Starting phenix.real_space_refine on Sun Jan 19 13:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129.map" model { file = "/net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vc1_43129/01_2025/8vc1_43129_neut.cif" } resolution = 2.85 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= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 132 5.16 5 C 8660 2.51 5 N 2032 2.21 5 O 2280 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-5571/modules/chem_data/mon_lib" Total number of atoms: 13128 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3043 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3043 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 239 Unusual residues: {'9Z9': 1, 'PC7': 5, 'PSC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PSC:plan-4': 2, 'PC7:plan-2': 1, 'PSC:plan-1': 1, 'PSC:plan-3': 2} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 239 Unusual residues: {'9Z9': 1, 'PC7': 5, 'PSC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PSC:plan-4': 2, 'PC7:plan-2': 1, 'PSC:plan-1': 1, 'PSC:plan-3': 2} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: B, D Time building chain proxies: 8.70, per 1000 atoms: 0.66 Number of scatterers: 13128 At special positions: 0 Unit cell: (105.41, 105.41, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 24 15.00 O 2280 8.00 N 2032 7.00 C 8660 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: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 83.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.791A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 113 through 136 removed outlier: 4.009A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 Processing helix chain 'A' and resid 178 through 230 removed outlier: 5.422A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 312 removed outlier: 3.626A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 340 Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 344 through 390 removed outlier: 3.514A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 444 removed outlier: 3.970A pdb=" N ILE A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.791A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 113 through 136 removed outlier: 4.009A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 Processing helix chain 'B' and resid 178 through 230 removed outlier: 5.421A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 213 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 312 removed outlier: 3.627A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 340 Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 344 through 390 removed outlier: 3.513A pdb=" N MET B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 365 " --> pdb=" O ARG B 361 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 444 removed outlier: 3.971A pdb=" N ILE B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 removed outlier: 3.791A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 113 Processing helix chain 'C' and resid 113 through 136 removed outlier: 4.009A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 Processing helix chain 'C' and resid 178 through 230 removed outlier: 5.422A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 312 removed outlier: 3.626A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 340 Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 344 through 390 removed outlier: 3.514A pdb=" N MET C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 444 removed outlier: 3.970A pdb=" N ILE C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 32 removed outlier: 3.790A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'D' and resid 113 through 136 removed outlier: 4.008A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 Processing helix chain 'D' and resid 178 through 230 removed outlier: 5.421A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D 213 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 312 removed outlier: 3.626A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 340 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 344 through 390 removed outlier: 3.514A pdb=" N MET D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 365 " --> pdb=" O ARG D 361 " (cutoff:3.500A) Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 444 removed outlier: 3.971A pdb=" N ILE D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.605A pdb=" N THR A 49 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.604A pdb=" N THR B 49 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.604A pdb=" N THR C 49 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.604A pdb=" N THR D 49 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 275 1072 hydrogen bonds defined for protein. 3180 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: 4.18 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1864 1.30 - 1.43: 3305 1.43 - 1.56: 7891 1.56 - 1.68: 100 1.68 - 1.81: 200 Bond restraints: 13360 Sorted by residual: bond pdb=" C1 PSC D 501 " pdb=" O01 PSC D 501 " ideal model delta sigma weight residual 1.331 1.431 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 PSC B 501 " pdb=" O01 PSC B 501 " ideal model delta sigma weight residual 1.331 1.431 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 PSC A 501 " pdb=" O01 PSC A 501 " ideal model delta sigma weight residual 1.331 1.431 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C1 PSC C 501 " pdb=" O01 PSC C 501 " ideal model delta sigma weight residual 1.331 1.430 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C19 PSC D 501 " pdb=" O03 PSC D 501 " ideal model delta sigma weight residual 1.326 1.424 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 13355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 17329 3.32 - 6.65: 555 6.65 - 9.97: 78 9.97 - 13.30: 18 13.30 - 16.62: 24 Bond angle restraints: 18004 Sorted by residual: angle pdb=" O3P PC7 D 506 " pdb=" P PC7 D 506 " pdb=" O4P PC7 D 506 " ideal model delta sigma weight residual 93.18 109.80 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 C 506 " pdb=" P PC7 C 506 " pdb=" O4P PC7 C 506 " ideal model delta sigma weight residual 93.18 109.80 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 B 506 " pdb=" P PC7 B 506 " pdb=" O4P PC7 B 506 " ideal model delta sigma weight residual 93.18 109.79 -16.61 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 A 506 " pdb=" P PC7 A 506 " pdb=" O4P PC7 A 506 " ideal model delta sigma weight residual 93.18 109.78 -16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O11 PSC C 502 " pdb=" P PSC C 502 " pdb=" O12 PSC C 502 " ideal model delta sigma weight residual 93.08 109.47 -16.39 3.00e+00 1.11e-01 2.98e+01 ... (remaining 17999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 8000 30.12 - 60.24: 390 60.24 - 90.36: 30 90.36 - 120.48: 12 120.48 - 150.60: 4 Dihedral angle restraints: 8436 sinusoidal: 3876 harmonic: 4560 Sorted by residual: dihedral pdb=" CA LEU A 37 " pdb=" C LEU A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU C 37 " pdb=" C LEU C 37 " pdb=" N ARG C 38 " pdb=" CA ARG C 38 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU B 37 " pdb=" C LEU B 37 " pdb=" N ARG B 38 " pdb=" CA ARG B 38 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1354 0.050 - 0.100: 608 0.100 - 0.150: 142 0.150 - 0.200: 32 0.200 - 0.250: 4 Chirality restraints: 2140 Sorted by residual: chirality pdb=" C02 PSC A 501 " pdb=" C01 PSC A 501 " pdb=" C03 PSC A 501 " pdb=" O01 PSC A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C02 PSC B 501 " pdb=" C01 PSC B 501 " pdb=" C03 PSC B 501 " pdb=" O01 PSC B 501 " both_signs ideal model delta sigma weight residual False 2.37 2.61 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C02 PSC D 501 " pdb=" C01 PSC D 501 " pdb=" C03 PSC D 501 " pdb=" O01 PSC D 501 " both_signs ideal model delta sigma weight residual False 2.37 2.61 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2137 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 124 " -0.016 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR A 124 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 124 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 124 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 124 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 124 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 124 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 124 " 0.017 2.00e-02 2.50e+03 1.68e-02 5.61e+00 pdb=" CG TYR C 124 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 124 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 124 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 124 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 124 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 124 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 124 " 0.016 2.00e-02 2.50e+03 1.67e-02 5.56e+00 pdb=" CG TYR B 124 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 124 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 124 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 124 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 124 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 124 " -0.009 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 919 2.74 - 3.28: 13555 3.28 - 3.82: 21479 3.82 - 4.36: 26609 4.36 - 4.90: 47138 Nonbonded interactions: 109700 Sorted by model distance: nonbonded pdb=" OE2 GLU B 375 " pdb=" NH1 ARG B 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU C 375 " pdb=" NH1 ARG C 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU A 375 " pdb=" NH1 ARG A 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU D 375 " pdb=" NH1 ARG D 378 " model vdw 2.197 3.120 nonbonded pdb=" NZ LYS A 146 " pdb=" O4P PC7 A 506 " model vdw 2.341 3.120 ... (remaining 109695 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' and (resid 16 through 444 or (resid 505 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name O11 or name O1P or nam \ e O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or \ (resid 506 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C2 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or (resid 507 and (name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ )))) selection = (chain 'B' and (resid 16 through 444 or (resid 505 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name O11 or name O1P or nam \ e O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or \ (resid 506 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C2 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or (resid 507 and (name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ )))) selection = (chain 'C' and (resid 16 through 444 or (resid 503 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name O11 or name O1P or nam \ e O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or \ resid 504 or (resid 505 and (name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)))) selection = (chain 'D' and (resid 16 through 444 or (resid 505 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C40 or name C41 or name O11 or name O1P or nam \ e O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or \ (resid 506 and (name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C2 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or (resid 507 and (name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.450 Find NCS groups from input model: 0.690 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.012 0.100 13360 Z= 0.784 Angle : 1.459 16.620 18004 Z= 0.644 Chirality : 0.059 0.250 2140 Planarity : 0.010 0.092 2088 Dihedral : 17.034 150.597 5492 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % 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: -1.02 (0.18), residues: 1548 helix: -0.46 (0.12), residues: 1244 sheet: -1.27 (0.54), residues: 88 loop : -0.57 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP D 354 HIS 0.009 0.004 HIS D 307 PHE 0.031 0.003 PHE A 271 TYR 0.036 0.005 TYR A 124 ARG 0.013 0.003 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 SER cc_start: 0.7735 (t) cc_final: 0.7434 (p) REVERT: A 193 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7814 (m100) REVERT: A 296 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7762 (mtt-85) REVERT: B 123 SER cc_start: 0.7708 (t) cc_final: 0.7372 (p) REVERT: B 193 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.7729 (m100) REVERT: C 123 SER cc_start: 0.7701 (t) cc_final: 0.7379 (p) REVERT: C 193 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.7812 (m100) REVERT: D 123 SER cc_start: 0.7688 (t) cc_final: 0.7369 (p) REVERT: D 193 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.7804 (m100) outliers start: 4 outliers final: 0 residues processed: 141 average time/residue: 1.6515 time to fit residues: 250.2066 Evaluate side-chains 129 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain D residue 193 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153464 restraints weight = 11511.464| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.84 r_work: 0.3690 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13360 Z= 0.226 Angle : 0.631 7.086 18004 Z= 0.320 Chirality : 0.039 0.154 2140 Planarity : 0.005 0.038 2088 Dihedral : 16.753 139.354 2736 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.26 % Allowed : 3.49 % Favored : 95.25 % 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: 2.40 (0.21), residues: 1548 helix: 2.00 (0.14), residues: 1264 sheet: -0.76 (0.59), residues: 88 loop : 0.26 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 354 HIS 0.004 0.001 HIS D 307 PHE 0.021 0.002 PHE C 56 TYR 0.019 0.002 TYR B 124 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.5885 (ttp) cc_final: 0.5612 (ttt) REVERT: A 310 ASP cc_start: 0.7982 (m-30) cc_final: 0.7776 (m-30) REVERT: A 373 MET cc_start: 0.7464 (mmt) cc_final: 0.7122 (mtt) REVERT: B 133 ARG cc_start: 0.6869 (mtm-85) cc_final: 0.6639 (mtm-85) REVERT: B 373 MET cc_start: 0.7551 (mmt) cc_final: 0.7162 (mtt) REVERT: B 419 MET cc_start: 0.8705 (mmt) cc_final: 0.8408 (mmm) REVERT: C 273 MET cc_start: 0.5743 (ttp) cc_final: 0.5468 (ttt) REVERT: C 306 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7515 (mtt90) REVERT: C 373 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7213 (mtt) REVERT: C 378 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6857 (ttt180) REVERT: C 419 MET cc_start: 0.8710 (mmt) cc_final: 0.8411 (mmm) REVERT: D 373 MET cc_start: 0.7538 (mmt) cc_final: 0.7167 (mtt) REVERT: D 378 ARG cc_start: 0.7691 (mtt180) cc_final: 0.6856 (ttt180) REVERT: D 419 MET cc_start: 0.8706 (mmt) cc_final: 0.8411 (mmm) outliers start: 17 outliers final: 4 residues processed: 142 average time/residue: 1.6885 time to fit residues: 256.8981 Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153739 restraints weight = 11719.417| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.96 r_work: 0.3649 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13360 Z= 0.198 Angle : 0.534 5.141 18004 Z= 0.272 Chirality : 0.037 0.145 2140 Planarity : 0.004 0.038 2088 Dihedral : 14.961 131.951 2728 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.26 % Allowed : 6.90 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.19 (0.21), residues: 1548 helix: 2.64 (0.14), residues: 1264 sheet: -0.77 (0.59), residues: 88 loop : -0.09 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS A 370 PHE 0.017 0.002 PHE D 205 TYR 0.019 0.002 TYR D 124 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.5906 (ttp) cc_final: 0.5677 (ttt) REVERT: A 303 GLU cc_start: 0.7311 (tt0) cc_final: 0.6983 (pt0) REVERT: A 310 ASP cc_start: 0.7776 (m-30) cc_final: 0.7518 (m-30) REVERT: A 378 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6602 (ttt180) REVERT: A 419 MET cc_start: 0.8524 (mmt) cc_final: 0.8294 (mmm) REVERT: B 200 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 273 MET cc_start: 0.5878 (ttp) cc_final: 0.5608 (ttt) REVERT: B 378 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6614 (ttt180) REVERT: B 419 MET cc_start: 0.8571 (mmt) cc_final: 0.8265 (mmm) REVERT: C 200 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 273 MET cc_start: 0.5835 (ttp) cc_final: 0.5634 (ttt) REVERT: C 378 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6596 (ttt180) REVERT: C 419 MET cc_start: 0.8575 (mmt) cc_final: 0.8275 (mmm) REVERT: D 200 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7489 (mt-10) REVERT: D 273 MET cc_start: 0.5774 (ttp) cc_final: 0.5534 (ttt) REVERT: D 378 ARG cc_start: 0.7343 (mtt180) cc_final: 0.6589 (ttt180) REVERT: D 419 MET cc_start: 0.8571 (mmt) cc_final: 0.8270 (mmm) outliers start: 17 outliers final: 4 residues processed: 152 average time/residue: 1.7970 time to fit residues: 291.7840 Evaluate side-chains 140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.204440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152296 restraints weight = 11630.255| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.14 r_work: 0.3562 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.199 Angle : 0.508 6.675 18004 Z= 0.261 Chirality : 0.036 0.139 2140 Planarity : 0.004 0.039 2088 Dihedral : 14.074 118.409 2728 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.56 % Allowed : 9.05 % Favored : 89.39 % 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: 3.51 (0.21), residues: 1548 helix: 2.88 (0.14), residues: 1264 sheet: -0.41 (0.61), residues: 88 loop : -0.33 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.003 0.001 HIS C 307 PHE 0.017 0.002 PHE B 205 TYR 0.020 0.001 TYR B 124 ARG 0.002 0.000 ARG D 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6714 (mt-10) REVERT: A 273 MET cc_start: 0.6161 (ttp) cc_final: 0.5940 (ttt) REVERT: A 303 GLU cc_start: 0.7475 (tt0) cc_final: 0.7207 (pt0) REVERT: A 310 ASP cc_start: 0.7849 (m-30) cc_final: 0.7606 (m-30) REVERT: A 378 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6958 (ttt180) REVERT: A 419 MET cc_start: 0.8619 (mmt) cc_final: 0.8356 (mmm) REVERT: B 38 ARG cc_start: 0.6683 (ptm-80) cc_final: 0.6468 (ptm-80) REVERT: B 378 ARG cc_start: 0.7515 (mtt180) cc_final: 0.6935 (ttt180) REVERT: B 419 MET cc_start: 0.8667 (mmt) cc_final: 0.8363 (mmm) REVERT: C 91 MET cc_start: 0.6082 (tpt) cc_final: 0.5821 (tpt) REVERT: C 273 MET cc_start: 0.6077 (ttp) cc_final: 0.5844 (ttt) REVERT: C 378 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6946 (ttt180) REVERT: C 419 MET cc_start: 0.8682 (mmt) cc_final: 0.8380 (mmm) REVERT: D 273 MET cc_start: 0.5967 (ttp) cc_final: 0.5695 (ttt) REVERT: D 378 ARG cc_start: 0.7513 (mtt180) cc_final: 0.6935 (ttt180) REVERT: D 419 MET cc_start: 0.8677 (mmt) cc_final: 0.8367 (mmm) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 1.7064 time to fit residues: 273.9009 Evaluate side-chains 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 119 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.205997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151880 restraints weight = 11722.600| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.90 r_work: 0.3587 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13360 Z= 0.174 Angle : 0.478 4.872 18004 Z= 0.247 Chirality : 0.035 0.134 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.728 91.101 2728 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.48 % Allowed : 9.42 % Favored : 89.09 % 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: 3.83 (0.21), residues: 1548 helix: 3.15 (0.14), residues: 1264 sheet: -0.44 (0.61), residues: 88 loop : -0.52 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS C 307 PHE 0.016 0.002 PHE D 205 TYR 0.018 0.001 TYR C 124 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6862 (mt-10) REVERT: A 273 MET cc_start: 0.6130 (ttp) cc_final: 0.5860 (ttt) REVERT: A 303 GLU cc_start: 0.7705 (tt0) cc_final: 0.7325 (pt0) REVERT: A 310 ASP cc_start: 0.7934 (m-30) cc_final: 0.7654 (m-30) REVERT: A 378 ARG cc_start: 0.7728 (mtt180) cc_final: 0.6976 (ttt180) REVERT: A 419 MET cc_start: 0.8658 (mmt) cc_final: 0.8396 (mmm) REVERT: B 219 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6859 (mt-10) REVERT: B 273 MET cc_start: 0.5976 (ttp) cc_final: 0.5701 (ttt) REVERT: B 303 GLU cc_start: 0.7672 (tt0) cc_final: 0.7309 (pt0) REVERT: B 378 ARG cc_start: 0.7710 (mtt180) cc_final: 0.6950 (ttt180) REVERT: B 419 MET cc_start: 0.8663 (mmt) cc_final: 0.8419 (mmm) REVERT: C 273 MET cc_start: 0.6080 (ttp) cc_final: 0.5805 (ttt) REVERT: C 378 ARG cc_start: 0.7737 (mtt180) cc_final: 0.6991 (ttt180) REVERT: C 419 MET cc_start: 0.8685 (mmt) cc_final: 0.8446 (mmm) REVERT: D 219 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6831 (mt-10) REVERT: D 273 MET cc_start: 0.5950 (ttp) cc_final: 0.5625 (ttt) REVERT: D 303 GLU cc_start: 0.7681 (tt0) cc_final: 0.7303 (pt0) REVERT: D 378 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6973 (ttt180) REVERT: D 419 MET cc_start: 0.8697 (mmt) cc_final: 0.8455 (mmm) outliers start: 20 outliers final: 11 residues processed: 156 average time/residue: 1.7944 time to fit residues: 298.3902 Evaluate side-chains 152 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 111 optimal weight: 0.0070 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.208247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153227 restraints weight = 12069.331| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.15 r_work: 0.3531 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13360 Z= 0.252 Angle : 0.539 8.164 18004 Z= 0.270 Chirality : 0.037 0.163 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.373 78.510 2728 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.52 % Allowed : 8.98 % Favored : 88.50 % 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: 3.63 (0.21), residues: 1548 helix: 3.01 (0.14), residues: 1264 sheet: -0.39 (0.63), residues: 88 loop : -0.65 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 193 HIS 0.003 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.021 0.001 TYR D 124 ARG 0.003 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6714 (mt-10) REVERT: A 273 MET cc_start: 0.6216 (ttp) cc_final: 0.5977 (ttt) REVERT: A 303 GLU cc_start: 0.7538 (tt0) cc_final: 0.7178 (pt0) REVERT: A 310 ASP cc_start: 0.7773 (m-30) cc_final: 0.7558 (m-30) REVERT: A 378 ARG cc_start: 0.7545 (mtt180) cc_final: 0.6957 (ttt180) REVERT: A 419 MET cc_start: 0.8627 (mmt) cc_final: 0.8330 (mmm) REVERT: B 219 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6719 (mt-10) REVERT: B 273 MET cc_start: 0.6074 (ttp) cc_final: 0.5814 (ttt) REVERT: B 303 GLU cc_start: 0.7529 (tt0) cc_final: 0.7159 (pt0) REVERT: B 378 ARG cc_start: 0.7573 (mtt180) cc_final: 0.6954 (ttt180) REVERT: B 419 MET cc_start: 0.8696 (mmt) cc_final: 0.8365 (mmm) REVERT: C 87 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.3747 (mmm) REVERT: C 219 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6701 (mt-10) REVERT: C 273 MET cc_start: 0.6163 (ttp) cc_final: 0.5912 (ttt) REVERT: C 303 GLU cc_start: 0.7525 (tt0) cc_final: 0.7161 (pt0) REVERT: C 378 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6956 (ttt180) REVERT: C 419 MET cc_start: 0.8695 (mmt) cc_final: 0.8362 (mmm) REVERT: D 219 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6718 (mt-10) REVERT: D 273 MET cc_start: 0.6129 (ttp) cc_final: 0.5827 (ttt) REVERT: D 303 GLU cc_start: 0.7531 (tt0) cc_final: 0.7160 (pt0) REVERT: D 378 ARG cc_start: 0.7570 (mtt180) cc_final: 0.6963 (ttt180) REVERT: D 419 MET cc_start: 0.8700 (mmt) cc_final: 0.8425 (mmm) outliers start: 34 outliers final: 13 residues processed: 157 average time/residue: 1.7915 time to fit residues: 300.6790 Evaluate side-chains 153 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.203857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149250 restraints weight = 11840.359| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.13 r_work: 0.3550 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13360 Z= 0.213 Angle : 0.506 7.345 18004 Z= 0.255 Chirality : 0.036 0.142 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.056 66.910 2728 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.67 % Allowed : 9.05 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.79 (0.21), residues: 1548 helix: 3.11 (0.14), residues: 1264 sheet: 0.28 (0.64), residues: 80 loop : -0.88 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 193 HIS 0.002 0.001 HIS C 392 PHE 0.019 0.002 PHE D 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.3871 (mmm) REVERT: A 219 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6641 (mt-10) REVERT: A 273 MET cc_start: 0.6167 (ttp) cc_final: 0.5914 (ttt) REVERT: A 303 GLU cc_start: 0.7479 (tt0) cc_final: 0.7111 (pt0) REVERT: A 310 ASP cc_start: 0.7720 (m-30) cc_final: 0.7480 (m-30) REVERT: A 378 ARG cc_start: 0.7526 (mtt180) cc_final: 0.6889 (ttt180) REVERT: A 419 MET cc_start: 0.8610 (mmt) cc_final: 0.8348 (mmm) REVERT: B 219 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6645 (mt-10) REVERT: B 273 MET cc_start: 0.6109 (ttp) cc_final: 0.5854 (ttt) REVERT: B 303 GLU cc_start: 0.7482 (tt0) cc_final: 0.7114 (pt0) REVERT: B 378 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6869 (ttt180) REVERT: B 419 MET cc_start: 0.8633 (mmt) cc_final: 0.8334 (mmm) REVERT: C 219 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6623 (mt-10) REVERT: C 273 MET cc_start: 0.6136 (ttp) cc_final: 0.5894 (ttt) REVERT: C 303 GLU cc_start: 0.7496 (tt0) cc_final: 0.7120 (pt0) REVERT: C 378 ARG cc_start: 0.7534 (mtt180) cc_final: 0.6895 (ttt180) REVERT: C 419 MET cc_start: 0.8635 (mmt) cc_final: 0.8338 (mmm) REVERT: D 219 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6633 (mt-10) REVERT: D 273 MET cc_start: 0.6084 (ttp) cc_final: 0.5791 (ttt) REVERT: D 303 GLU cc_start: 0.7498 (tt0) cc_final: 0.7128 (pt0) REVERT: D 378 ARG cc_start: 0.7511 (mtt180) cc_final: 0.6887 (ttt180) REVERT: D 419 MET cc_start: 0.8641 (mmt) cc_final: 0.8340 (mmm) outliers start: 36 outliers final: 12 residues processed: 154 average time/residue: 1.7685 time to fit residues: 290.8918 Evaluate side-chains 156 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149759 restraints weight = 11803.344| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.90 r_work: 0.3562 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.201 Angle : 0.509 11.427 18004 Z= 0.255 Chirality : 0.036 0.169 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.926 61.451 2728 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 10.16 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.84 (0.21), residues: 1548 helix: 3.16 (0.14), residues: 1264 sheet: 0.26 (0.64), residues: 80 loop : -0.86 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 193 HIS 0.002 0.001 HIS A 392 PHE 0.019 0.002 PHE B 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6814 (mt-10) REVERT: A 273 MET cc_start: 0.6073 (ttp) cc_final: 0.5780 (ttt) REVERT: A 303 GLU cc_start: 0.7722 (tt0) cc_final: 0.7311 (pt0) REVERT: A 310 ASP cc_start: 0.7889 (m-30) cc_final: 0.7676 (m-30) REVERT: A 378 ARG cc_start: 0.7735 (mtt180) cc_final: 0.6974 (ttt180) REVERT: A 419 MET cc_start: 0.8669 (mmt) cc_final: 0.8399 (mmm) REVERT: B 219 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6836 (mt-10) REVERT: B 273 MET cc_start: 0.6090 (ttp) cc_final: 0.5780 (ttt) REVERT: B 303 GLU cc_start: 0.7682 (tt0) cc_final: 0.7265 (pt0) REVERT: B 378 ARG cc_start: 0.7726 (mtt180) cc_final: 0.6959 (ttt180) REVERT: B 419 MET cc_start: 0.8692 (mmt) cc_final: 0.8402 (mmm) REVERT: C 126 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: C 219 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6825 (mt-10) REVERT: C 273 MET cc_start: 0.6057 (ttp) cc_final: 0.5761 (ttt) REVERT: C 303 GLU cc_start: 0.7726 (tt0) cc_final: 0.7297 (pt0) REVERT: C 378 ARG cc_start: 0.7719 (mtt180) cc_final: 0.6973 (ttt180) REVERT: C 419 MET cc_start: 0.8684 (mmt) cc_final: 0.8388 (mmm) REVERT: D 219 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6835 (mt-10) REVERT: D 273 MET cc_start: 0.6069 (ttp) cc_final: 0.5707 (ttt) REVERT: D 303 GLU cc_start: 0.7755 (tt0) cc_final: 0.7333 (pt0) REVERT: D 378 ARG cc_start: 0.7685 (mtt180) cc_final: 0.6938 (ttt180) REVERT: D 419 MET cc_start: 0.8696 (mmt) cc_final: 0.8400 (mmm) outliers start: 25 outliers final: 12 residues processed: 148 average time/residue: 1.8129 time to fit residues: 286.1934 Evaluate side-chains 155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151774 restraints weight = 11963.947| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.86 r_work: 0.3467 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.197 Angle : 0.499 9.026 18004 Z= 0.251 Chirality : 0.036 0.192 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.794 56.713 2728 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.93 % Allowed : 10.76 % Favored : 87.31 % 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: 3.91 (0.21), residues: 1548 helix: 3.19 (0.14), residues: 1264 sheet: 0.36 (0.63), residues: 80 loop : -0.75 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS C 392 PHE 0.019 0.002 PHE A 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6813 (mt-10) REVERT: A 273 MET cc_start: 0.6041 (ttp) cc_final: 0.5753 (ttt) REVERT: A 303 GLU cc_start: 0.7752 (tt0) cc_final: 0.7313 (pt0) REVERT: A 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7684 (m-30) REVERT: A 378 ARG cc_start: 0.7713 (mtt180) cc_final: 0.6916 (ttt180) REVERT: A 419 MET cc_start: 0.8623 (mmt) cc_final: 0.8348 (mmm) REVERT: B 219 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6842 (mt-10) REVERT: B 273 MET cc_start: 0.6016 (ttp) cc_final: 0.5718 (ttt) REVERT: B 303 GLU cc_start: 0.7697 (tt0) cc_final: 0.7263 (pt0) REVERT: B 378 ARG cc_start: 0.7694 (mtt180) cc_final: 0.6905 (ttt180) REVERT: B 419 MET cc_start: 0.8630 (mmt) cc_final: 0.8335 (mmm) REVERT: C 122 LEU cc_start: 0.8354 (mm) cc_final: 0.8085 (mt) REVERT: C 126 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: C 219 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6832 (mt-10) REVERT: C 273 MET cc_start: 0.6042 (ttp) cc_final: 0.5749 (ttt) REVERT: C 303 GLU cc_start: 0.7719 (tt0) cc_final: 0.7275 (pt0) REVERT: C 378 ARG cc_start: 0.7728 (mtt180) cc_final: 0.6934 (ttt180) REVERT: C 419 MET cc_start: 0.8624 (mmt) cc_final: 0.8330 (mmm) REVERT: D 219 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6838 (mt-10) REVERT: D 303 GLU cc_start: 0.7725 (tt0) cc_final: 0.7289 (pt0) REVERT: D 378 ARG cc_start: 0.7682 (mtt180) cc_final: 0.6913 (ttt180) REVERT: D 419 MET cc_start: 0.8631 (mmt) cc_final: 0.8331 (mmm) outliers start: 26 outliers final: 13 residues processed: 153 average time/residue: 1.7907 time to fit residues: 292.3461 Evaluate side-chains 154 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 0.0030 chunk 126 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 63 optimal weight: 0.7980 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.206599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154347 restraints weight = 11886.160| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.84 r_work: 0.3510 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13360 Z= 0.160 Angle : 0.477 9.154 18004 Z= 0.241 Chirality : 0.035 0.190 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.677 59.713 2728 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.74 % Allowed : 12.46 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.12 (0.21), residues: 1548 helix: 3.35 (0.14), residues: 1264 sheet: 0.26 (0.63), residues: 80 loop : -0.71 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 193 HIS 0.002 0.000 HIS C 392 PHE 0.018 0.002 PHE A 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG A 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: A 219 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6770 (mt-10) REVERT: A 273 MET cc_start: 0.6049 (ttp) cc_final: 0.5784 (ttt) REVERT: A 303 GLU cc_start: 0.7682 (tt0) cc_final: 0.7262 (pt0) REVERT: A 310 ASP cc_start: 0.7857 (m-30) cc_final: 0.7569 (m-30) REVERT: A 378 ARG cc_start: 0.7689 (mtt180) cc_final: 0.6945 (ttt180) REVERT: A 419 MET cc_start: 0.8583 (mmt) cc_final: 0.8315 (mmm) REVERT: B 126 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: B 219 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6790 (mt-10) REVERT: B 273 MET cc_start: 0.6033 (ttp) cc_final: 0.5745 (ttt) REVERT: B 303 GLU cc_start: 0.7651 (tt0) cc_final: 0.7234 (pt0) REVERT: B 378 ARG cc_start: 0.7667 (mtt180) cc_final: 0.6930 (ttt180) REVERT: B 419 MET cc_start: 0.8561 (mmt) cc_final: 0.8255 (mmm) REVERT: C 126 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: C 219 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6775 (mt-10) REVERT: C 273 MET cc_start: 0.6024 (ttp) cc_final: 0.5770 (ttt) REVERT: C 303 GLU cc_start: 0.7656 (tt0) cc_final: 0.7226 (pt0) REVERT: C 378 ARG cc_start: 0.7670 (mtt180) cc_final: 0.6911 (ttt180) REVERT: C 419 MET cc_start: 0.8544 (mmt) cc_final: 0.8242 (mmm) REVERT: D 126 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: D 219 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6778 (mt-10) REVERT: D 273 MET cc_start: 0.6033 (ttp) cc_final: 0.5715 (ttt) REVERT: D 303 GLU cc_start: 0.7647 (tt0) cc_final: 0.7234 (pt0) REVERT: D 378 ARG cc_start: 0.7625 (mtt180) cc_final: 0.6891 (ttt180) REVERT: D 419 MET cc_start: 0.8557 (mmt) cc_final: 0.8250 (mmm) outliers start: 10 outliers final: 6 residues processed: 141 average time/residue: 1.8520 time to fit residues: 278.9996 Evaluate side-chains 146 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 115 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.201522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148348 restraints weight = 12026.885| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.84 r_work: 0.3492 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13360 Z= 0.159 Angle : 0.471 4.998 18004 Z= 0.239 Chirality : 0.035 0.138 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.466 59.825 2728 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.19 % Allowed : 12.31 % Favored : 86.50 % 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: 4.19 (0.21), residues: 1548 helix: 3.40 (0.14), residues: 1264 sheet: 0.32 (0.62), residues: 80 loop : -0.70 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 193 HIS 0.002 0.000 HIS B 392 PHE 0.018 0.001 PHE A 205 TYR 0.019 0.001 TYR C 124 ARG 0.002 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8628.89 seconds wall clock time: 154 minutes 18.81 seconds (9258.81 seconds total)