Starting phenix.real_space_refine on Thu Jul 31 20:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vc1_43129/07_2025/8vc1_43129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vc1_43129/07_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_43129/07_2025/8vc1_43129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vc1_43129/07_2025/8vc1_43129.map" model { file = "/net/cci-nas-00/data/ceres_data/8vc1_43129/07_2025/8vc1_43129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vc1_43129/07_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-5711/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: 8.85, per 1000 atoms: 0.67 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=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 16 " distance=0.00 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 32 " distance=0.00 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 55 " distance=0.00 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 68 " distance=0.00 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 98 " distance=0.00 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 148 " distance=0.00 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 167 " distance=0.00 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 229 " distance=0.00 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 282 " distance=0.00 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 288 " distance=0.00 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 299 " distance=0.00 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 302 " distance=0.00 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 355 " distance=0.00 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 369 " distance=0.00 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 384 " distance=0.00 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 420 " distance=0.00 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: 3.38 Conformation dependent library (CDL) restraints added in 1.5 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: 0.99 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: 4.08 Time building geometry restraints manager: 4.00 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: 422 60.24 - 90.36: 30 90.36 - 120.48: 12 120.48 - 150.60: 4 Dihedral angle restraints: 8468 sinusoidal: 3908 harmonic: 4560 Sorted by residual: dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 16 " pdb=" CB CYS B 16 " ideal model delta sinusoidal sigma weight residual 19.10 19.10 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 32 " pdb=" SG CYS B 32 " pdb=" SG CYS B 32 " pdb=" CB CYS B 32 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 55 " pdb=" CB CYS B 55 " ideal model delta sinusoidal sigma weight residual 60.85 22.92 37.93 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 8465 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.860 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- 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= 0.485 Angle : 1.458 16.620 18020 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 Details of bonding type rmsd hydrogen bonds : bond 0.19361 ( 1072) hydrogen bonds : angle 7.17532 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.01186 (13360) covalent geometry : angle 1.45890 (18004) *********************** 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: 1.5106 time to fit residues: 229.7656 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 : 1.265 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153464 restraints weight = 11511.468| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.84 r_work: 0.3693 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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= 0.159 Angle : 0.631 7.086 18020 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 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 1072) hydrogen bonds : angle 4.11386 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00340 (13360) covalent geometry : angle 0.63086 (18004) *********************** 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 : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.5835 (ttp) cc_final: 0.5560 (ttt) REVERT: A 310 ASP cc_start: 0.7935 (m-30) cc_final: 0.7720 (m-30) REVERT: A 373 MET cc_start: 0.7411 (mmt) cc_final: 0.7066 (mtt) REVERT: B 133 ARG cc_start: 0.6806 (mtm-85) cc_final: 0.6579 (mtm-85) REVERT: B 306 ARG cc_start: 0.7597 (mtt90) cc_final: 0.7397 (mtt90) REVERT: B 310 ASP cc_start: 0.7971 (m-30) cc_final: 0.7764 (m-30) REVERT: B 373 MET cc_start: 0.7490 (mmt) cc_final: 0.7102 (mtt) REVERT: B 419 MET cc_start: 0.8671 (mmt) cc_final: 0.8370 (mmm) REVERT: C 273 MET cc_start: 0.5698 (ttp) cc_final: 0.5422 (ttt) REVERT: C 306 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7434 (mtt90) REVERT: C 310 ASP cc_start: 0.7970 (m-30) cc_final: 0.7767 (m-30) REVERT: C 373 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7163 (mtt) REVERT: C 378 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6756 (ttt180) REVERT: C 419 MET cc_start: 0.8676 (mmt) cc_final: 0.8374 (mmm) REVERT: D 310 ASP cc_start: 0.7974 (m-30) cc_final: 0.7767 (m-30) REVERT: D 373 MET cc_start: 0.7480 (mmt) cc_final: 0.7111 (mtt) REVERT: D 378 ARG cc_start: 0.7630 (mtt180) cc_final: 0.6756 (ttt180) REVERT: D 419 MET cc_start: 0.8670 (mmt) cc_final: 0.8372 (mmm) outliers start: 17 outliers final: 4 residues processed: 142 average time/residue: 1.6643 time to fit residues: 253.6541 Evaluate side-chains 128 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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: 1.9990 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.204701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152577 restraints weight = 11721.942| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.03 r_work: 0.3655 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2054 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= 0.140 Angle : 0.536 5.315 18020 Z= 0.273 Chirality : 0.037 0.144 2140 Planarity : 0.004 0.038 2088 Dihedral : 15.001 132.440 2728 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.41 % Allowed : 7.05 % Favored : 91.54 % 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: 3.18 (0.21), residues: 1548 helix: 2.63 (0.14), residues: 1264 sheet: -0.77 (0.59), residues: 88 loop : -0.12 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS A 370 PHE 0.017 0.002 PHE D 205 TYR 0.020 0.002 TYR D 124 ARG 0.002 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.05412 ( 1072) hydrogen bonds : angle 3.90849 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00303 (13360) covalent geometry : angle 0.53655 (18004) *********************** 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 170 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.5884 (ttp) cc_final: 0.5630 (ttt) REVERT: A 303 GLU cc_start: 0.7555 (tt0) cc_final: 0.7175 (pt0) REVERT: A 310 ASP cc_start: 0.7939 (m-30) cc_final: 0.7692 (m-30) REVERT: A 378 ARG cc_start: 0.7585 (mtt180) cc_final: 0.6687 (ttt180) REVERT: A 419 MET cc_start: 0.8592 (mmt) cc_final: 0.8367 (mmm) REVERT: B 200 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 273 MET cc_start: 0.5845 (ttp) cc_final: 0.5532 (ttt) REVERT: B 306 ARG cc_start: 0.7530 (mtt90) cc_final: 0.7274 (mtt90) REVERT: B 310 ASP cc_start: 0.7941 (m-30) cc_final: 0.7680 (m-30) REVERT: B 378 ARG cc_start: 0.7588 (mtt180) cc_final: 0.6693 (ttt180) REVERT: B 419 MET cc_start: 0.8633 (mmt) cc_final: 0.8340 (mmm) REVERT: C 273 MET cc_start: 0.5819 (ttp) cc_final: 0.5597 (ttt) REVERT: C 306 ARG cc_start: 0.7533 (mtt90) cc_final: 0.7292 (mtt90) REVERT: C 310 ASP cc_start: 0.7941 (m-30) cc_final: 0.7682 (m-30) REVERT: C 378 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6692 (ttt180) REVERT: C 419 MET cc_start: 0.8626 (mmt) cc_final: 0.8332 (mmm) REVERT: D 273 MET cc_start: 0.5769 (ttp) cc_final: 0.5507 (ttt) REVERT: D 310 ASP cc_start: 0.7934 (m-30) cc_final: 0.7684 (m-30) REVERT: D 378 ARG cc_start: 0.7557 (mtt180) cc_final: 0.6678 (ttt180) REVERT: D 419 MET cc_start: 0.8630 (mmt) cc_final: 0.8333 (mmm) outliers start: 19 outliers final: 6 residues processed: 158 average time/residue: 1.6608 time to fit residues: 280.9506 Evaluate side-chains 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain D residue 123 SER 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: 0.6980 chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.207145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152616 restraints weight = 11782.658| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.88 r_work: 0.3509 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13360 Z= 0.171 Angle : 0.560 7.342 18020 Z= 0.283 Chirality : 0.038 0.147 2140 Planarity : 0.004 0.040 2088 Dihedral : 14.422 126.180 2728 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 9.20 % Favored : 88.80 % 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: 3.17 (0.21), residues: 1548 helix: 2.64 (0.14), residues: 1264 sheet: -0.43 (0.61), residues: 88 loop : -0.46 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 193 HIS 0.003 0.001 HIS A 307 PHE 0.018 0.002 PHE B 205 TYR 0.021 0.002 TYR D 124 ARG 0.003 0.000 ARG B 298 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 1072) hydrogen bonds : angle 3.84956 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00413 (13360) covalent geometry : angle 0.56065 (18004) *********************** 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 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6929 (mt-10) REVERT: A 273 MET cc_start: 0.6122 (ttp) cc_final: 0.5847 (ttt) REVERT: A 303 GLU cc_start: 0.7778 (tt0) cc_final: 0.7395 (pt0) REVERT: A 310 ASP cc_start: 0.8003 (m-30) cc_final: 0.7768 (m-30) REVERT: A 378 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6992 (ttt180) REVERT: A 419 MET cc_start: 0.8707 (mmt) cc_final: 0.8452 (mmm) REVERT: B 38 ARG cc_start: 0.6680 (ptm-80) cc_final: 0.6416 (ptm-80) REVERT: B 219 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6904 (mt-10) REVERT: B 303 GLU cc_start: 0.7821 (tt0) cc_final: 0.7436 (pt0) REVERT: B 306 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7545 (mtt90) REVERT: B 310 ASP cc_start: 0.8018 (m-30) cc_final: 0.7792 (m-30) REVERT: B 378 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7003 (ttt180) REVERT: B 419 MET cc_start: 0.8761 (mmt) cc_final: 0.8469 (mmm) REVERT: C 219 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6933 (mt-10) REVERT: C 273 MET cc_start: 0.6078 (ttp) cc_final: 0.5782 (ttt) REVERT: C 303 GLU cc_start: 0.7798 (tt0) cc_final: 0.7432 (pt0) REVERT: C 306 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7547 (mtt90) REVERT: C 310 ASP cc_start: 0.8075 (m-30) cc_final: 0.7843 (m-30) REVERT: C 378 ARG cc_start: 0.7774 (mtt180) cc_final: 0.6985 (ttt180) REVERT: C 419 MET cc_start: 0.8766 (mmt) cc_final: 0.8474 (mmm) REVERT: D 219 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6954 (mt-10) REVERT: D 273 MET cc_start: 0.6075 (ttp) cc_final: 0.5764 (ttt) REVERT: D 303 GLU cc_start: 0.7790 (tt0) cc_final: 0.7414 (pt0) REVERT: D 310 ASP cc_start: 0.8041 (m-30) cc_final: 0.7801 (m-30) REVERT: D 378 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7000 (ttt180) REVERT: D 419 MET cc_start: 0.8761 (mmt) cc_final: 0.8467 (mmm) outliers start: 27 outliers final: 12 residues processed: 161 average time/residue: 1.6883 time to fit residues: 291.2239 Evaluate side-chains 152 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 102 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 0.0770 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 140 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.206027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152286 restraints weight = 11746.648| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.90 r_work: 0.3596 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2580 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= 0.117 Angle : 0.471 5.500 18020 Z= 0.244 Chirality : 0.035 0.130 2140 Planarity : 0.004 0.040 2088 Dihedral : 13.278 103.782 2728 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.26 % Allowed : 9.94 % Favored : 88.80 % 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: 3.71 (0.21), residues: 1548 helix: 3.06 (0.14), residues: 1264 sheet: -0.44 (0.61), residues: 88 loop : -0.53 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.000 HIS A 22 PHE 0.015 0.002 PHE D 205 TYR 0.017 0.001 TYR A 124 ARG 0.001 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 1072) hydrogen bonds : angle 3.65317 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00239 (13360) covalent geometry : angle 0.47170 (18004) *********************** 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 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.6133 (ttp) cc_final: 0.5838 (ttt) REVERT: A 310 ASP cc_start: 0.7929 (m-30) cc_final: 0.7653 (m-30) REVERT: A 378 ARG cc_start: 0.7699 (mtt180) cc_final: 0.6944 (ttt180) REVERT: A 419 MET cc_start: 0.8661 (mmt) cc_final: 0.8438 (mmm) REVERT: B 273 MET cc_start: 0.5942 (ttp) cc_final: 0.5655 (ttt) REVERT: B 306 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7453 (mtt90) REVERT: B 310 ASP cc_start: 0.7957 (m-30) cc_final: 0.7684 (m-30) REVERT: B 378 ARG cc_start: 0.7709 (mtt180) cc_final: 0.6952 (ttt180) REVERT: B 419 MET cc_start: 0.8679 (mmt) cc_final: 0.8425 (mmm) REVERT: C 273 MET cc_start: 0.6068 (ttp) cc_final: 0.5788 (ttt) REVERT: C 310 ASP cc_start: 0.7975 (m-30) cc_final: 0.7698 (m-30) REVERT: C 378 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6962 (ttt180) REVERT: C 419 MET cc_start: 0.8679 (mmt) cc_final: 0.8427 (mmm) REVERT: D 273 MET cc_start: 0.6028 (ttp) cc_final: 0.5713 (ttt) REVERT: D 310 ASP cc_start: 0.7941 (m-30) cc_final: 0.7667 (m-30) REVERT: D 378 ARG cc_start: 0.7685 (mtt180) cc_final: 0.6946 (ttt180) REVERT: D 419 MET cc_start: 0.8683 (mmt) cc_final: 0.8424 (mmm) outliers start: 17 outliers final: 7 residues processed: 138 average time/residue: 2.0496 time to fit residues: 301.2397 Evaluate side-chains 137 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain D residue 91 MET 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4255 r_free = 0.4255 target = 0.200955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146008 restraints weight = 11945.778| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.92 r_work: 0.3518 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13360 Z= 0.185 Angle : 0.580 8.534 18020 Z= 0.289 Chirality : 0.038 0.149 2140 Planarity : 0.005 0.040 2088 Dihedral : 12.756 92.082 2728 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.15 % Allowed : 9.87 % 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: 3.33 (0.21), residues: 1548 helix: 2.80 (0.14), residues: 1264 sheet: -0.46 (0.63), residues: 88 loop : -0.72 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 193 HIS 0.003 0.001 HIS C 392 PHE 0.019 0.002 PHE A 205 TYR 0.022 0.002 TYR C 124 ARG 0.004 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.05701 ( 1072) hydrogen bonds : angle 3.78552 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00461 (13360) covalent geometry : angle 0.58030 (18004) *********************** 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 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.3953 (mmm) REVERT: A 193 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.8209 (m100) REVERT: A 219 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6884 (mt-10) REVERT: A 273 MET cc_start: 0.6149 (ttp) cc_final: 0.5854 (ttt) REVERT: A 303 GLU cc_start: 0.7799 (tt0) cc_final: 0.7388 (pt0) REVERT: A 310 ASP cc_start: 0.7985 (m-30) cc_final: 0.7776 (m-30) REVERT: A 378 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7016 (ttt180) REVERT: A 419 MET cc_start: 0.8675 (mmt) cc_final: 0.8438 (mmm) REVERT: B 193 TRP cc_start: 0.8595 (OUTLIER) cc_final: 0.8224 (m100) REVERT: B 219 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6896 (mt-10) REVERT: B 273 MET cc_start: 0.6056 (ttp) cc_final: 0.5768 (ttt) REVERT: B 303 GLU cc_start: 0.7814 (tt0) cc_final: 0.7369 (pt0) REVERT: B 310 ASP cc_start: 0.7985 (m-30) cc_final: 0.7770 (m-30) REVERT: B 378 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6992 (ttt180) REVERT: B 419 MET cc_start: 0.8747 (mmt) cc_final: 0.8419 (mmm) REVERT: C 193 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.8228 (m100) REVERT: C 219 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6866 (mt-10) REVERT: C 273 MET cc_start: 0.6138 (ttp) cc_final: 0.5849 (ttt) REVERT: C 303 GLU cc_start: 0.7799 (tt0) cc_final: 0.7380 (pt0) REVERT: C 310 ASP cc_start: 0.8001 (m-30) cc_final: 0.7793 (m-30) REVERT: C 378 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7004 (ttt180) REVERT: C 419 MET cc_start: 0.8747 (mmt) cc_final: 0.8418 (mmm) REVERT: D 193 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8228 (m100) REVERT: D 219 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6874 (mt-10) REVERT: D 273 MET cc_start: 0.6106 (ttp) cc_final: 0.5779 (ttt) REVERT: D 303 GLU cc_start: 0.7788 (tt0) cc_final: 0.7342 (pt0) REVERT: D 310 ASP cc_start: 0.8014 (m-30) cc_final: 0.7797 (m-30) REVERT: D 378 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7000 (ttt180) REVERT: D 419 MET cc_start: 0.8745 (mmt) cc_final: 0.8410 (mmm) outliers start: 29 outliers final: 7 residues processed: 156 average time/residue: 2.0338 time to fit residues: 338.6816 Evaluate side-chains 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 193 TRP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 193 TRP 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: 0.6980 chunk 139 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.203333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148893 restraints weight = 11852.285| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.91 r_work: 0.3554 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13360 Z= 0.137 Angle : 0.502 5.444 18020 Z= 0.256 Chirality : 0.036 0.143 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.275 77.418 2728 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.15 % Allowed : 9.94 % Favored : 87.91 % 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: 3.61 (0.21), residues: 1548 helix: 3.01 (0.14), residues: 1264 sheet: -0.45 (0.62), residues: 88 loop : -0.77 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS A 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 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 1072) hydrogen bonds : angle 3.65721 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00315 (13360) covalent geometry : angle 0.50267 (18004) *********************** 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 167 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6831 (mt-10) REVERT: A 273 MET cc_start: 0.6108 (ttp) cc_final: 0.5818 (ttt) REVERT: A 303 GLU cc_start: 0.7751 (tt0) cc_final: 0.7330 (pt0) REVERT: A 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7686 (m-30) REVERT: A 378 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6977 (ttt180) REVERT: A 419 MET cc_start: 0.8664 (mmt) cc_final: 0.8405 (mmm) REVERT: B 219 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6839 (mt-10) REVERT: B 273 MET cc_start: 0.6057 (ttp) cc_final: 0.5769 (ttt) REVERT: B 303 GLU cc_start: 0.7718 (tt0) cc_final: 0.7311 (pt0) REVERT: B 310 ASP cc_start: 0.7887 (m-30) cc_final: 0.7640 (m-30) REVERT: B 378 ARG cc_start: 0.7774 (mtt180) cc_final: 0.6978 (ttt180) REVERT: B 419 MET cc_start: 0.8709 (mmt) cc_final: 0.8352 (mmm) REVERT: C 219 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6828 (mt-10) REVERT: C 273 MET cc_start: 0.6078 (ttp) cc_final: 0.5780 (ttt) REVERT: C 303 GLU cc_start: 0.7704 (tt0) cc_final: 0.7285 (pt0) REVERT: C 310 ASP cc_start: 0.7908 (m-30) cc_final: 0.7679 (m-30) REVERT: C 378 ARG cc_start: 0.7777 (mtt180) cc_final: 0.6995 (ttt180) REVERT: C 419 MET cc_start: 0.8709 (mmt) cc_final: 0.8409 (mmm) REVERT: D 219 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6868 (mt-10) REVERT: D 273 MET cc_start: 0.6075 (ttp) cc_final: 0.5725 (ttt) REVERT: D 303 GLU cc_start: 0.7724 (tt0) cc_final: 0.7313 (pt0) REVERT: D 310 ASP cc_start: 0.7900 (m-30) cc_final: 0.7669 (m-30) REVERT: D 378 ARG cc_start: 0.7764 (mtt180) cc_final: 0.6983 (ttt180) REVERT: D 419 MET cc_start: 0.8715 (mmt) cc_final: 0.8358 (mmm) outliers start: 29 outliers final: 9 residues processed: 148 average time/residue: 1.9370 time to fit residues: 307.7809 Evaluate side-chains 145 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 102 VAL Chi-restraints excluded: chain D residue 123 SER 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: 0.7980 chunk 39 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 55 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 358 HIS C 202 GLN D 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152671 restraints weight = 11810.939| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.84 r_work: 0.3576 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13360 Z= 0.120 Angle : 0.476 4.897 18020 Z= 0.244 Chirality : 0.035 0.138 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.845 58.930 2728 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.48 % Allowed : 10.83 % Favored : 87.69 % 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: 3.94 (0.21), residues: 1548 helix: 3.22 (0.14), residues: 1264 sheet: 0.26 (0.63), residues: 80 loop : -0.80 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.000 HIS C 392 PHE 0.017 0.002 PHE A 205 TYR 0.017 0.001 TYR D 124 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1072) hydrogen bonds : angle 3.56230 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00258 (13360) covalent geometry : angle 0.47581 (18004) *********************** 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 161 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6792 (mt-10) REVERT: A 273 MET cc_start: 0.6079 (ttp) cc_final: 0.5789 (ttt) REVERT: A 303 GLU cc_start: 0.7640 (tt0) cc_final: 0.7236 (pt0) REVERT: A 310 ASP cc_start: 0.7828 (m-30) cc_final: 0.7585 (m-30) REVERT: A 378 ARG cc_start: 0.7687 (mtt180) cc_final: 0.6936 (ttt180) REVERT: A 419 MET cc_start: 0.8619 (mmt) cc_final: 0.8342 (mmm) REVERT: B 219 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6823 (mt-10) REVERT: B 273 MET cc_start: 0.6032 (ttp) cc_final: 0.5737 (ttt) REVERT: B 303 GLU cc_start: 0.7625 (tt0) cc_final: 0.7236 (pt0) REVERT: B 306 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7332 (mpt90) REVERT: B 310 ASP cc_start: 0.7872 (m-30) cc_final: 0.7601 (m-30) REVERT: B 378 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6945 (ttt180) REVERT: B 419 MET cc_start: 0.8667 (mmt) cc_final: 0.8364 (mmm) REVERT: C 219 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6808 (mt-10) REVERT: C 273 MET cc_start: 0.6063 (ttp) cc_final: 0.5760 (ttt) REVERT: C 303 GLU cc_start: 0.7633 (tt0) cc_final: 0.7236 (pt0) REVERT: C 310 ASP cc_start: 0.7838 (m-30) cc_final: 0.7606 (m-30) REVERT: C 378 ARG cc_start: 0.7724 (mtt180) cc_final: 0.6971 (ttt180) REVERT: C 419 MET cc_start: 0.8665 (mmt) cc_final: 0.8360 (mmm) REVERT: D 219 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6791 (mt-10) REVERT: D 273 MET cc_start: 0.6068 (ttp) cc_final: 0.5719 (ttt) REVERT: D 303 GLU cc_start: 0.7637 (tt0) cc_final: 0.7240 (pt0) REVERT: D 310 ASP cc_start: 0.7825 (m-30) cc_final: 0.7574 (m-30) REVERT: D 378 ARG cc_start: 0.7688 (mtt180) cc_final: 0.6934 (ttt180) REVERT: D 419 MET cc_start: 0.8637 (mmt) cc_final: 0.8323 (mmm) outliers start: 20 outliers final: 11 residues processed: 149 average time/residue: 1.8231 time to fit residues: 291.5125 Evaluate side-chains 148 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 91 MET Chi-restraints excluded: chain C residue 102 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 3.9990 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: 0.9990 chunk 138 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.204028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149499 restraints weight = 11887.152| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.92 r_work: 0.3559 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13360 Z= 0.133 Angle : 0.501 5.673 18020 Z= 0.254 Chirality : 0.036 0.142 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.827 57.401 2728 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 11.05 % Favored : 87.39 % 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: 3.88 (0.21), residues: 1548 helix: 3.17 (0.14), residues: 1264 sheet: 0.34 (0.63), residues: 80 loop : -0.79 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 193 HIS 0.002 0.001 HIS C 370 PHE 0.019 0.002 PHE A 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 1072) hydrogen bonds : angle 3.57974 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00305 (13360) covalent geometry : angle 0.50147 (18004) *********************** 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 162 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6794 (mt-10) REVERT: A 303 GLU cc_start: 0.7696 (tt0) cc_final: 0.7276 (pt0) REVERT: A 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7631 (m-30) REVERT: A 378 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6968 (ttt180) REVERT: A 419 MET cc_start: 0.8661 (mmt) cc_final: 0.8386 (mmm) REVERT: B 219 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6829 (mt-10) REVERT: B 273 MET cc_start: 0.6067 (ttp) cc_final: 0.5769 (ttt) REVERT: B 303 GLU cc_start: 0.7687 (tt0) cc_final: 0.7282 (pt0) REVERT: B 310 ASP cc_start: 0.7847 (m-30) cc_final: 0.7627 (m-30) REVERT: B 378 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6966 (ttt180) REVERT: B 419 MET cc_start: 0.8689 (mmt) cc_final: 0.8384 (mmm) REVERT: C 126 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: C 219 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6821 (mt-10) REVERT: C 273 MET cc_start: 0.6093 (ttp) cc_final: 0.5790 (ttt) REVERT: C 303 GLU cc_start: 0.7689 (tt0) cc_final: 0.7269 (pt0) REVERT: C 310 ASP cc_start: 0.7868 (m-30) cc_final: 0.7642 (m-30) REVERT: C 378 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6980 (ttt180) REVERT: C 419 MET cc_start: 0.8680 (mmt) cc_final: 0.8372 (mmm) REVERT: D 126 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: D 219 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6790 (mt-10) REVERT: D 273 MET cc_start: 0.6071 (ttp) cc_final: 0.5711 (ttt) REVERT: D 303 GLU cc_start: 0.7705 (tt0) cc_final: 0.7289 (pt0) REVERT: D 310 ASP cc_start: 0.7843 (m-30) cc_final: 0.7618 (m-30) REVERT: D 378 ARG cc_start: 0.7733 (mtt180) cc_final: 0.6965 (ttt180) REVERT: D 419 MET cc_start: 0.8691 (mmt) cc_final: 0.8383 (mmm) outliers start: 21 outliers final: 12 residues processed: 148 average time/residue: 1.9129 time to fit residues: 302.4050 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 : 1.230 ------------------------------------------------------------------------------- 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 123 SER 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 143 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 126 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.200031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146628 restraints weight = 11968.676| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.83 r_work: 0.3474 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13360 Z= 0.122 Angle : 0.483 5.193 18020 Z= 0.246 Chirality : 0.035 0.142 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.775 59.885 2728 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.26 % Allowed : 11.57 % Favored : 87.17 % 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: 4.00 (0.21), residues: 1548 helix: 3.26 (0.14), residues: 1264 sheet: 0.32 (0.62), residues: 80 loop : -0.80 (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 D 392 PHE 0.018 0.002 PHE B 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1072) hydrogen bonds : angle 3.53556 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00270 (13360) covalent geometry : angle 0.48370 (18004) ********************** 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 162 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: A 219 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6814 (mt-10) REVERT: A 303 GLU cc_start: 0.7699 (tt0) cc_final: 0.7269 (pt0) REVERT: A 310 ASP cc_start: 0.7950 (m-30) cc_final: 0.7690 (m-30) REVERT: A 378 ARG cc_start: 0.7723 (mtt180) cc_final: 0.6922 (ttt180) REVERT: A 419 MET cc_start: 0.8576 (mmt) cc_final: 0.8359 (mmm) REVERT: B 126 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: B 219 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6820 (mt-10) REVERT: B 273 MET cc_start: 0.6058 (ttp) cc_final: 0.5775 (ttt) REVERT: B 297 MET cc_start: 0.8521 (mtp) cc_final: 0.8244 (mtt) REVERT: B 303 GLU cc_start: 0.7712 (tt0) cc_final: 0.7293 (pt0) REVERT: B 310 ASP cc_start: 0.7933 (m-30) cc_final: 0.7656 (m-30) REVERT: B 378 ARG cc_start: 0.7710 (mtt180) cc_final: 0.6909 (ttt180) REVERT: B 419 MET cc_start: 0.8627 (mmt) cc_final: 0.8316 (mmm) REVERT: C 126 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: C 219 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6818 (mt-10) REVERT: C 303 GLU cc_start: 0.7699 (tt0) cc_final: 0.7277 (pt0) REVERT: C 310 ASP cc_start: 0.7943 (m-30) cc_final: 0.7686 (m-30) REVERT: C 378 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6948 (ttt180) REVERT: C 419 MET cc_start: 0.8581 (mmt) cc_final: 0.8273 (mmm) REVERT: D 126 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: D 219 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6812 (mt-10) REVERT: D 303 GLU cc_start: 0.7684 (tt0) cc_final: 0.7269 (pt0) REVERT: D 310 ASP cc_start: 0.7929 (m-30) cc_final: 0.7659 (m-30) REVERT: D 378 ARG cc_start: 0.7732 (mtt180) cc_final: 0.6943 (ttt180) REVERT: D 419 MET cc_start: 0.8584 (mmt) cc_final: 0.8272 (mmm) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 1.6579 time to fit residues: 270.3365 Evaluate side-chains 156 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 123 SER 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: 0.8980 chunk 114 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.197832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142574 restraints weight = 12041.594| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.90 r_work: 0.3557 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3090 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= 0.122 Angle : 0.486 5.517 18020 Z= 0.248 Chirality : 0.035 0.139 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.732 58.697 2728 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.19 % Allowed : 11.80 % Favored : 87.02 % 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: 3.99 (0.21), residues: 1548 helix: 3.26 (0.14), residues: 1264 sheet: 0.35 (0.62), residues: 80 loop : -0.81 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 193 HIS 0.002 0.000 HIS B 358 PHE 0.013 0.002 PHE A 56 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1072) hydrogen bonds : angle 3.53388 ( 3180) SS BOND : angle 0.00000 ( 16) covalent geometry : bond 0.00268 (13360) covalent geometry : angle 0.48660 (18004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10024.25 seconds wall clock time: 179 minutes 13.32 seconds (10753.32 seconds total)