Starting phenix.real_space_refine on Mon Aug 5 16:15:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_43129_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_43129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_43129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_43129_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/08_2024/8vc1_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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13128 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "D" 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: "B" 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 Chain: "D" 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 Time building chain proxies: 7.27, per 1000 atoms: 0.55 Number of scatterers: 13128 At special positions: 0 Unit cell: (105.41, 105.41, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 24 15.00 O 2280 8.00 N 2032 7.00 C 8660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.54 Conformation dependent library (CDL) restraints added in 2.2 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: 4.05 Time building geometry restraints manager: 5.98 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: 97.32 - 104.67: 237 104.67 - 112.02: 6600 112.02 - 119.37: 4739 119.37 - 126.72: 6300 126.72 - 134.07: 128 Bond angle restraints: 18004 Sorted by residual: angle pdb=" O3P PC7 D 506 " pdb=" P PC7 D 506 " pdb=" O4P PC7 D 506 " ideal model delta sigma weight residual 93.18 109.80 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 C 506 " pdb=" P PC7 C 506 " pdb=" O4P PC7 C 506 " ideal model delta sigma weight residual 93.18 109.80 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 B 506 " pdb=" P PC7 B 506 " pdb=" O4P PC7 B 506 " ideal model delta sigma weight residual 93.18 109.79 -16.61 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O3P PC7 A 506 " pdb=" P PC7 A 506 " pdb=" O4P PC7 A 506 " ideal model delta sigma weight residual 93.18 109.78 -16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O11 PSC C 502 " pdb=" P PSC C 502 " pdb=" O12 PSC C 502 " ideal model delta sigma weight residual 93.08 109.47 -16.39 3.00e+00 1.11e-01 2.98e+01 ... (remaining 17999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 8000 30.12 - 60.24: 390 60.24 - 90.36: 30 90.36 - 120.48: 12 120.48 - 150.60: 4 Dihedral angle restraints: 8436 sinusoidal: 3876 harmonic: 4560 Sorted by residual: dihedral pdb=" CA LEU A 37 " pdb=" C LEU A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU C 37 " pdb=" C LEU C 37 " pdb=" N ARG C 38 " pdb=" CA ARG C 38 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA LEU B 37 " pdb=" C LEU B 37 " pdb=" N ARG B 38 " pdb=" CA ARG B 38 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 8433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1354 0.050 - 0.100: 608 0.100 - 0.150: 142 0.150 - 0.200: 32 0.200 - 0.250: 4 Chirality restraints: 2140 Sorted by residual: chirality pdb=" C02 PSC A 501 " pdb=" C01 PSC A 501 " pdb=" C03 PSC A 501 " pdb=" O01 PSC A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.62 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C02 PSC B 501 " pdb=" C01 PSC B 501 " pdb=" C03 PSC B 501 " pdb=" O01 PSC B 501 " both_signs ideal model delta sigma weight residual False 2.37 2.61 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C02 PSC D 501 " pdb=" C01 PSC D 501 " pdb=" C03 PSC D 501 " pdb=" O01 PSC D 501 " both_signs ideal model delta sigma weight residual False 2.37 2.61 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2137 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 124 " -0.016 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR A 124 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 124 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 124 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 124 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 124 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 124 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 124 " 0.017 2.00e-02 2.50e+03 1.68e-02 5.61e+00 pdb=" CG TYR C 124 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 124 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 124 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 124 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 124 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR C 124 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 124 " 0.016 2.00e-02 2.50e+03 1.67e-02 5.56e+00 pdb=" CG TYR B 124 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 124 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 124 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 124 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 124 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 124 " -0.009 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 919 2.74 - 3.28: 13555 3.28 - 3.82: 21479 3.82 - 4.36: 26609 4.36 - 4.90: 47138 Nonbonded interactions: 109700 Sorted by model distance: nonbonded pdb=" OE2 GLU B 375 " pdb=" NH1 ARG B 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU C 375 " pdb=" NH1 ARG C 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU A 375 " pdb=" NH1 ARG A 378 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU D 375 " pdb=" NH1 ARG D 378 " model vdw 2.197 3.120 nonbonded pdb=" NZ LYS A 146 " pdb=" O4P PC7 A 506 " model vdw 2.341 3.120 ... (remaining 109695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.540 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: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.600 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.100 13360 Z= 0.784 Angle : 1.459 16.620 18004 Z= 0.644 Chirality : 0.059 0.250 2140 Planarity : 0.010 0.092 2088 Dihedral : 17.034 150.597 5492 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 1548 helix: -0.46 (0.12), residues: 1244 sheet: -1.27 (0.54), residues: 88 loop : -0.57 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP D 354 HIS 0.009 0.004 HIS D 307 PHE 0.031 0.003 PHE A 271 TYR 0.036 0.005 TYR A 124 ARG 0.013 0.003 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.401 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: 1.5152 time to fit residues: 230.4129 Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13360 Z= 0.226 Angle : 0.631 7.086 18004 Z= 0.320 Chirality : 0.039 0.154 2140 Planarity : 0.005 0.038 2088 Dihedral : 16.753 139.354 2736 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.26 % Allowed : 3.49 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.21), residues: 1548 helix: 2.00 (0.14), residues: 1264 sheet: -0.76 (0.59), residues: 88 loop : 0.26 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 354 HIS 0.004 0.001 HIS D 307 PHE 0.021 0.002 PHE C 56 TYR 0.019 0.002 TYR B 124 ARG 0.004 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7654 (mmt) cc_final: 0.7281 (mtt) REVERT: B 133 ARG cc_start: 0.7076 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: B 373 MET cc_start: 0.7705 (mmt) cc_final: 0.7283 (mtt) REVERT: B 419 MET cc_start: 0.8822 (mmt) cc_final: 0.8553 (mmm) REVERT: C 373 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7385 (mtt) REVERT: C 378 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7321 (ttt180) REVERT: C 419 MET cc_start: 0.8837 (mmt) cc_final: 0.8567 (mmm) REVERT: D 373 MET cc_start: 0.7728 (mmt) cc_final: 0.7318 (mtt) REVERT: D 378 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7329 (ttt180) REVERT: D 419 MET cc_start: 0.8816 (mmt) cc_final: 0.8548 (mmm) outliers start: 17 outliers final: 4 residues processed: 142 average time/residue: 1.5889 time to fit residues: 242.9159 Evaluate side-chains 127 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 78 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13360 Z= 0.454 Angle : 0.713 11.002 18004 Z= 0.351 Chirality : 0.044 0.172 2140 Planarity : 0.005 0.051 2088 Dihedral : 15.504 143.134 2728 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.23 % Allowed : 8.46 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1548 helix: 1.93 (0.14), residues: 1264 sheet: -1.36 (0.65), residues: 48 loop : -0.20 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 193 HIS 0.005 0.002 HIS C 392 PHE 0.024 0.003 PHE D 205 TYR 0.024 0.002 TYR D 124 ARG 0.004 0.001 ARG D 117 *********************** 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 179 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 303 GLU cc_start: 0.7484 (tt0) cc_final: 0.7187 (pt0) REVERT: A 378 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7288 (ttt180) REVERT: A 419 MET cc_start: 0.8795 (mmt) cc_final: 0.8524 (mmm) REVERT: B 200 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 219 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7019 (mt-10) REVERT: B 303 GLU cc_start: 0.7474 (tt0) cc_final: 0.7165 (pt0) REVERT: B 378 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7291 (ttt180) REVERT: B 419 MET cc_start: 0.8851 (mmt) cc_final: 0.8568 (mmm) REVERT: C 200 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 303 GLU cc_start: 0.7464 (tt0) cc_final: 0.7155 (pt0) REVERT: C 378 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7292 (ttt180) REVERT: C 419 MET cc_start: 0.8849 (mmt) cc_final: 0.8570 (mmm) REVERT: D 200 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7678 (mt-10) REVERT: D 219 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7077 (mt-10) REVERT: D 273 MET cc_start: 0.6101 (ttp) cc_final: 0.5883 (ttt) REVERT: D 303 GLU cc_start: 0.7463 (tt0) cc_final: 0.7160 (pt0) REVERT: D 378 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7292 (ttt180) REVERT: D 419 MET cc_start: 0.8854 (mmt) cc_final: 0.8574 (mmm) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 1.6184 time to fit residues: 277.5141 Evaluate side-chains 161 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL 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 129 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 129 VAL 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 140 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13360 Z= 0.256 Angle : 0.547 6.478 18004 Z= 0.280 Chirality : 0.037 0.153 2140 Planarity : 0.005 0.038 2088 Dihedral : 14.798 137.527 2728 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 8.31 % Favored : 88.95 % 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: 2.86 (0.21), residues: 1548 helix: 2.46 (0.14), residues: 1264 sheet: -0.59 (0.59), residues: 88 loop : -0.78 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 193 HIS 0.002 0.001 HIS A 358 PHE 0.019 0.002 PHE A 205 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG B 385 *********************** 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 181 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.8075 (m100) REVERT: A 200 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 219 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6984 (mt-10) REVERT: A 303 GLU cc_start: 0.7424 (tt0) cc_final: 0.7112 (pt0) REVERT: A 378 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7299 (ttt180) REVERT: A 419 MET cc_start: 0.8722 (mmt) cc_final: 0.8501 (mmm) REVERT: B 193 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8074 (m100) REVERT: B 200 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7603 (mt-10) REVERT: B 219 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6964 (mt-10) REVERT: B 303 GLU cc_start: 0.7391 (tt0) cc_final: 0.7109 (pt0) REVERT: B 378 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7299 (ttt180) REVERT: B 419 MET cc_start: 0.8791 (mmt) cc_final: 0.8470 (mmm) REVERT: C 193 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.8069 (m100) REVERT: C 200 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 216 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mt) REVERT: C 219 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6956 (mt-10) REVERT: C 303 GLU cc_start: 0.7380 (tt0) cc_final: 0.7076 (pt0) REVERT: C 378 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7302 (ttt180) REVERT: C 419 MET cc_start: 0.8790 (mmt) cc_final: 0.8472 (mmm) REVERT: D 193 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.8068 (m100) REVERT: D 200 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7598 (mt-10) REVERT: D 216 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8416 (mt) REVERT: D 219 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6998 (mt-10) REVERT: D 273 MET cc_start: 0.6051 (ttp) cc_final: 0.5850 (ttt) REVERT: D 303 GLU cc_start: 0.7376 (tt0) cc_final: 0.7062 (pt0) REVERT: D 378 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7300 (ttt180) REVERT: D 419 MET cc_start: 0.8793 (mmt) cc_final: 0.8471 (mmm) outliers start: 37 outliers final: 16 residues processed: 164 average time/residue: 1.6039 time to fit residues: 281.5869 Evaluate side-chains 167 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 193 TRP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13360 Z= 0.234 Angle : 0.525 6.622 18004 Z= 0.267 Chirality : 0.037 0.144 2140 Planarity : 0.004 0.039 2088 Dihedral : 14.194 128.113 2728 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.37 % Allowed : 9.50 % Favored : 88.13 % 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: 3.16 (0.21), residues: 1548 helix: 2.69 (0.14), residues: 1264 sheet: -0.46 (0.61), residues: 88 loop : -0.91 (0.45), residues: 196 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 0.017 0.002 PHE C 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG A 298 *********************** 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 189 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3921 (mmm) REVERT: A 193 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.8125 (m100) REVERT: A 200 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 219 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6869 (mt-10) REVERT: A 303 GLU cc_start: 0.7378 (tt0) cc_final: 0.7053 (pt0) REVERT: A 378 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7298 (ttt180) REVERT: A 419 MET cc_start: 0.8720 (mmt) cc_final: 0.8477 (mmm) REVERT: B 87 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.3680 (mmm) REVERT: B 193 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8130 (m100) REVERT: B 200 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 303 GLU cc_start: 0.7371 (tt0) cc_final: 0.7054 (pt0) REVERT: B 378 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7292 (ttt180) REVERT: B 419 MET cc_start: 0.8769 (mmt) cc_final: 0.8428 (mmm) REVERT: C 193 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.8132 (m100) REVERT: C 200 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 219 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6855 (mt-10) REVERT: C 303 GLU cc_start: 0.7378 (tt0) cc_final: 0.7052 (pt0) REVERT: C 378 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7305 (ttt180) REVERT: C 419 MET cc_start: 0.8762 (mmt) cc_final: 0.8423 (mmm) REVERT: D 87 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3838 (mmm) REVERT: D 193 TRP cc_start: 0.8487 (OUTLIER) cc_final: 0.8126 (m100) REVERT: D 200 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 216 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (mt) REVERT: D 219 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6875 (mt-10) REVERT: D 273 MET cc_start: 0.6062 (ttp) cc_final: 0.5851 (ttt) REVERT: D 303 GLU cc_start: 0.7357 (tt0) cc_final: 0.7050 (pt0) REVERT: D 378 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7304 (ttt180) REVERT: D 419 MET cc_start: 0.8764 (mmt) cc_final: 0.8422 (mmm) outliers start: 32 outliers final: 13 residues processed: 176 average time/residue: 1.6246 time to fit residues: 306.7351 Evaluate side-chains 173 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 102 VAL 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 87 MET Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP 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 193 TRP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 193 TRP 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 50 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13360 Z= 0.234 Angle : 0.522 6.377 18004 Z= 0.266 Chirality : 0.037 0.143 2140 Planarity : 0.004 0.040 2088 Dihedral : 13.112 110.486 2728 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.52 % Allowed : 9.79 % 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: 3.31 (0.21), residues: 1548 helix: 2.80 (0.14), residues: 1264 sheet: -0.42 (0.62), residues: 88 loop : -0.91 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS B 392 PHE 0.019 0.002 PHE D 205 TYR 0.018 0.001 TYR D 124 ARG 0.002 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 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 186 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.3890 (mmm) REVERT: A 193 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8131 (m100) REVERT: A 200 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 219 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6875 (mt-10) REVERT: A 303 GLU cc_start: 0.7384 (tt0) cc_final: 0.7048 (pt0) REVERT: A 336 MET cc_start: 0.7136 (mmp) cc_final: 0.6918 (mmp) REVERT: A 378 ARG cc_start: 0.7593 (mtt180) cc_final: 0.7273 (ttt180) REVERT: A 419 MET cc_start: 0.8730 (mmt) cc_final: 0.8458 (mmm) REVERT: B 193 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.8125 (m100) REVERT: B 200 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 219 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6869 (mt-10) REVERT: B 303 GLU cc_start: 0.7385 (tt0) cc_final: 0.7056 (pt0) REVERT: B 378 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7281 (ttt180) REVERT: B 419 MET cc_start: 0.8765 (mmt) cc_final: 0.8454 (mmm) REVERT: C 193 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (m100) REVERT: C 219 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6877 (mt-10) REVERT: C 303 GLU cc_start: 0.7380 (tt0) cc_final: 0.7043 (pt0) REVERT: C 378 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7275 (ttt180) REVERT: C 419 MET cc_start: 0.8775 (mmt) cc_final: 0.8461 (mmm) REVERT: D 193 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.8133 (m100) REVERT: D 200 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 219 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6925 (mt-10) REVERT: D 303 GLU cc_start: 0.7356 (tt0) cc_final: 0.7034 (pt0) REVERT: D 336 MET cc_start: 0.7131 (mmp) cc_final: 0.6898 (mmp) REVERT: D 378 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7275 (ttt180) REVERT: D 419 MET cc_start: 0.8769 (mmt) cc_final: 0.8456 (mmm) outliers start: 34 outliers final: 17 residues processed: 171 average time/residue: 1.6037 time to fit residues: 293.7791 Evaluate side-chains 166 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 102 VAL 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 91 MET Chi-restraints excluded: chain B residue 102 VAL 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 B residue 423 ASP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13360 Z= 0.313 Angle : 0.573 8.183 18004 Z= 0.286 Chirality : 0.038 0.152 2140 Planarity : 0.005 0.041 2088 Dihedral : 12.867 98.815 2728 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.04 % Allowed : 10.09 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.11 (0.21), residues: 1548 helix: 2.66 (0.14), residues: 1264 sheet: -0.33 (0.62), residues: 88 loop : -1.04 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 193 HIS 0.003 0.001 HIS B 392 PHE 0.020 0.002 PHE D 205 TYR 0.020 0.002 TYR A 124 ARG 0.003 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.8118 (m100) REVERT: A 200 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 219 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6936 (mt-10) REVERT: A 303 GLU cc_start: 0.7409 (tt0) cc_final: 0.7056 (pt0) REVERT: A 378 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7260 (ttt180) REVERT: A 419 MET cc_start: 0.8743 (mmt) cc_final: 0.8458 (mmm) REVERT: B 193 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.8103 (m100) REVERT: B 200 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 219 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6900 (mt-10) REVERT: B 303 GLU cc_start: 0.7410 (tt0) cc_final: 0.7059 (pt0) REVERT: B 378 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7261 (ttt180) REVERT: B 419 MET cc_start: 0.8788 (mmt) cc_final: 0.8473 (mmm) REVERT: C 193 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.8115 (m100) REVERT: C 219 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6891 (mt-10) REVERT: C 303 GLU cc_start: 0.7406 (tt0) cc_final: 0.7051 (pt0) REVERT: C 378 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7259 (ttt180) REVERT: C 419 MET cc_start: 0.8773 (mmt) cc_final: 0.8458 (mmm) REVERT: D 193 TRP cc_start: 0.8526 (OUTLIER) cc_final: 0.8120 (m100) REVERT: D 200 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 216 LEU cc_start: 0.8607 (mt) cc_final: 0.8391 (mt) REVERT: D 303 GLU cc_start: 0.7407 (tt0) cc_final: 0.7054 (pt0) REVERT: D 378 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7259 (ttt180) REVERT: D 419 MET cc_start: 0.8779 (mmt) cc_final: 0.8463 (mmm) outliers start: 41 outliers final: 20 residues processed: 172 average time/residue: 1.6046 time to fit residues: 296.3242 Evaluate side-chains 167 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 193 TRP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 423 ASP 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 C residue 193 TRP Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2823 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= 0.195 Angle : 0.496 5.227 18004 Z= 0.254 Chirality : 0.036 0.143 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.381 82.836 2728 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.15 % Allowed : 11.57 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.21), residues: 1548 helix: 2.96 (0.14), residues: 1264 sheet: -0.24 (0.63), residues: 88 loop : -0.98 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.002 0.001 HIS C 358 PHE 0.017 0.002 PHE C 205 TYR 0.017 0.001 TYR A 124 ARG 0.001 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6871 (mt-10) REVERT: A 303 GLU cc_start: 0.7379 (tt0) cc_final: 0.7040 (pt0) REVERT: A 378 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7274 (ttt180) REVERT: A 419 MET cc_start: 0.8709 (mmt) cc_final: 0.8409 (mmm) REVERT: B 193 TRP cc_start: 0.8468 (OUTLIER) cc_final: 0.8114 (m100) REVERT: B 219 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6867 (mt-10) REVERT: B 303 GLU cc_start: 0.7383 (tt0) cc_final: 0.7054 (pt0) REVERT: B 378 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7275 (ttt180) REVERT: B 419 MET cc_start: 0.8740 (mmt) cc_final: 0.8408 (mmm) REVERT: C 193 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.8112 (m100) REVERT: C 219 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6871 (mt-10) REVERT: C 303 GLU cc_start: 0.7379 (tt0) cc_final: 0.7035 (pt0) REVERT: C 378 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7276 (ttt180) REVERT: C 419 MET cc_start: 0.8738 (mmt) cc_final: 0.8409 (mmm) REVERT: D 219 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6840 (mt-10) REVERT: D 303 GLU cc_start: 0.7384 (tt0) cc_final: 0.7049 (pt0) REVERT: D 378 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7274 (ttt180) REVERT: D 419 MET cc_start: 0.8742 (mmt) cc_final: 0.8411 (mmm) outliers start: 29 outliers final: 15 residues processed: 158 average time/residue: 1.7028 time to fit residues: 287.9904 Evaluate side-chains 160 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 91 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 423 ASP 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 C residue 423 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 0.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS D 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2969 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= 0.179 Angle : 0.489 5.051 18004 Z= 0.250 Chirality : 0.035 0.142 2140 Planarity : 0.004 0.041 2088 Dihedral : 12.018 68.169 2728 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.78 % Allowed : 12.31 % Favored : 85.91 % 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: 3.79 (0.21), residues: 1548 helix: 3.11 (0.14), residues: 1264 sheet: 0.47 (0.65), residues: 80 loop : -0.91 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.003 0.001 HIS B 392 PHE 0.017 0.002 PHE C 205 TYR 0.017 0.001 TYR D 124 ARG 0.002 0.000 ARG D 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6828 (mt-10) REVERT: A 303 GLU cc_start: 0.7364 (tt0) cc_final: 0.7039 (pt0) REVERT: A 336 MET cc_start: 0.7134 (mmp) cc_final: 0.6879 (mmt) REVERT: A 378 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7269 (ttt180) REVERT: A 419 MET cc_start: 0.8684 (mmt) cc_final: 0.8380 (mmm) REVERT: B 219 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6832 (mt-10) REVERT: B 303 GLU cc_start: 0.7354 (tt0) cc_final: 0.7052 (pt0) REVERT: B 378 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7264 (ttt180) REVERT: B 419 MET cc_start: 0.8707 (mmt) cc_final: 0.8428 (mmm) REVERT: C 219 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6831 (mt-10) REVERT: C 303 GLU cc_start: 0.7364 (tt0) cc_final: 0.7037 (pt0) REVERT: C 378 ARG cc_start: 0.7572 (mtt180) cc_final: 0.7276 (ttt180) REVERT: C 419 MET cc_start: 0.8743 (mmt) cc_final: 0.8465 (mmm) REVERT: D 219 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6832 (mt-10) REVERT: D 303 GLU cc_start: 0.7350 (tt0) cc_final: 0.7048 (pt0) REVERT: D 336 MET cc_start: 0.7152 (mmp) cc_final: 0.6895 (mmt) REVERT: D 378 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7266 (ttt180) REVERT: D 419 MET cc_start: 0.8746 (mmt) cc_final: 0.8464 (mmm) outliers start: 24 outliers final: 10 residues processed: 145 average time/residue: 1.7225 time to fit residues: 266.8168 Evaluate side-chains 150 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13360 Z= 0.257 Angle : 0.540 6.900 18004 Z= 0.272 Chirality : 0.037 0.147 2140 Planarity : 0.004 0.041 2088 Dihedral : 12.034 67.852 2728 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 12.98 % Favored : 85.68 % 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: 3.59 (0.21), residues: 1548 helix: 2.95 (0.14), residues: 1264 sheet: 0.46 (0.64), residues: 80 loop : -0.87 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.002 0.001 HIS A 392 PHE 0.019 0.002 PHE C 205 TYR 0.019 0.001 TYR D 124 ARG 0.003 0.000 ARG D 298 ********************** 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 154 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6901 (mt-10) REVERT: A 303 GLU cc_start: 0.7402 (tt0) cc_final: 0.7064 (pt0) REVERT: A 336 MET cc_start: 0.7154 (mmp) cc_final: 0.6922 (mmt) REVERT: A 378 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7261 (ttt180) REVERT: A 419 MET cc_start: 0.8690 (mmt) cc_final: 0.8391 (mmm) REVERT: B 126 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: B 193 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.8138 (m100) REVERT: B 219 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6861 (mt-10) REVERT: B 303 GLU cc_start: 0.7409 (tt0) cc_final: 0.7071 (pt0) REVERT: B 378 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7261 (ttt180) REVERT: B 419 MET cc_start: 0.8746 (mmt) cc_final: 0.8410 (mmm) REVERT: C 219 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6863 (mt-10) REVERT: C 303 GLU cc_start: 0.7399 (tt0) cc_final: 0.7062 (pt0) REVERT: C 378 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7265 (ttt180) REVERT: C 419 MET cc_start: 0.8743 (mmt) cc_final: 0.8413 (mmm) REVERT: D 219 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6868 (mt-10) REVERT: D 303 GLU cc_start: 0.7409 (tt0) cc_final: 0.7066 (pt0) REVERT: D 336 MET cc_start: 0.7128 (mmp) cc_final: 0.6891 (mmt) REVERT: D 378 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7261 (ttt180) REVERT: D 419 MET cc_start: 0.8747 (mmt) cc_final: 0.8412 (mmm) outliers start: 18 outliers final: 11 residues processed: 142 average time/residue: 1.7855 time to fit residues: 270.3591 Evaluate side-chains 148 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142070 restraints weight = 12010.820| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.90 r_work: 0.3542 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3084 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= 0.171 Angle : 0.484 5.016 18004 Z= 0.248 Chirality : 0.035 0.138 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.782 59.948 2728 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.63 % Allowed : 12.91 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.90 (0.21), residues: 1548 helix: 3.18 (0.14), residues: 1264 sheet: 0.43 (0.63), residues: 80 loop : -0.80 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 193 HIS 0.002 0.001 HIS C 358 PHE 0.017 0.002 PHE C 205 TYR 0.017 0.001 TYR D 124 ARG 0.001 0.000 ARG A 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.53 seconds wall clock time: 84 minutes 14.38 seconds (5054.38 seconds total)