Starting phenix.real_space_refine on Sun Jul 21 08:38:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/07_2024/8vc1_43129_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/07_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_43129/07_2024/8vc1_43129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/07_2024/8vc1_43129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/07_2024/8vc1_43129_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/07_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-5388/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: 7.82, per 1000 atoms: 0.60 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: 5.11 Conformation dependent library (CDL) restraints added in 2.3 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 83.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 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: 3.97 Time building geometry restraints manager: 5.57 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 2.520 nonbonded pdb=" OE2 GLU C 375 " pdb=" NH1 ARG C 378 " model vdw 2.196 2.520 nonbonded pdb=" OE2 GLU A 375 " pdb=" NH1 ARG A 378 " model vdw 2.196 2.520 nonbonded pdb=" OE2 GLU D 375 " pdb=" NH1 ARG D 378 " model vdw 2.197 2.520 nonbonded pdb=" NZ LYS A 146 " pdb=" O4P PC7 A 506 " model vdw 2.341 2.520 ... (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 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: 1.010 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.600 Find NCS groups from input model: 0.770 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- 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 : 1.299 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: 1.4635 time to fit residues: 222.6846 Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 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: 0.7664 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13360 Z= 0.216 Angle : 0.621 6.653 18004 Z= 0.316 Chirality : 0.038 0.154 2140 Planarity : 0.004 0.037 2088 Dihedral : 16.903 139.113 2736 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.78 % Allowed : 3.93 % Favored : 94.29 % 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: 2.47 (0.21), residues: 1548 helix: 2.04 (0.14), residues: 1264 sheet: -0.75 (0.58), residues: 88 loop : 0.31 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 193 HIS 0.003 0.001 HIS A 307 PHE 0.022 0.002 PHE A 56 TYR 0.018 0.002 TYR B 124 ARG 0.003 0.001 ARG D 296 *********************** 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 156 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7299 (mtt) REVERT: A 419 MET cc_start: 0.8820 (mmt) cc_final: 0.8573 (mmm) REVERT: B 133 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6785 (mtm-85) REVERT: B 373 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7298 (mtt) REVERT: B 419 MET cc_start: 0.8832 (mmt) cc_final: 0.8585 (mmm) REVERT: C 373 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7366 (mtt) REVERT: C 419 MET cc_start: 0.8842 (mmt) cc_final: 0.8591 (mmm) REVERT: D 273 MET cc_start: 0.6192 (ttp) cc_final: 0.5905 (ttt) REVERT: D 373 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7351 (mtt) REVERT: D 419 MET cc_start: 0.8827 (mmt) cc_final: 0.8577 (mmm) outliers start: 24 outliers final: 9 residues processed: 137 average time/residue: 1.5878 time to fit residues: 233.8346 Evaluate side-chains 131 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain D residue 129 VAL 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 78 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13360 Z= 0.447 Angle : 0.714 11.317 18004 Z= 0.351 Chirality : 0.043 0.176 2140 Planarity : 0.005 0.051 2088 Dihedral : 15.547 143.735 2728 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.08 % Allowed : 8.31 % Favored : 89.61 % 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: 2.31 (0.21), residues: 1548 helix: 1.96 (0.14), residues: 1264 sheet: -1.13 (0.67), residues: 48 loop : -0.15 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 180 HIS 0.005 0.002 HIS D 307 PHE 0.025 0.003 PHE C 205 TYR 0.024 0.002 TYR D 124 ARG 0.004 0.001 ARG C 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 177 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 303 GLU cc_start: 0.7481 (tt0) cc_final: 0.7145 (pt0) REVERT: A 378 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7284 (ttt180) REVERT: A 419 MET cc_start: 0.8858 (mmt) cc_final: 0.8583 (mmm) REVERT: B 133 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6885 (mtp180) REVERT: B 200 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 219 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7112 (mt-10) REVERT: B 303 GLU cc_start: 0.7498 (tt0) cc_final: 0.7174 (pt0) REVERT: B 378 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7281 (ttt180) REVERT: B 419 MET cc_start: 0.8842 (mmt) cc_final: 0.8528 (mmm) REVERT: C 200 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 303 GLU cc_start: 0.7486 (tt0) cc_final: 0.7191 (pt0) REVERT: C 378 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7295 (ttt180) REVERT: C 419 MET cc_start: 0.8844 (mmt) cc_final: 0.8536 (mmm) REVERT: D 91 MET cc_start: 0.5468 (tpt) cc_final: 0.5243 (tpt) REVERT: D 200 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 219 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7148 (mt-10) REVERT: D 303 GLU cc_start: 0.7504 (tt0) cc_final: 0.7172 (pt0) REVERT: D 378 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7290 (ttt180) REVERT: D 419 MET cc_start: 0.8847 (mmt) cc_final: 0.8535 (mmm) outliers start: 28 outliers final: 14 residues processed: 156 average time/residue: 1.5739 time to fit residues: 263.4094 Evaluate side-chains 155 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL 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 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 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: 2.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.2315 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= 0.250 Angle : 0.538 6.481 18004 Z= 0.274 Chirality : 0.037 0.151 2140 Planarity : 0.004 0.039 2088 Dihedral : 14.828 137.640 2728 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.45 % Allowed : 8.46 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.21), residues: 1548 helix: 2.53 (0.14), residues: 1264 sheet: -0.51 (0.60), residues: 88 loop : -0.73 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 307 PHE 0.019 0.002 PHE D 205 TYR 0.018 0.001 TYR B 124 ARG 0.003 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.8138 (m100) REVERT: A 200 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 303 GLU cc_start: 0.7470 (tt0) cc_final: 0.7152 (pt0) REVERT: A 373 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7066 (mtt) REVERT: A 378 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7261 (ttt180) REVERT: A 419 MET cc_start: 0.8786 (mmt) cc_final: 0.8476 (mmm) REVERT: B 193 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.8062 (m100) REVERT: B 200 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 219 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7031 (mt-10) REVERT: B 303 GLU cc_start: 0.7467 (tt0) cc_final: 0.7159 (pt0) REVERT: B 373 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7103 (mtt) REVERT: B 378 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7263 (ttt180) REVERT: B 419 MET cc_start: 0.8782 (mmt) cc_final: 0.8472 (mmm) REVERT: C 193 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.8138 (m100) REVERT: C 200 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 303 GLU cc_start: 0.7463 (tt0) cc_final: 0.7148 (pt0) REVERT: C 373 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7434 (mtt) REVERT: C 378 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7265 (ttt180) REVERT: C 419 MET cc_start: 0.8781 (mmt) cc_final: 0.8478 (mmm) REVERT: D 91 MET cc_start: 0.5515 (tpt) cc_final: 0.5225 (tpt) REVERT: D 193 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.8137 (m100) REVERT: D 200 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 219 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6991 (mt-10) REVERT: D 303 GLU cc_start: 0.7465 (tt0) cc_final: 0.7153 (pt0) REVERT: D 378 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7265 (ttt180) REVERT: D 419 MET cc_start: 0.8784 (mmt) cc_final: 0.8469 (mmm) outliers start: 33 outliers final: 10 residues processed: 157 average time/residue: 1.6285 time to fit residues: 273.2462 Evaluate side-chains 160 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 373 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 MET 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 373 MET Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=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: 0.7980 chunk 62 optimal weight: 0.9990 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: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.192 Angle : 0.496 6.153 18004 Z= 0.253 Chirality : 0.036 0.142 2140 Planarity : 0.004 0.039 2088 Dihedral : 13.946 124.408 2728 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.67 % Allowed : 9.64 % 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: 3.44 (0.21), residues: 1548 helix: 2.87 (0.14), residues: 1264 sheet: -0.40 (0.61), residues: 88 loop : -0.70 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS C 307 PHE 0.019 0.002 PHE B 205 TYR 0.017 0.001 TYR A 124 ARG 0.003 0.000 ARG B 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 191 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8460 (OUTLIER) cc_final: 0.8098 (m100) REVERT: A 200 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 303 GLU cc_start: 0.7385 (tt0) cc_final: 0.7073 (pt0) REVERT: A 378 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7208 (ttt180) REVERT: A 419 MET cc_start: 0.8747 (mmt) cc_final: 0.8421 (mmm) REVERT: B 193 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.8102 (m100) REVERT: B 200 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 219 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6887 (mt-10) REVERT: B 303 GLU cc_start: 0.7389 (tt0) cc_final: 0.7083 (pt0) REVERT: B 378 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7233 (ttt180) REVERT: B 419 MET cc_start: 0.8755 (mmt) cc_final: 0.8437 (mmm) REVERT: C 193 TRP cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (m100) REVERT: C 200 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 219 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6921 (mt-10) REVERT: C 303 GLU cc_start: 0.7387 (tt0) cc_final: 0.7074 (pt0) REVERT: C 378 ARG cc_start: 0.7474 (mtt180) cc_final: 0.7233 (ttt180) REVERT: C 419 MET cc_start: 0.8752 (mmt) cc_final: 0.8437 (mmm) REVERT: D 193 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.8101 (m100) REVERT: D 200 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7588 (mt-10) REVERT: D 303 GLU cc_start: 0.7386 (tt0) cc_final: 0.7082 (pt0) REVERT: D 378 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7254 (ttt180) REVERT: D 419 MET cc_start: 0.8754 (mmt) cc_final: 0.8435 (mmm) outliers start: 36 outliers final: 15 residues processed: 174 average time/residue: 1.6153 time to fit residues: 301.5993 Evaluate side-chains 170 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LEU Chi-restraints excluded: chain A residue 273 MET 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 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 216 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13360 Z= 0.177 Angle : 0.484 6.212 18004 Z= 0.247 Chirality : 0.035 0.139 2140 Planarity : 0.004 0.040 2088 Dihedral : 13.013 106.668 2728 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.67 % Allowed : 9.72 % Favored : 87.61 % 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: 3.73 (0.21), residues: 1548 helix: 3.08 (0.14), residues: 1264 sheet: -0.32 (0.62), residues: 88 loop : -0.63 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 193 HIS 0.002 0.000 HIS C 392 PHE 0.018 0.002 PHE B 205 TYR 0.018 0.001 TYR A 124 ARG 0.003 0.000 ARG C 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 182 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.8094 (m100) REVERT: A 303 GLU cc_start: 0.7382 (tt0) cc_final: 0.7077 (pt0) REVERT: A 378 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7206 (ttt180) REVERT: A 419 MET cc_start: 0.8778 (mmt) cc_final: 0.8439 (mmm) REVERT: B 193 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.8092 (m100) REVERT: B 303 GLU cc_start: 0.7383 (tt0) cc_final: 0.7081 (pt0) REVERT: B 336 MET cc_start: 0.7130 (mmp) cc_final: 0.6876 (mmt) REVERT: B 378 ARG cc_start: 0.7436 (mtt180) cc_final: 0.7230 (ttt180) REVERT: B 419 MET cc_start: 0.8770 (mmt) cc_final: 0.8433 (mmm) REVERT: C 193 TRP cc_start: 0.8460 (OUTLIER) cc_final: 0.8095 (m100) REVERT: C 303 GLU cc_start: 0.7381 (tt0) cc_final: 0.7074 (pt0) REVERT: C 378 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7207 (ttt180) REVERT: C 419 MET cc_start: 0.8766 (mmt) cc_final: 0.8438 (mmm) REVERT: D 193 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.8095 (m100) REVERT: D 303 GLU cc_start: 0.7389 (tt0) cc_final: 0.7079 (pt0) REVERT: D 378 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7225 (ttt180) REVERT: D 419 MET cc_start: 0.8769 (mmt) cc_final: 0.8433 (mmm) outliers start: 36 outliers final: 19 residues processed: 162 average time/residue: 1.7293 time to fit residues: 299.1543 Evaluate side-chains 165 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET 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 216 LEU Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 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 126 GLU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU 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 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 145 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 93 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 D 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2827 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= 0.180 Angle : 0.485 5.425 18004 Z= 0.246 Chirality : 0.035 0.140 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.142 78.136 2728 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.82 % Allowed : 10.46 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.21), residues: 1548 helix: 3.19 (0.14), residues: 1264 sheet: -0.38 (0.60), residues: 88 loop : -0.63 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 193 HIS 0.002 0.000 HIS D 370 PHE 0.019 0.002 PHE C 205 TYR 0.018 0.001 TYR B 124 ARG 0.002 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 190 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.3770 (mmm) REVERT: A 216 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8346 (mt) REVERT: A 219 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6859 (mt-10) REVERT: A 303 GLU cc_start: 0.7388 (tt0) cc_final: 0.7080 (pt0) REVERT: A 419 MET cc_start: 0.8756 (mmt) cc_final: 0.8450 (mmm) REVERT: B 219 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6843 (mt-10) REVERT: B 303 GLU cc_start: 0.7395 (tt0) cc_final: 0.7089 (pt0) REVERT: B 378 ARG cc_start: 0.7422 (mtt180) cc_final: 0.7217 (ttt180) REVERT: B 419 MET cc_start: 0.8760 (mmt) cc_final: 0.8461 (mmm) REVERT: C 219 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6860 (mt-10) REVERT: C 303 GLU cc_start: 0.7389 (tt0) cc_final: 0.7077 (pt0) REVERT: C 378 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7212 (ttt180) REVERT: C 419 MET cc_start: 0.8747 (mmt) cc_final: 0.8450 (mmm) REVERT: D 219 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6839 (mt-10) REVERT: D 303 GLU cc_start: 0.7390 (tt0) cc_final: 0.7084 (pt0) REVERT: D 378 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7213 (ttt180) REVERT: D 419 MET cc_start: 0.8751 (mmt) cc_final: 0.8451 (mmm) outliers start: 38 outliers final: 17 residues processed: 164 average time/residue: 1.6177 time to fit residues: 284.0917 Evaluate side-chains 168 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 126 GLU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 216 LEU 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 216 LEU 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 60 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 D 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2855 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= 0.230 Angle : 0.513 6.546 18004 Z= 0.258 Chirality : 0.036 0.145 2140 Planarity : 0.004 0.041 2088 Dihedral : 12.096 72.483 2728 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.37 % Allowed : 12.02 % Favored : 85.61 % 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: 3.75 (0.21), residues: 1548 helix: 3.11 (0.14), residues: 1264 sheet: -0.41 (0.60), residues: 88 loop : -0.70 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 193 HIS 0.002 0.001 HIS D 370 PHE 0.020 0.002 PHE C 205 TYR 0.019 0.001 TYR B 124 ARG 0.003 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 182 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8146 (mtt-85) REVERT: A 216 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (mt) REVERT: A 219 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6838 (mt-10) REVERT: A 303 GLU cc_start: 0.7429 (tt0) cc_final: 0.7091 (pt0) REVERT: A 336 MET cc_start: 0.7248 (mmp) cc_final: 0.6990 (mmp) REVERT: A 419 MET cc_start: 0.8759 (mmt) cc_final: 0.8448 (mmm) REVERT: B 219 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6876 (mt-10) REVERT: B 303 GLU cc_start: 0.7407 (tt0) cc_final: 0.7083 (pt0) REVERT: B 378 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7213 (ttt180) REVERT: B 419 MET cc_start: 0.8757 (mmt) cc_final: 0.8452 (mmm) REVERT: C 216 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8386 (mt) REVERT: C 219 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6875 (mt-10) REVERT: C 303 GLU cc_start: 0.7429 (tt0) cc_final: 0.7086 (pt0) REVERT: C 378 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7205 (ttt180) REVERT: C 419 MET cc_start: 0.8743 (mmt) cc_final: 0.8443 (mmm) REVERT: D 87 MET cc_start: 0.4553 (OUTLIER) cc_final: 0.3660 (mmm) REVERT: D 219 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6862 (mt-10) REVERT: D 303 GLU cc_start: 0.7410 (tt0) cc_final: 0.7090 (pt0) REVERT: D 419 MET cc_start: 0.8751 (mmt) cc_final: 0.8449 (mmm) outliers start: 32 outliers final: 16 residues processed: 158 average time/residue: 1.6683 time to fit residues: 281.6171 Evaluate side-chains 165 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 216 LEU 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 C residue 126 GLU Chi-restraints excluded: chain C residue 216 LEU 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 126 GLU Chi-restraints excluded: chain D residue 216 LEU 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 131 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 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: 0.7723 moved from start: 0.2939 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= 0.222 Angle : 0.505 5.999 18004 Z= 0.254 Chirality : 0.036 0.144 2140 Planarity : 0.004 0.041 2088 Dihedral : 12.017 65.497 2728 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.08 % Allowed : 12.98 % Favored : 84.94 % 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: 3.78 (0.21), residues: 1548 helix: 3.13 (0.14), residues: 1264 sheet: -0.36 (0.60), residues: 88 loop : -0.75 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 193 HIS 0.003 0.001 HIS C 392 PHE 0.020 0.002 PHE C 205 TYR 0.019 0.001 TYR B 124 ARG 0.003 0.000 ARG C 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 171 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 219 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6786 (mt-10) REVERT: A 303 GLU cc_start: 0.7425 (tt0) cc_final: 0.7084 (pt0) REVERT: A 419 MET cc_start: 0.8732 (mmt) cc_final: 0.8431 (mmm) REVERT: B 216 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8331 (mt) REVERT: B 219 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6862 (mt-10) REVERT: B 303 GLU cc_start: 0.7399 (tt0) cc_final: 0.7076 (pt0) REVERT: B 419 MET cc_start: 0.8746 (mmt) cc_final: 0.8443 (mmm) REVERT: C 216 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8357 (mt) REVERT: C 219 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6866 (mt-10) REVERT: C 303 GLU cc_start: 0.7419 (tt0) cc_final: 0.7077 (pt0) REVERT: C 378 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7201 (ttt180) REVERT: C 419 MET cc_start: 0.8712 (mmt) cc_final: 0.8421 (mmm) REVERT: D 216 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8319 (mt) REVERT: D 219 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6847 (mt-10) REVERT: D 303 GLU cc_start: 0.7406 (tt0) cc_final: 0.7083 (pt0) REVERT: D 419 MET cc_start: 0.8729 (mmt) cc_final: 0.8434 (mmm) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 1.6324 time to fit residues: 264.4153 Evaluate side-chains 161 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 216 LEU 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 C residue 126 GLU Chi-restraints excluded: chain C residue 216 LEU 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 216 LEU 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 148 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13360 Z= 0.193 Angle : 0.488 5.671 18004 Z= 0.247 Chirality : 0.035 0.143 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.880 59.604 2728 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.48 % Allowed : 13.80 % Favored : 84.72 % 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: 3.92 (0.21), residues: 1548 helix: 3.23 (0.14), residues: 1264 sheet: -0.26 (0.61), residues: 88 loop : -0.75 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.002 0.000 HIS D 370 PHE 0.019 0.002 PHE A 205 TYR 0.018 0.001 TYR B 124 ARG 0.003 0.000 ARG A 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 166 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8135 (mtt-85) REVERT: A 216 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 219 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6785 (mt-10) REVERT: A 303 GLU cc_start: 0.7423 (tt0) cc_final: 0.7094 (pt0) REVERT: A 336 MET cc_start: 0.7144 (mmp) cc_final: 0.6891 (mmt) REVERT: A 419 MET cc_start: 0.8713 (mmt) cc_final: 0.8405 (mmm) REVERT: B 126 GLU cc_start: 0.7138 (pt0) cc_final: 0.6872 (mp0) REVERT: B 216 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 219 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6854 (mt-10) REVERT: B 303 GLU cc_start: 0.7396 (tt0) cc_final: 0.7085 (pt0) REVERT: B 419 MET cc_start: 0.8727 (mmt) cc_final: 0.8418 (mmm) REVERT: C 126 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: C 216 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 219 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6851 (mt-10) REVERT: C 303 GLU cc_start: 0.7400 (tt0) cc_final: 0.7072 (pt0) REVERT: C 378 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7204 (ttt180) REVERT: C 419 MET cc_start: 0.8702 (mmt) cc_final: 0.8404 (mmm) REVERT: D 126 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: D 216 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8331 (mt) REVERT: D 219 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6813 (mt-10) REVERT: D 303 GLU cc_start: 0.7390 (tt0) cc_final: 0.7081 (pt0) REVERT: D 419 MET cc_start: 0.8709 (mmt) cc_final: 0.8408 (mmm) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 1.7117 time to fit residues: 282.2598 Evaluate side-chains 162 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 216 LEU 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 C residue 126 GLU Chi-restraints excluded: chain C residue 216 LEU 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 216 LEU 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 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.202680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148284 restraints weight = 11806.869| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.90 r_work: 0.3537 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13360 Z= 0.217 Angle : 0.507 6.123 18004 Z= 0.254 Chirality : 0.036 0.145 2140 Planarity : 0.004 0.041 2088 Dihedral : 11.855 60.212 2728 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.56 % Allowed : 13.65 % Favored : 84.79 % 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: 3.89 (0.21), residues: 1548 helix: 3.18 (0.14), residues: 1264 sheet: -0.16 (0.61), residues: 88 loop : -0.56 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS C 392 PHE 0.020 0.002 PHE A 205 TYR 0.019 0.001 TYR D 124 ARG 0.004 0.000 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4523.62 seconds wall clock time: 80 minutes 1.05 seconds (4801.05 seconds total)