Starting phenix.real_space_refine on Thu Sep 18 03:53:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vc1_43129/09_2025/8vc1_43129_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vc1_43129/09_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_43129/09_2025/8vc1_43129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vc1_43129/09_2025/8vc1_43129.map" model { file = "/net/cci-nas-00/data/ceres_data/8vc1_43129/09_2025/8vc1_43129_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vc1_43129/09_2025/8vc1_43129_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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-3': 2, 'PSC:plan-4': 2, 'PSC:plan-1': 1, 'PC7:plan-2': 1} 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: {'PC7:plan-2': 1, 'PSC:plan-3': 2, 'PSC:plan-4': 2, 'PSC:plan-1': 1} Unresolved non-hydrogen planarities: 21 Restraints were copied for chains: B, D Time building chain proxies: 3.63, per 1000 atoms: 0.28 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: 1.28 Conformation dependent library (CDL) restraints added in 593.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.44 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: 2.09 Time building geometry restraints manager: 1.65 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 0.00 0.00 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 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 ... (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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.003 ARG D 385 TYR 0.036 0.005 TYR A 124 PHE 0.031 0.003 PHE A 271 TRP 0.017 0.005 TRP D 354 HIS 0.009 0.004 HIS D 307 Details of bonding type rmsd covalent geometry : bond 0.01186 (13360) covalent geometry : angle 1.45890 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.19361 ( 1072) hydrogen bonds : angle 7.17532 ( 3180) *********************** 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 : 0.457 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: 0.7389 time to fit residues: 112.0538 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 : 0.491 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.212238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158059 restraints weight = 11672.453| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.88 r_work: 0.3587 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1562 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= 0.157 Angle : 0.623 6.682 18020 Z= 0.318 Chirality : 0.038 0.157 2140 Planarity : 0.004 0.037 2088 Dihedral : 16.902 139.606 2736 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.48 % Allowed : 3.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.21), residues: 1548 helix: 2.03 (0.14), residues: 1264 sheet: -0.76 (0.59), residues: 88 loop : 0.28 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 213 TYR 0.018 0.002 TYR B 124 PHE 0.022 0.002 PHE A 56 TRP 0.003 0.001 TRP D 193 HIS 0.003 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00321 (13360) covalent geometry : angle 0.62336 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.06119 ( 1072) hydrogen bonds : angle 4.16152 ( 3180) *********************** 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 152 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.5964 (ttp) cc_final: 0.5683 (ttt) REVERT: A 373 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: A 419 MET cc_start: 0.8743 (mmt) cc_final: 0.8466 (mmm) REVERT: B 133 ARG cc_start: 0.6938 (mtm-85) cc_final: 0.6697 (mtm-85) REVERT: B 273 MET cc_start: 0.6105 (ttp) cc_final: 0.5745 (ttt) REVERT: B 373 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7239 (mtt) REVERT: B 419 MET cc_start: 0.8750 (mmt) cc_final: 0.8469 (mmm) REVERT: C 273 MET cc_start: 0.5822 (ttp) cc_final: 0.5546 (ttt) REVERT: C 373 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7278 (mtt) REVERT: C 419 MET cc_start: 0.8758 (mmt) cc_final: 0.8471 (mmm) REVERT: D 273 MET cc_start: 0.6134 (ttp) cc_final: 0.5754 (ttt) REVERT: D 373 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7282 (mtt) REVERT: D 419 MET cc_start: 0.8753 (mmt) cc_final: 0.8471 (mmm) outliers start: 20 outliers final: 4 residues processed: 136 average time/residue: 0.7780 time to fit residues: 113.2409 Evaluate side-chains 129 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 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 Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 21 optimal weight: 0.0070 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.206376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154478 restraints weight = 11692.686| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.07 r_work: 0.3591 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2097 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= 0.131 Angle : 0.519 4.871 18020 Z= 0.267 Chirality : 0.037 0.140 2140 Planarity : 0.004 0.038 2088 Dihedral : 14.932 130.301 2728 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.11 % Allowed : 6.23 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.21), residues: 1548 helix: 2.73 (0.14), residues: 1264 sheet: -0.80 (0.59), residues: 88 loop : -0.06 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.019 0.001 TYR D 124 PHE 0.017 0.002 PHE C 56 TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00263 (13360) covalent geometry : angle 0.51946 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.05192 ( 1072) hydrogen bonds : angle 3.87099 ( 3180) *********************** 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 160 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.5287 (tpt) cc_final: 0.5064 (tpt) REVERT: A 273 MET cc_start: 0.6019 (ttp) cc_final: 0.5755 (ttt) REVERT: A 378 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6991 (ttt180) REVERT: A 419 MET cc_start: 0.8668 (mmt) cc_final: 0.8400 (mmm) REVERT: B 200 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7545 (mt-10) REVERT: B 273 MET cc_start: 0.6011 (ttp) cc_final: 0.5706 (ttt) REVERT: B 378 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7000 (ttt180) REVERT: B 419 MET cc_start: 0.8677 (mmt) cc_final: 0.8415 (mmm) REVERT: C 273 MET cc_start: 0.5972 (ttp) cc_final: 0.5742 (ttt) REVERT: C 378 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7001 (ttt180) REVERT: C 419 MET cc_start: 0.8670 (mmt) cc_final: 0.8409 (mmm) REVERT: D 91 MET cc_start: 0.5509 (tpt) cc_final: 0.5275 (tpt) REVERT: D 273 MET cc_start: 0.6112 (ttp) cc_final: 0.5830 (ttt) REVERT: D 378 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6993 (ttt180) REVERT: D 419 MET cc_start: 0.8670 (mmt) cc_final: 0.8404 (mmm) outliers start: 15 outliers final: 2 residues processed: 147 average time/residue: 0.8660 time to fit residues: 135.5830 Evaluate side-chains 138 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.205471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151764 restraints weight = 11739.716| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.89 r_work: 0.3583 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2408 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= 0.128 Angle : 0.501 7.317 18020 Z= 0.257 Chirality : 0.036 0.135 2140 Planarity : 0.004 0.040 2088 Dihedral : 13.927 113.942 2728 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.56 % Allowed : 7.57 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.21), residues: 1548 helix: 2.99 (0.14), residues: 1264 sheet: -0.52 (0.61), residues: 88 loop : -0.37 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.020 0.001 TYR B 124 PHE 0.017 0.002 PHE B 205 TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00280 (13360) covalent geometry : angle 0.50140 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04889 ( 1072) hydrogen bonds : angle 3.71980 ( 3180) *********************** 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 164 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 MET cc_start: 0.6005 (ttp) cc_final: 0.5763 (ttt) REVERT: A 378 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7014 (ttt180) REVERT: A 419 MET cc_start: 0.8707 (mmt) cc_final: 0.8404 (mmm) REVERT: B 273 MET cc_start: 0.6002 (ttp) cc_final: 0.5655 (ttt) REVERT: B 378 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7020 (ttt180) REVERT: B 419 MET cc_start: 0.8701 (mmt) cc_final: 0.8404 (mmm) REVERT: C 273 MET cc_start: 0.5918 (ttp) cc_final: 0.5694 (ttt) REVERT: C 378 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7015 (ttt180) REVERT: C 419 MET cc_start: 0.8720 (mmt) cc_final: 0.8432 (mmm) REVERT: D 273 MET cc_start: 0.6004 (ttp) cc_final: 0.5648 (ttt) REVERT: D 378 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7011 (ttt180) REVERT: D 419 MET cc_start: 0.8710 (mmt) cc_final: 0.8425 (mmm) outliers start: 21 outliers final: 5 residues processed: 148 average time/residue: 0.8291 time to fit residues: 130.9539 Evaluate side-chains 142 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 362 MET 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 31 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.210502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156267 restraints weight = 12011.752| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.24 r_work: 0.3543 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2591 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= 0.131 Angle : 0.491 5.427 18020 Z= 0.252 Chirality : 0.036 0.135 2140 Planarity : 0.004 0.039 2088 Dihedral : 12.908 91.419 2728 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.71 % Allowed : 9.05 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.21), residues: 1548 helix: 3.11 (0.14), residues: 1264 sheet: -0.21 (0.62), residues: 84 loop : -0.68 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.019 0.001 TYR C 124 PHE 0.016 0.002 PHE D 205 TRP 0.005 0.001 TRP B 193 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00294 (13360) covalent geometry : angle 0.49091 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04866 ( 1072) hydrogen bonds : angle 3.65775 ( 3180) *********************** 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 176 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6658 (mt-10) REVERT: A 273 MET cc_start: 0.6132 (ttp) cc_final: 0.5886 (ttt) REVERT: A 303 GLU cc_start: 0.7462 (tt0) cc_final: 0.7083 (pt0) REVERT: A 378 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6859 (ttt180) REVERT: A 419 MET cc_start: 0.8621 (mmt) cc_final: 0.8374 (mmm) REVERT: B 219 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6649 (mt-10) REVERT: B 273 MET cc_start: 0.5947 (ttp) cc_final: 0.5674 (ttt) REVERT: B 303 GLU cc_start: 0.7489 (tt0) cc_final: 0.7155 (pt0) REVERT: B 378 ARG cc_start: 0.7504 (mtt180) cc_final: 0.6847 (ttt180) REVERT: B 419 MET cc_start: 0.8628 (mmt) cc_final: 0.8387 (mmm) REVERT: C 219 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6618 (mt-10) REVERT: C 273 MET cc_start: 0.6018 (ttp) cc_final: 0.5782 (ttt) REVERT: C 303 GLU cc_start: 0.7470 (tt0) cc_final: 0.7138 (pt0) REVERT: C 378 ARG cc_start: 0.7505 (mtt180) cc_final: 0.6866 (ttt180) REVERT: C 419 MET cc_start: 0.8622 (mmt) cc_final: 0.8385 (mmm) REVERT: D 87 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.3840 (mmm) REVERT: D 219 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6634 (mt-10) REVERT: D 273 MET cc_start: 0.5949 (ttp) cc_final: 0.5672 (ttt) REVERT: D 303 GLU cc_start: 0.7469 (tt0) cc_final: 0.7141 (pt0) REVERT: D 378 ARG cc_start: 0.7495 (mtt180) cc_final: 0.6862 (ttt180) REVERT: D 419 MET cc_start: 0.8619 (mmt) cc_final: 0.8376 (mmm) outliers start: 23 outliers final: 9 residues processed: 158 average time/residue: 0.8360 time to fit residues: 140.6785 Evaluate side-chains 155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 87 MET Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 LEU 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 18 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.203089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148864 restraints weight = 11801.355| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.89 r_work: 0.3559 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13360 Z= 0.150 Angle : 0.526 6.609 18020 Z= 0.266 Chirality : 0.037 0.144 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.304 73.948 2728 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.97 % Allowed : 8.61 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.68 (0.21), residues: 1548 helix: 3.04 (0.14), residues: 1264 sheet: 0.20 (0.64), residues: 80 loop : -0.90 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 298 TYR 0.021 0.001 TYR A 124 PHE 0.020 0.002 PHE A 205 TRP 0.004 0.001 TRP C 193 HIS 0.002 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00354 (13360) covalent geometry : angle 0.52612 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.05132 ( 1072) hydrogen bonds : angle 3.68202 ( 3180) *********************** 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 184 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6841 (mt-10) REVERT: A 273 MET cc_start: 0.6170 (ttp) cc_final: 0.5895 (ttt) REVERT: A 303 GLU cc_start: 0.7732 (tt0) cc_final: 0.7331 (pt0) REVERT: A 378 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7001 (ttt180) REVERT: A 419 MET cc_start: 0.8738 (mmt) cc_final: 0.8475 (mmm) REVERT: B 219 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6871 (mt-10) REVERT: B 303 GLU cc_start: 0.7737 (tt0) cc_final: 0.7321 (pt0) REVERT: B 378 ARG cc_start: 0.7758 (mtt180) cc_final: 0.6994 (ttt180) REVERT: B 419 MET cc_start: 0.8735 (mmt) cc_final: 0.8480 (mmm) REVERT: C 219 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6862 (mt-10) REVERT: C 273 MET cc_start: 0.6114 (ttp) cc_final: 0.5832 (ttt) REVERT: C 303 GLU cc_start: 0.7746 (tt0) cc_final: 0.7343 (pt0) REVERT: C 378 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7017 (ttt180) REVERT: C 419 MET cc_start: 0.8737 (mmt) cc_final: 0.8423 (mmm) REVERT: D 219 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6857 (mt-10) REVERT: D 273 MET cc_start: 0.6029 (ttp) cc_final: 0.5674 (ttt) REVERT: D 303 GLU cc_start: 0.7737 (tt0) cc_final: 0.7309 (pt0) REVERT: D 378 ARG cc_start: 0.7712 (mtt180) cc_final: 0.6980 (ttt180) REVERT: D 419 MET cc_start: 0.8746 (mmt) cc_final: 0.8489 (mmm) outliers start: 40 outliers final: 13 residues processed: 156 average time/residue: 0.8091 time to fit residues: 134.6819 Evaluate side-chains 155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 216 LEU 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 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 LEU 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 4 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 0.0470 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 = 0.205057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150917 restraints weight = 11835.942| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.23 r_work: 0.3563 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13360 Z= 0.123 Angle : 0.485 5.827 18020 Z= 0.246 Chirality : 0.035 0.136 2140 Planarity : 0.004 0.040 2088 Dihedral : 11.956 62.034 2728 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.08 % Allowed : 9.42 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (0.21), residues: 1548 helix: 3.22 (0.14), residues: 1264 sheet: 0.21 (0.63), residues: 80 loop : -0.76 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.017 0.001 TYR B 124 PHE 0.018 0.002 PHE B 205 TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00269 (13360) covalent geometry : angle 0.48477 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04692 ( 1072) hydrogen bonds : angle 3.58970 ( 3180) *********************** 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 170 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6642 (mt-10) REVERT: A 273 MET cc_start: 0.6148 (ttp) cc_final: 0.5878 (ttt) REVERT: A 303 GLU cc_start: 0.7434 (tt0) cc_final: 0.7051 (pt0) REVERT: A 378 ARG cc_start: 0.7500 (mtt180) cc_final: 0.6850 (ttt180) REVERT: A 419 MET cc_start: 0.8587 (mmt) cc_final: 0.8288 (mmm) REVERT: B 219 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6624 (mt-10) REVERT: B 273 MET cc_start: 0.5940 (ttp) cc_final: 0.5671 (ttt) REVERT: B 303 GLU cc_start: 0.7438 (tt0) cc_final: 0.7076 (pt0) REVERT: B 378 ARG cc_start: 0.7495 (mtt180) cc_final: 0.6851 (ttt180) REVERT: B 419 MET cc_start: 0.8587 (mmt) cc_final: 0.8303 (mmm) REVERT: C 219 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6601 (mt-10) REVERT: C 273 MET cc_start: 0.6152 (ttp) cc_final: 0.5897 (ttt) REVERT: C 303 GLU cc_start: 0.7412 (tt0) cc_final: 0.7051 (pt0) REVERT: C 378 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6858 (ttt180) REVERT: C 419 MET cc_start: 0.8603 (mmt) cc_final: 0.8320 (mmm) REVERT: D 219 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6591 (mt-10) REVERT: D 273 MET cc_start: 0.5970 (ttp) cc_final: 0.5679 (ttt) REVERT: D 303 GLU cc_start: 0.7437 (tt0) cc_final: 0.7073 (pt0) REVERT: D 378 ARG cc_start: 0.7468 (mtt180) cc_final: 0.6841 (ttt180) REVERT: D 419 MET cc_start: 0.8587 (mmt) cc_final: 0.8298 (mmm) outliers start: 28 outliers final: 10 residues processed: 145 average time/residue: 0.8279 time to fit residues: 127.9722 Evaluate side-chains 151 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 362 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.205632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151643 restraints weight = 11732.199| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.90 r_work: 0.3583 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13360 Z= 0.122 Angle : 0.480 4.930 18020 Z= 0.244 Chirality : 0.035 0.139 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.671 57.345 2728 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.71 % Allowed : 10.76 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.05 (0.21), residues: 1548 helix: 3.30 (0.14), residues: 1264 sheet: 0.24 (0.63), residues: 80 loop : -0.76 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.019 0.001 TYR B 124 PHE 0.018 0.002 PHE A 205 TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS C 392 Details of bonding type rmsd covalent geometry : bond 0.00267 (13360) covalent geometry : angle 0.47988 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04565 ( 1072) hydrogen bonds : angle 3.54209 ( 3180) *********************** 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 174 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: A 219 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6637 (mt-10) REVERT: A 273 MET cc_start: 0.6160 (ttp) cc_final: 0.5883 (ttt) REVERT: A 303 GLU cc_start: 0.7446 (tt0) cc_final: 0.7056 (pt0) REVERT: A 378 ARG cc_start: 0.7494 (mtt180) cc_final: 0.6863 (ttt180) REVERT: A 419 MET cc_start: 0.8543 (mmt) cc_final: 0.8245 (mmm) REVERT: B 126 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: B 219 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6602 (mt-10) REVERT: B 273 MET cc_start: 0.5951 (ttp) cc_final: 0.5681 (ttt) REVERT: B 303 GLU cc_start: 0.7446 (tt0) cc_final: 0.7089 (pt0) REVERT: B 378 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6889 (ttt180) REVERT: B 419 MET cc_start: 0.8539 (mmt) cc_final: 0.8248 (mmm) REVERT: C 126 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: C 219 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6540 (mt-10) REVERT: C 273 MET cc_start: 0.6106 (ttp) cc_final: 0.5835 (ttt) REVERT: C 303 GLU cc_start: 0.7421 (tt0) cc_final: 0.7048 (pt0) REVERT: C 378 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6848 (ttt180) REVERT: C 419 MET cc_start: 0.8587 (mmt) cc_final: 0.8308 (mmm) REVERT: D 126 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: D 219 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6545 (mt-10) REVERT: D 273 MET cc_start: 0.6002 (ttp) cc_final: 0.5711 (ttt) REVERT: D 303 GLU cc_start: 0.7430 (tt0) cc_final: 0.7071 (pt0) REVERT: D 378 ARG cc_start: 0.7474 (mtt180) cc_final: 0.6881 (ttt180) REVERT: D 419 MET cc_start: 0.8543 (mmt) cc_final: 0.8252 (mmm) outliers start: 23 outliers final: 6 residues processed: 155 average time/residue: 0.8150 time to fit residues: 134.9199 Evaluate side-chains 157 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.197830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.142963 restraints weight = 11998.595| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.88 r_work: 0.3565 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13360 Z= 0.123 Angle : 0.484 5.003 18020 Z= 0.247 Chirality : 0.035 0.142 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.664 58.121 2728 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.85 % Allowed : 10.68 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.02 (0.21), residues: 1548 helix: 3.27 (0.14), residues: 1264 sheet: 0.28 (0.63), residues: 80 loop : -0.72 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.018 0.001 TYR A 124 PHE 0.013 0.002 PHE A 203 TRP 0.005 0.001 TRP B 193 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00275 (13360) covalent geometry : angle 0.48373 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04579 ( 1072) hydrogen bonds : angle 3.54800 ( 3180) *********************** 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 169 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 219 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6881 (mt-10) REVERT: A 273 MET cc_start: 0.6147 (ttp) cc_final: 0.5856 (ttt) REVERT: A 303 GLU cc_start: 0.7821 (tt0) cc_final: 0.7385 (pt0) REVERT: A 378 ARG cc_start: 0.7752 (mtt180) cc_final: 0.6991 (ttt180) REVERT: A 419 MET cc_start: 0.8597 (mmt) cc_final: 0.8306 (mmm) REVERT: B 126 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: B 219 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6855 (mt-10) REVERT: B 273 MET cc_start: 0.5982 (ttp) cc_final: 0.5689 (ttt) REVERT: B 303 GLU cc_start: 0.7804 (tt0) cc_final: 0.7383 (pt0) REVERT: B 378 ARG cc_start: 0.7755 (mtt180) cc_final: 0.6996 (ttt180) REVERT: B 419 MET cc_start: 0.8584 (mmt) cc_final: 0.8296 (mmm) REVERT: C 126 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: C 219 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6838 (mt-10) REVERT: C 273 MET cc_start: 0.6099 (ttp) cc_final: 0.5814 (ttt) REVERT: C 303 GLU cc_start: 0.7783 (tt0) cc_final: 0.7358 (pt0) REVERT: C 378 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7017 (ttt180) REVERT: C 419 MET cc_start: 0.8623 (mmt) cc_final: 0.8338 (mmm) REVERT: D 126 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: D 219 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6834 (mt-10) REVERT: D 303 GLU cc_start: 0.7813 (tt0) cc_final: 0.7389 (pt0) REVERT: D 378 ARG cc_start: 0.7766 (mtt180) cc_final: 0.6996 (ttt180) REVERT: D 419 MET cc_start: 0.8582 (mmt) cc_final: 0.8292 (mmm) outliers start: 25 outliers final: 8 residues processed: 150 average time/residue: 0.8469 time to fit residues: 135.7590 Evaluate side-chains 156 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 362 MET 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 3 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 150 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 HIS C 358 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.199813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146359 restraints weight = 11966.639| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.83 r_work: 0.3428 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13360 Z= 0.232 Angle : 0.631 9.582 18020 Z= 0.311 Chirality : 0.040 0.162 2140 Planarity : 0.005 0.043 2088 Dihedral : 12.135 66.965 2728 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 11.65 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.21 (0.21), residues: 1548 helix: 2.68 (0.14), residues: 1264 sheet: 0.27 (0.64), residues: 80 loop : -0.88 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 298 TYR 0.021 0.002 TYR C 124 PHE 0.015 0.002 PHE A 203 TRP 0.003 0.001 TRP B 193 HIS 0.004 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00597 (13360) covalent geometry : angle 0.63121 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.06079 ( 1072) hydrogen bonds : angle 3.81185 ( 3180) ********************** 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 167 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6869 (mt-10) REVERT: A 303 GLU cc_start: 0.7835 (tt0) cc_final: 0.7363 (pt0) REVERT: A 378 ARG cc_start: 0.7750 (mtt180) cc_final: 0.6962 (ttt180) REVERT: A 419 MET cc_start: 0.8669 (mmt) cc_final: 0.8348 (mmm) REVERT: B 216 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 219 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6855 (mt-10) REVERT: B 273 MET cc_start: 0.5999 (ttp) cc_final: 0.5684 (ttt) REVERT: B 303 GLU cc_start: 0.7847 (tt0) cc_final: 0.7385 (pt0) REVERT: B 378 ARG cc_start: 0.7750 (mtt180) cc_final: 0.6964 (ttt180) REVERT: B 419 MET cc_start: 0.8669 (mmt) cc_final: 0.8349 (mmm) REVERT: C 193 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8259 (m100) REVERT: C 219 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6848 (mt-10) REVERT: C 303 GLU cc_start: 0.7851 (tt0) cc_final: 0.7388 (pt0) REVERT: C 378 ARG cc_start: 0.7736 (mtt180) cc_final: 0.6971 (ttt180) REVERT: C 419 MET cc_start: 0.8682 (mmt) cc_final: 0.8370 (mmm) REVERT: D 193 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.8258 (m100) REVERT: D 216 LEU cc_start: 0.8441 (mp) cc_final: 0.8240 (mt) REVERT: D 219 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6812 (mt-10) REVERT: D 303 GLU cc_start: 0.7826 (tt0) cc_final: 0.7370 (pt0) REVERT: D 378 ARG cc_start: 0.7705 (mtt180) cc_final: 0.6960 (ttt180) REVERT: D 419 MET cc_start: 0.8664 (mmt) cc_final: 0.8344 (mmm) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 0.8219 time to fit residues: 138.7674 Evaluate side-chains 161 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 TRP 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 109 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145399 restraints weight = 11936.373| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.82 r_work: 0.3483 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2995 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= 0.128 Angle : 0.499 5.570 18020 Z= 0.255 Chirality : 0.036 0.152 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.950 59.694 2728 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 11.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.21), residues: 1548 helix: 3.07 (0.14), residues: 1264 sheet: 0.27 (0.62), residues: 80 loop : -0.92 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 298 TYR 0.018 0.001 TYR C 124 PHE 0.015 0.002 PHE D 56 TRP 0.006 0.001 TRP B 193 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd covalent geometry : bond 0.00282 (13360) covalent geometry : angle 0.49969 (18004) SS BOND : angle 0.00000 ( 16) hydrogen bonds : bond 0.04870 ( 1072) hydrogen bonds : angle 3.63093 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.87 seconds wall clock time: 76 minutes 51.35 seconds (4611.35 seconds total)