.466A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.786A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.249A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.733A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.924A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 60 removed outlier: 4.066A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.681A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 397 through 420 removed outlier: 3.905A pdb=" N LEU B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 6.444A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.669A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.343A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.397A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.819A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.514A pdb=" N GLY B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.775A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.689A pdb=" N THR C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.656A pdb=" N LEU C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.604A pdb=" N LYS C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.652A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.748A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 6.416A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323 removed outlier: 3.764A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.939A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580 Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 323 removed outlier: 7.457A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.804A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580 Processing sheet with id=AB3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.805A pdb=" N LEU C 152 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 153 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 39 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 161 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 37 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 46 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 53 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.805A pdb=" N LEU C 152 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 153 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 39 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 161 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 37 " --> pdb=" O VAL C 161 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3772 1.34 - 1.46: 2432 1.46 - 1.58: 5426 1.58 - 1.69: 8 1.69 - 1.81: 97 Bond restraints: 11735 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 11730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 15758 3.71 - 7.42: 36 7.42 - 11.13: 8 11.13 - 14.83: 0 14.83 - 18.54: 2 Bond angle restraints: 15804 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 108.41 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.11 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta sigma weight residual 110.92 105.37 5.55 1.59e+00 3.96e-01 1.22e+01 angle pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" C ASN B 46 " ideal model delta sigma weight residual 111.02 107.02 4.00 1.22e+00 6.72e-01 1.08e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 110.25 9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 15799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 7164 34.84 - 69.68: 74 69.68 - 104.52: 5 104.52 - 139.35: 0 139.35 - 174.19: 1 Dihedral angle restraints: 7244 sinusoidal: 3081 harmonic: 4163 Sorted by residual: dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -150.66 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C ASN B 46 " pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta harmonic sigma weight residual -122.60 -114.21 -8.39 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA ALA C 133 " pdb=" C ALA C 133 " pdb=" N TYR C 134 " pdb=" CA TYR C 134 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 7241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1520 0.056 - 0.112: 223 0.112 - 0.168: 13 0.168 - 0.224: 0 0.224 - 0.280: 3 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ASN B 46 " pdb=" N ASN B 46 " pdb=" C ASN B 46 " pdb=" CB ASN B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1756 not shown) Planarity restraints: 2011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 371 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 517 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE A 517 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 517 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 518 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 ... (remaining 2008 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 17 2.35 - 2.99: 6299 2.99 - 3.63: 16858 3.63 - 4.26: 25190 4.26 - 4.90: 42571 Nonbonded interactions: 90935 Sorted by model distance: nonbonded pdb=" O2A ANP A 801 " pdb="MG MG A 802 " model vdw 1.718 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 1.887 2.250 nonbonded pdb=" PG ANP A 801 " pdb="MG MG A 802 " model vdw 2.112 2.530 nonbonded pdb=" N3B ANP A 801 " pdb=" O2A ANP A 801 " model vdw 2.122 3.120 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.125 2.170 ... (remaining 90930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 220 or resid 275 through 691 or resid 801 throu \ gh 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.340 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.090 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.150 11735 Z= 0.261 Angle : 0.584 18.543 15804 Z= 0.287 Chirality : 0.040 0.280 1759 Planarity : 0.003 0.044 2011 Dihedral : 11.607 174.192 4548 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.64 % Allowed : 7.04 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1411 helix: 1.31 (0.23), residues: 568 sheet: 0.07 (0.33), residues: 258 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 312 HIS 0.004 0.001 HIS B 632 PHE 0.009 0.001 PHE A 668 TYR 0.016 0.001 TYR B 211 ARG 0.005 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 366 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8536 (tpp) cc_final: 0.7945 (tmm) REVERT: A 606 MET cc_start: 0.8543 (ttm) cc_final: 0.8244 (tpp) REVERT: A 611 LEU cc_start: 0.9302 (mm) cc_final: 0.8687 (tp) REVERT: A 621 MET cc_start: 0.8701 (mmm) cc_final: 0.8458 (mmt) REVERT: A 626 LEU cc_start: 0.9202 (tp) cc_final: 0.8961 (tp) REVERT: B 25 MET cc_start: 0.8724 (tpp) cc_final: 0.8415 (tpp) REVERT: B 49 ASP cc_start: 0.8465 (m-30) cc_final: 0.8134 (m-30) REVERT: B 114 MET cc_start: 0.8558 (tpp) cc_final: 0.7980 (tpt) REVERT: B 311 ASP cc_start: 0.8560 (t0) cc_final: 0.8198 (t0) REVERT: B 362 ILE cc_start: 0.9469 (mm) cc_final: 0.9219 (tp) REVERT: B 436 ASN cc_start: 0.9027 (m110) cc_final: 0.8595 (m-40) REVERT: B 564 CYS cc_start: 0.9126 (m) cc_final: 0.8449 (m) REVERT: B 606 MET cc_start: 0.8595 (mmt) cc_final: 0.8312 (mmt) REVERT: B 681 TYR cc_start: 0.8381 (m-10) cc_final: 0.8081 (m-80) REVERT: C 5 HIS cc_start: 0.6998 (m90) cc_final: 0.6354 (m170) REVERT: C 40 PHE cc_start: 0.8601 (p90) cc_final: 0.7880 (p90) REVERT: C 45 MET cc_start: 0.9074 (mpp) cc_final: 0.8498 (mpp) REVERT: C 95 ASP cc_start: 0.8931 (m-30) cc_final: 0.8669 (m-30) REVERT: C 139 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5880 (t80) REVERT: C 150 GLN cc_start: 0.7908 (mp10) cc_final: 0.7279 (mp-120) outliers start: 21 outliers final: 6 residues processed: 381 average time/residue: 0.2797 time to fit residues: 146.3286 Evaluate side-chains 222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 80 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 407 ASN B 609 GLN C 146 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11735 Z= 0.210 Angle : 0.627 11.608 15804 Z= 0.323 Chirality : 0.042 0.187 1759 Planarity : 0.004 0.052 2011 Dihedral : 7.985 173.152 1608 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.49 % Allowed : 16.03 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1411 helix: 1.56 (0.22), residues: 560 sheet: 0.44 (0.33), residues: 263 loop : -0.62 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 312 HIS 0.006 0.001 HIS A 676 PHE 0.017 0.001 PHE B 133 TYR 0.013 0.002 TYR A 457 ARG 0.003 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8396 (mm-40) REVERT: A 114 MET cc_start: 0.8901 (tpp) cc_final: 0.8561 (tmm) REVERT: A 602 MET cc_start: 0.9210 (tpp) cc_final: 0.8976 (tpp) REVERT: A 603 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9183 (tp30) REVERT: A 606 MET cc_start: 0.8737 (ttm) cc_final: 0.7971 (tpp) REVERT: A 621 MET cc_start: 0.8368 (mmm) cc_final: 0.7506 (mpp) REVERT: B 35 ASN cc_start: 0.8615 (m-40) cc_final: 0.8317 (m-40) REVERT: B 49 ASP cc_start: 0.7984 (m-30) cc_final: 0.7753 (m-30) REVERT: B 203 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8610 (tppt) REVERT: B 337 ARG cc_start: 0.8519 (mtp180) cc_final: 0.8303 (ttm110) REVERT: B 362 ILE cc_start: 0.9479 (mm) cc_final: 0.9216 (tp) REVERT: B 436 ASN cc_start: 0.9029 (m110) cc_final: 0.8527 (m-40) REVERT: B 553 MET cc_start: 0.9011 (tmm) cc_final: 0.8770 (ppp) REVERT: B 564 CYS cc_start: 0.9149 (m) cc_final: 0.8904 (m) REVERT: B 566 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 567 MET cc_start: 0.8923 (mtm) cc_final: 0.8668 (mtm) REVERT: B 681 TYR cc_start: 0.8524 (m-10) cc_final: 0.8228 (m-80) REVERT: C 45 MET cc_start: 0.9191 (mpp) cc_final: 0.8542 (mpp) REVERT: C 75 GLU cc_start: 0.9023 (pp20) cc_final: 0.8386 (mp0) REVERT: C 84 MET cc_start: 0.8779 (tpp) cc_final: 0.8424 (tpp) REVERT: C 95 ASP cc_start: 0.8997 (m-30) cc_final: 0.8672 (m-30) REVERT: C 102 TYR cc_start: 0.9059 (t80) cc_final: 0.8672 (t80) REVERT: C 143 ASP cc_start: 0.9676 (m-30) cc_final: 0.9456 (p0) outliers start: 19 outliers final: 11 residues processed: 235 average time/residue: 0.2479 time to fit residues: 84.8613 Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11735 Z= 0.438 Angle : 0.721 7.608 15804 Z= 0.381 Chirality : 0.043 0.149 1759 Planarity : 0.004 0.044 2011 Dihedral : 8.373 173.571 1607 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.97 % Allowed : 16.73 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1411 helix: 1.08 (0.22), residues: 572 sheet: 0.46 (0.33), residues: 252 loop : -0.86 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 312 HIS 0.012 0.001 HIS C 5 PHE 0.018 0.002 PHE B 429 TYR 0.019 0.002 TYR B 426 ARG 0.008 0.001 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.9032 (pp) cc_final: 0.8433 (pp) REVERT: A 42 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 394 MET cc_start: 0.8809 (ptp) cc_final: 0.8504 (ptm) REVERT: A 567 MET cc_start: 0.9067 (mmm) cc_final: 0.8771 (mmm) REVERT: A 602 MET cc_start: 0.9277 (tpp) cc_final: 0.9036 (tpp) REVERT: A 606 MET cc_start: 0.8911 (ttm) cc_final: 0.8660 (tpt) REVERT: B 49 ASP cc_start: 0.8038 (m-30) cc_final: 0.7835 (m-30) REVERT: B 200 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8553 (tm-30) REVERT: B 311 ASP cc_start: 0.8655 (t0) cc_final: 0.8423 (t0) REVERT: B 385 ASP cc_start: 0.8928 (t0) cc_final: 0.8513 (p0) REVERT: B 553 MET cc_start: 0.8952 (tmm) cc_final: 0.8417 (ppp) REVERT: B 564 CYS cc_start: 0.9193 (m) cc_final: 0.8944 (m) REVERT: B 567 MET cc_start: 0.8951 (mtm) cc_final: 0.8671 (mtm) REVERT: B 616 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7778 (p) REVERT: B 681 TYR cc_start: 0.8610 (m-10) cc_final: 0.8313 (m-80) REVERT: C 40 PHE cc_start: 0.9199 (p90) cc_final: 0.8872 (p90) REVERT: C 45 MET cc_start: 0.9190 (mpp) cc_final: 0.8636 (mpp) REVERT: C 62 GLN cc_start: 0.9478 (tp-100) cc_final: 0.9245 (tp-100) REVERT: C 102 TYR cc_start: 0.9092 (t80) cc_final: 0.8785 (t80) outliers start: 38 outliers final: 25 residues processed: 197 average time/residue: 0.2028 time to fit residues: 61.2367 Evaluate side-chains 175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 436 ASN C 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11735 Z= 0.167 Angle : 0.603 10.485 15804 Z= 0.306 Chirality : 0.041 0.163 1759 Planarity : 0.003 0.045 2011 Dihedral : 7.783 167.100 1607 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.50 % Allowed : 17.04 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1411 helix: 1.31 (0.22), residues: 571 sheet: 0.69 (0.33), residues: 265 loop : -0.76 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 157 HIS 0.005 0.001 HIS C 5 PHE 0.017 0.001 PHE C 42 TYR 0.011 0.001 TYR A 457 ARG 0.006 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8654 (mtmm) REVERT: A 513 MET cc_start: 0.8750 (mtt) cc_final: 0.8535 (mtt) REVERT: A 567 MET cc_start: 0.9234 (mmm) cc_final: 0.8849 (mmm) REVERT: A 602 MET cc_start: 0.9223 (tpp) cc_final: 0.8970 (tpp) REVERT: A 606 MET cc_start: 0.8770 (ttm) cc_final: 0.7755 (tpp) REVERT: A 617 MET cc_start: 0.7136 (mmm) cc_final: 0.6306 (mmm) REVERT: A 660 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8671 (mt-10) REVERT: B 200 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 311 ASP cc_start: 0.8608 (t0) cc_final: 0.8339 (t0) REVERT: B 362 ILE cc_start: 0.9430 (mm) cc_final: 0.8986 (tp) REVERT: B 365 SER cc_start: 0.8507 (t) cc_final: 0.8037 (p) REVERT: B 385 ASP cc_start: 0.8591 (t0) cc_final: 0.8143 (p0) REVERT: B 553 MET cc_start: 0.8989 (tmm) cc_final: 0.8489 (ppp) REVERT: B 564 CYS cc_start: 0.9177 (m) cc_final: 0.8796 (m) REVERT: B 567 MET cc_start: 0.8916 (mtm) cc_final: 0.8671 (mtm) REVERT: B 681 TYR cc_start: 0.8507 (m-10) cc_final: 0.8197 (m-80) REVERT: C 45 MET cc_start: 0.9149 (mpp) cc_final: 0.8616 (mpp) REVERT: C 72 PHE cc_start: 0.6984 (p90) cc_final: 0.6780 (p90) REVERT: C 75 GLU cc_start: 0.9010 (pp20) cc_final: 0.8340 (mp0) REVERT: C 95 ASP cc_start: 0.9073 (m-30) cc_final: 0.8575 (m-30) REVERT: C 102 TYR cc_start: 0.8990 (t80) cc_final: 0.8640 (t80) REVERT: C 143 ASP cc_start: 0.9673 (m-30) cc_final: 0.9445 (p0) outliers start: 32 outliers final: 14 residues processed: 211 average time/residue: 0.1993 time to fit residues: 63.8199 Evaluate side-chains 178 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11735 Z= 0.333 Angle : 0.672 12.249 15804 Z= 0.348 Chirality : 0.043 0.171 1759 Planarity : 0.004 0.040 2011 Dihedral : 7.950 173.051 1603 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.74 % Allowed : 17.67 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1411 helix: 1.10 (0.22), residues: 572 sheet: 0.61 (0.33), residues: 261 loop : -0.88 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.004 0.001 HIS B 458 PHE 0.027 0.002 PHE A 208 TYR 0.016 0.002 TYR A 457 ARG 0.005 0.001 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8638 (mtmm) REVERT: A 513 MET cc_start: 0.8689 (mtt) cc_final: 0.8457 (mtt) REVERT: A 567 MET cc_start: 0.9321 (mmm) cc_final: 0.8854 (mmm) REVERT: A 602 MET cc_start: 0.9262 (tpp) cc_final: 0.9040 (tpp) REVERT: A 606 MET cc_start: 0.8807 (ttm) cc_final: 0.8558 (tpt) REVERT: A 621 MET cc_start: 0.8267 (mmt) cc_final: 0.7889 (mmm) REVERT: B 114 MET cc_start: 0.8007 (tpt) cc_final: 0.7752 (tpt) REVERT: B 200 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 311 ASP cc_start: 0.8654 (t0) cc_final: 0.8347 (t0) REVERT: B 346 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8478 (p0) REVERT: B 365 SER cc_start: 0.8808 (t) cc_final: 0.8319 (p) REVERT: B 385 ASP cc_start: 0.8851 (t0) cc_final: 0.8309 (p0) REVERT: B 553 MET cc_start: 0.8972 (tmm) cc_final: 0.8508 (ppp) REVERT: B 564 CYS cc_start: 0.9250 (m) cc_final: 0.9009 (m) REVERT: B 567 MET cc_start: 0.8932 (mtm) cc_final: 0.8613 (ptp) REVERT: B 617 MET cc_start: 0.8942 (mtp) cc_final: 0.8572 (mmm) REVERT: B 681 TYR cc_start: 0.8541 (m-10) cc_final: 0.8199 (m-80) REVERT: C 40 PHE cc_start: 0.9080 (p90) cc_final: 0.8691 (p90) REVERT: C 45 MET cc_start: 0.9122 (mpp) cc_final: 0.8663 (mpp) REVERT: C 84 MET cc_start: 0.8559 (tpp) cc_final: 0.8327 (tpp) REVERT: C 102 TYR cc_start: 0.9062 (t80) cc_final: 0.8749 (t80) outliers start: 35 outliers final: 22 residues processed: 186 average time/residue: 0.1997 time to fit residues: 57.4852 Evaluate side-chains 175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 135 optimal weight: 0.0070 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11735 Z= 0.275 Angle : 0.652 14.698 15804 Z= 0.332 Chirality : 0.042 0.187 1759 Planarity : 0.003 0.040 2011 Dihedral : 7.905 172.897 1603 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.66 % Allowed : 18.92 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1411 helix: 1.07 (0.22), residues: 572 sheet: 0.64 (0.33), residues: 263 loop : -0.93 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.009 0.001 HIS C 5 PHE 0.018 0.002 PHE C 40 TYR 0.015 0.002 TYR A 457 ARG 0.003 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8605 (mtmm) REVERT: A 513 MET cc_start: 0.8641 (mtt) cc_final: 0.8424 (mtt) REVERT: A 567 MET cc_start: 0.9314 (mmm) cc_final: 0.8933 (mmm) REVERT: A 602 MET cc_start: 0.9286 (tpp) cc_final: 0.9023 (tpp) REVERT: A 606 MET cc_start: 0.8883 (ttm) cc_final: 0.8515 (tpt) REVERT: A 621 MET cc_start: 0.8227 (mmt) cc_final: 0.7962 (tpp) REVERT: B 200 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8473 (tm-30) REVERT: B 311 ASP cc_start: 0.8524 (t0) cc_final: 0.8195 (t0) REVERT: B 362 ILE cc_start: 0.9420 (mm) cc_final: 0.9137 (tp) REVERT: B 365 SER cc_start: 0.8777 (t) cc_final: 0.8189 (p) REVERT: B 385 ASP cc_start: 0.8809 (t0) cc_final: 0.8374 (p0) REVERT: B 553 MET cc_start: 0.8961 (tmm) cc_final: 0.8500 (ppp) REVERT: B 564 CYS cc_start: 0.9199 (m) cc_final: 0.8879 (m) REVERT: B 567 MET cc_start: 0.8949 (mtm) cc_final: 0.8653 (ptp) REVERT: B 602 MET cc_start: 0.8348 (tpp) cc_final: 0.8014 (tpp) REVERT: B 617 MET cc_start: 0.8904 (mtp) cc_final: 0.8441 (mmm) REVERT: B 681 TYR cc_start: 0.8550 (m-10) cc_final: 0.8254 (m-80) REVERT: C 40 PHE cc_start: 0.9107 (p90) cc_final: 0.8698 (p90) REVERT: C 45 MET cc_start: 0.9168 (mpp) cc_final: 0.8666 (mpp) REVERT: C 75 GLU cc_start: 0.9043 (pp20) cc_final: 0.8332 (mp0) REVERT: C 84 MET cc_start: 0.8505 (tpp) cc_final: 0.8259 (tpp) REVERT: C 95 ASP cc_start: 0.9123 (m-30) cc_final: 0.8665 (m-30) REVERT: C 102 TYR cc_start: 0.9052 (t80) cc_final: 0.8727 (t80) REVERT: C 139 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6216 (t80) REVERT: C 143 ASP cc_start: 0.9672 (m-30) cc_final: 0.9413 (p0) outliers start: 34 outliers final: 26 residues processed: 189 average time/residue: 0.2192 time to fit residues: 65.1550 Evaluate side-chains 174 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11735 Z= 0.274 Angle : 0.664 12.588 15804 Z= 0.337 Chirality : 0.043 0.249 1759 Planarity : 0.003 0.040 2011 Dihedral : 7.879 173.592 1603 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.81 % Allowed : 19.08 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1411 helix: 1.01 (0.22), residues: 572 sheet: 0.70 (0.33), residues: 263 loop : -1.00 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.007 0.001 HIS C 5 PHE 0.016 0.001 PHE B 429 TYR 0.018 0.002 TYR A 457 ARG 0.003 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8661 (mtmm) REVERT: A 513 MET cc_start: 0.8483 (mtt) cc_final: 0.8230 (mtt) REVERT: A 567 MET cc_start: 0.9345 (mmm) cc_final: 0.9010 (mmm) REVERT: A 602 MET cc_start: 0.9277 (tpp) cc_final: 0.8791 (tpp) REVERT: A 606 MET cc_start: 0.8776 (ttm) cc_final: 0.8516 (tpt) REVERT: A 621 MET cc_start: 0.8148 (mmt) cc_final: 0.7738 (tpp) REVERT: A 683 MET cc_start: 0.8957 (ppp) cc_final: 0.8740 (ppp) REVERT: B 311 ASP cc_start: 0.8520 (t0) cc_final: 0.8207 (t0) REVERT: B 385 ASP cc_start: 0.8845 (t0) cc_final: 0.8389 (p0) REVERT: B 513 MET cc_start: 0.8427 (mmm) cc_final: 0.7813 (mmt) REVERT: B 515 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8432 (mm-30) REVERT: B 553 MET cc_start: 0.8942 (tmm) cc_final: 0.8531 (ppp) REVERT: B 563 LEU cc_start: 0.9324 (tp) cc_final: 0.8939 (tp) REVERT: B 564 CYS cc_start: 0.9192 (m) cc_final: 0.8967 (m) REVERT: B 567 MET cc_start: 0.8950 (mtm) cc_final: 0.8681 (ptp) REVERT: B 584 LEU cc_start: 0.8392 (mp) cc_final: 0.7738 (mt) REVERT: B 590 CYS cc_start: 0.7792 (m) cc_final: 0.7245 (m) REVERT: B 602 MET cc_start: 0.8411 (tpp) cc_final: 0.8031 (tpp) REVERT: B 617 MET cc_start: 0.8969 (mtp) cc_final: 0.8549 (mmm) REVERT: B 681 TYR cc_start: 0.8564 (m-10) cc_final: 0.8275 (m-80) REVERT: C 40 PHE cc_start: 0.9116 (p90) cc_final: 0.8797 (p90) REVERT: C 45 MET cc_start: 0.9173 (mpp) cc_final: 0.8700 (mpp) REVERT: C 84 MET cc_start: 0.8440 (tpp) cc_final: 0.8209 (tpp) REVERT: C 95 ASP cc_start: 0.9096 (m-30) cc_final: 0.8605 (m-30) REVERT: C 102 TYR cc_start: 0.9079 (t80) cc_final: 0.8763 (t80) REVERT: C 139 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6108 (t80) outliers start: 36 outliers final: 29 residues processed: 185 average time/residue: 0.2097 time to fit residues: 60.8485 Evaluate side-chains 177 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN B 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11735 Z= 0.218 Angle : 0.657 12.549 15804 Z= 0.328 Chirality : 0.043 0.246 1759 Planarity : 0.003 0.039 2011 Dihedral : 7.782 172.607 1603 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 20.17 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1411 helix: 1.05 (0.22), residues: 570 sheet: 0.65 (0.33), residues: 268 loop : -0.98 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 598 HIS 0.004 0.001 HIS C 98 PHE 0.015 0.001 PHE B 429 TYR 0.018 0.001 TYR A 457 ARG 0.002 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (mtmm) REVERT: A 513 MET cc_start: 0.8408 (mtt) cc_final: 0.8187 (mtt) REVERT: A 567 MET cc_start: 0.9376 (mmm) cc_final: 0.8975 (mmm) REVERT: A 602 MET cc_start: 0.9389 (tpp) cc_final: 0.9107 (tpp) REVERT: A 606 MET cc_start: 0.8887 (ttm) cc_final: 0.8499 (tpt) REVERT: A 621 MET cc_start: 0.7994 (mmt) cc_final: 0.7683 (mmm) REVERT: B 114 MET cc_start: 0.8124 (tpt) cc_final: 0.7859 (tpt) REVERT: B 311 ASP cc_start: 0.8584 (t0) cc_final: 0.8210 (t0) REVERT: B 385 ASP cc_start: 0.8775 (t0) cc_final: 0.8324 (p0) REVERT: B 513 MET cc_start: 0.8505 (mmm) cc_final: 0.7923 (mmm) REVERT: B 553 MET cc_start: 0.8956 (tmm) cc_final: 0.8493 (ppp) REVERT: B 564 CYS cc_start: 0.9223 (m) cc_final: 0.8094 (m) REVERT: B 567 MET cc_start: 0.8853 (mtm) cc_final: 0.8512 (mtm) REVERT: B 584 LEU cc_start: 0.8358 (mp) cc_final: 0.7769 (mt) REVERT: B 590 CYS cc_start: 0.7773 (m) cc_final: 0.7313 (m) REVERT: B 617 MET cc_start: 0.8912 (mtp) cc_final: 0.8500 (mmm) REVERT: B 681 TYR cc_start: 0.8535 (m-10) cc_final: 0.8228 (m-80) REVERT: C 21 ILE cc_start: 0.9183 (mm) cc_final: 0.8951 (mm) REVERT: C 45 MET cc_start: 0.9191 (mpp) cc_final: 0.8682 (mpp) REVERT: C 58 LYS cc_start: 0.9447 (tttt) cc_final: 0.9159 (ttpt) REVERT: C 75 GLU cc_start: 0.9025 (pp20) cc_final: 0.8314 (mp0) REVERT: C 84 MET cc_start: 0.8402 (tpp) cc_final: 0.8101 (tpp) REVERT: C 95 ASP cc_start: 0.9103 (m-30) cc_final: 0.8635 (m-30) REVERT: C 102 TYR cc_start: 0.9076 (t80) cc_final: 0.8773 (t80) REVERT: C 143 ASP cc_start: 0.9656 (m-30) cc_final: 0.9391 (p0) outliers start: 34 outliers final: 26 residues processed: 185 average time/residue: 0.1774 time to fit residues: 51.4984 Evaluate side-chains 174 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11735 Z= 0.208 Angle : 0.671 14.046 15804 Z= 0.332 Chirality : 0.044 0.330 1759 Planarity : 0.003 0.037 2011 Dihedral : 7.791 172.984 1603 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.27 % Allowed : 20.72 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1411 helix: 1.11 (0.22), residues: 570 sheet: 0.71 (0.33), residues: 271 loop : -1.05 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 598 HIS 0.004 0.001 HIS C 98 PHE 0.022 0.001 PHE C 154 TYR 0.018 0.001 TYR A 373 ARG 0.002 0.000 ARG B 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.9410 (mmm) cc_final: 0.9082 (mmm) REVERT: A 602 MET cc_start: 0.9387 (tpp) cc_final: 0.9096 (tpp) REVERT: A 606 MET cc_start: 0.8861 (ttm) cc_final: 0.8504 (tpt) REVERT: A 619 TYR cc_start: 0.6937 (m-10) cc_final: 0.6619 (m-80) REVERT: A 621 MET cc_start: 0.7985 (mmt) cc_final: 0.7630 (mmm) REVERT: B 311 ASP cc_start: 0.8539 (t0) cc_final: 0.8151 (t0) REVERT: B 385 ASP cc_start: 0.8726 (t0) cc_final: 0.8329 (p0) REVERT: B 513 MET cc_start: 0.8479 (mmm) cc_final: 0.7886 (mmm) REVERT: B 553 MET cc_start: 0.8962 (tmm) cc_final: 0.8505 (ppp) REVERT: B 567 MET cc_start: 0.8861 (mtm) cc_final: 0.8537 (mtm) REVERT: B 584 LEU cc_start: 0.8329 (mp) cc_final: 0.7820 (mp) REVERT: B 590 CYS cc_start: 0.7888 (m) cc_final: 0.7660 (m) REVERT: B 617 MET cc_start: 0.8854 (mtp) cc_final: 0.8464 (mmm) REVERT: C 45 MET cc_start: 0.9189 (mpp) cc_final: 0.8674 (mpp) REVERT: C 58 LYS cc_start: 0.9443 (tttt) cc_final: 0.9148 (ttpt) REVERT: C 75 GLU cc_start: 0.9004 (pp20) cc_final: 0.8303 (mp0) REVERT: C 95 ASP cc_start: 0.9134 (m-30) cc_final: 0.8690 (m-30) REVERT: C 102 TYR cc_start: 0.9078 (t80) cc_final: 0.8775 (t80) REVERT: C 139 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6232 (t80) REVERT: C 143 ASP cc_start: 0.9653 (m-30) cc_final: 0.9383 (p0) outliers start: 29 outliers final: 24 residues processed: 176 average time/residue: 0.1973 time to fit residues: 54.0641 Evaluate side-chains 167 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11735 Z= 0.247 Angle : 0.712 13.257 15804 Z= 0.354 Chirality : 0.045 0.338 1759 Planarity : 0.003 0.038 2011 Dihedral : 7.798 173.732 1601 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 21.27 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1411 helix: 0.98 (0.22), residues: 573 sheet: 0.68 (0.33), residues: 271 loop : -1.08 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 598 HIS 0.004 0.001 HIS C 5 PHE 0.024 0.001 PHE C 154 TYR 0.044 0.002 TYR B 681 ARG 0.003 0.000 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 MET cc_start: 0.9411 (mmm) cc_final: 0.9090 (mmm) REVERT: A 602 MET cc_start: 0.9400 (tpp) cc_final: 0.9166 (tpp) REVERT: A 619 TYR cc_start: 0.6827 (m-10) cc_final: 0.6569 (m-80) REVERT: B 49 ASP cc_start: 0.7362 (t0) cc_final: 0.6981 (t70) REVERT: B 311 ASP cc_start: 0.8568 (t0) cc_final: 0.8173 (t0) REVERT: B 385 ASP cc_start: 0.8770 (t0) cc_final: 0.8365 (p0) REVERT: B 513 MET cc_start: 0.8502 (mmm) cc_final: 0.7887 (mmm) REVERT: B 515 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 553 MET cc_start: 0.8961 (tmm) cc_final: 0.8514 (ppp) REVERT: B 567 MET cc_start: 0.8873 (mtm) cc_final: 0.8596 (mtm) REVERT: B 584 LEU cc_start: 0.8351 (mp) cc_final: 0.7879 (mp) REVERT: B 590 CYS cc_start: 0.8238 (m) cc_final: 0.7983 (m) REVERT: B 617 MET cc_start: 0.8875 (mtp) cc_final: 0.8479 (mmm) REVERT: B 681 TYR cc_start: 0.8536 (m-80) cc_final: 0.8180 (m-80) REVERT: C 45 MET cc_start: 0.9175 (mpp) cc_final: 0.8709 (mpp) REVERT: C 75 GLU cc_start: 0.9003 (pp20) cc_final: 0.8295 (mp0) REVERT: C 95 ASP cc_start: 0.9142 (m-30) cc_final: 0.8689 (m-30) REVERT: C 102 TYR cc_start: 0.9075 (t80) cc_final: 0.8804 (t80) REVERT: C 139 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6200 (t80) REVERT: C 143 ASP cc_start: 0.9654 (m-30) cc_final: 0.9375 (p0) outliers start: 26 outliers final: 24 residues processed: 163 average time/residue: 0.1961 time to fit residues: 50.3313 Evaluate side-chains 167 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 0.0970 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** 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 = 0.3274 r_free = 0.3274 target = 0.064296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049758 restraints weight = 50242.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051736 restraints weight = 28228.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053101 restraints weight = 18954.747| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11735 Z= 0.227 Angle : 0.729 14.177 15804 Z= 0.357 Chirality : 0.045 0.351 1759 Planarity : 0.003 0.050 2011 Dihedral : 7.757 172.479 1601 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.35 % Allowed : 21.19 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1411 helix: 0.90 (0.22), residues: 574 sheet: 0.78 (0.34), residues: 266 loop : -1.11 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 312 HIS 0.003 0.001 HIS A 315 PHE 0.026 0.001 PHE C 154 TYR 0.039 0.002 TYR B 681 ARG 0.003 0.000 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.77 seconds wall clock time: 42 minutes 31.60 seconds (2551.60 seconds total)