Starting phenix.real_space_refine on Sat Mar 16 00:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/03_2024/8vc1_43129_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/03_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_43129/03_2024/8vc1_43129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/03_2024/8vc1_43129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/03_2024/8vc1_43129_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc1_43129/03_2024/8vc1_43129_neut_updated.pdb" } 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-5265/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: 7.66, per 1000 atoms: 0.58 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: 5.45 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... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 78.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.791A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 79 Processing helix chain 'A' and resid 90 through 112 Processing helix chain 'A' and resid 114 through 135 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 141 through 176 removed outlier: 4.475A pdb=" N THR A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 229 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 287 through 311 removed outlier: 3.626A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 339 Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 345 through 389 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 395 through 409 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 424 through 443 removed outlier: 3.554A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.791A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 79 Processing helix chain 'B' and resid 90 through 112 Processing helix chain 'B' and resid 114 through 135 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 141 through 176 removed outlier: 4.475A pdb=" N THR B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 229 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 287 through 311 removed outlier: 3.627A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 339 Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 345 through 389 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 395 through 409 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 424 through 443 removed outlier: 3.554A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.791A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 79 Processing helix chain 'C' and resid 90 through 112 Processing helix chain 'C' and resid 114 through 135 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 141 through 176 removed outlier: 4.474A pdb=" N THR C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 229 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 287 through 311 removed outlier: 3.626A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 339 Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 345 through 389 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 395 through 409 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 424 through 443 removed outlier: 3.554A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 removed outlier: 3.790A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 90 through 112 Processing helix chain 'D' and resid 114 through 135 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 141 through 176 removed outlier: 4.475A pdb=" N THR D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 229 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 287 through 311 removed outlier: 3.626A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 339 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 345 through 389 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 395 through 409 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 424 through 443 removed outlier: 3.553A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.605A pdb=" N THR A 49 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 273 through 275 Processing sheet with id= C, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.604A pdb=" N THR B 49 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 273 through 275 Processing sheet with id= E, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.604A pdb=" N THR C 49 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 273 through 275 Processing sheet with id= G, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.604A pdb=" N THR D 49 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 273 through 275 988 hydrogen bonds defined for protein. 2964 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: 3.74 Time building geometry restraints manager: 5.87 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: 927 2.74 - 3.28: 13635 3.28 - 3.82: 21559 3.82 - 4.36: 26769 4.36 - 4.90: 47146 Nonbonded interactions: 110036 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 110031 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: 1.410 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: 5.840 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.840 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.350 ------------------------------------------------------------------------------- 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= 0.788 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 : 1.199 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: 1.4514 time to fit residues: 221.1171 Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.5980 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13360 Z= 0.216 Angle : 0.615 6.866 18004 Z= 0.308 Chirality : 0.038 0.155 2140 Planarity : 0.004 0.037 2088 Dihedral : 16.851 139.322 2736 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.78 % Allowed : 4.08 % Favored : 94.14 % 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: 2.35 (0.21), residues: 1548 helix: 1.97 (0.14), residues: 1260 sheet: -0.83 (0.58), residues: 88 loop : 0.24 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 354 HIS 0.003 0.001 HIS B 307 PHE 0.022 0.002 PHE A 56 TYR 0.019 0.002 TYR B 124 ARG 0.003 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 154 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7300 (mtt) REVERT: B 133 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6749 (mtm-85) REVERT: B 373 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7265 (mtt) REVERT: B 419 MET cc_start: 0.8839 (mmt) cc_final: 0.8589 (mmm) REVERT: C 373 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7358 (mtt) REVERT: C 419 MET cc_start: 0.8855 (mmt) cc_final: 0.8606 (mmm) REVERT: D 273 MET cc_start: 0.6189 (ttp) cc_final: 0.5909 (ttt) REVERT: D 373 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: D 419 MET cc_start: 0.8831 (mmt) cc_final: 0.8585 (mmm) outliers start: 24 outliers final: 8 residues processed: 138 average time/residue: 1.4111 time to fit residues: 210.9052 Evaluate side-chains 129 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 3.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13360 Z= 0.303 Angle : 0.608 7.469 18004 Z= 0.302 Chirality : 0.039 0.155 2140 Planarity : 0.004 0.037 2088 Dihedral : 15.207 138.056 2728 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.71 % Allowed : 7.64 % Favored : 90.65 % 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: 2.71 (0.21), residues: 1548 helix: 2.26 (0.14), residues: 1260 sheet: -1.34 (0.64), residues: 48 loop : -0.00 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.003 0.001 HIS D 370 PHE 0.021 0.002 PHE D 205 TYR 0.022 0.002 TYR D 124 ARG 0.004 0.000 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 176 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 303 GLU cc_start: 0.7485 (tt0) cc_final: 0.7203 (pt0) REVERT: A 378 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7305 (ttt180) REVERT: A 419 MET cc_start: 0.8807 (mmt) cc_final: 0.8564 (mmm) REVERT: B 200 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 303 GLU cc_start: 0.7461 (tt0) cc_final: 0.7238 (pt0) REVERT: B 378 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7298 (ttt180) REVERT: B 419 MET cc_start: 0.8802 (mmt) cc_final: 0.8562 (mmm) REVERT: C 200 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 303 GLU cc_start: 0.7458 (tt0) cc_final: 0.7233 (pt0) REVERT: C 378 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7307 (ttt180) REVERT: C 419 MET cc_start: 0.8807 (mmt) cc_final: 0.8572 (mmm) REVERT: D 200 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 303 GLU cc_start: 0.7451 (tt0) cc_final: 0.7235 (pt0) REVERT: D 378 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7307 (ttt180) REVERT: D 419 MET cc_start: 0.8806 (mmt) cc_final: 0.8567 (mmm) outliers start: 23 outliers final: 8 residues processed: 162 average time/residue: 1.6807 time to fit residues: 291.2631 Evaluate side-chains 152 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 102 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: 0.9980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13360 Z= 0.271 Angle : 0.546 6.908 18004 Z= 0.275 Chirality : 0.038 0.146 2140 Planarity : 0.004 0.038 2088 Dihedral : 14.611 131.832 2728 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 9.05 % 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: 3.02 (0.21), residues: 1548 helix: 2.50 (0.14), residues: 1260 sheet: 0.18 (1.04), residues: 40 loop : -0.41 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 193 HIS 0.003 0.001 HIS A 307 PHE 0.020 0.002 PHE A 205 TYR 0.021 0.002 TYR B 124 ARG 0.008 0.000 ARG B 38 *********************** 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 172 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 303 GLU cc_start: 0.7476 (tt0) cc_final: 0.7150 (pt0) REVERT: A 378 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7260 (ttt180) REVERT: B 200 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7668 (mt-10) REVERT: B 219 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7035 (mt-10) REVERT: B 303 GLU cc_start: 0.7471 (tt0) cc_final: 0.7160 (pt0) REVERT: B 378 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7267 (ttt180) REVERT: C 200 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 303 GLU cc_start: 0.7466 (tt0) cc_final: 0.7150 (pt0) REVERT: C 378 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7271 (ttt180) REVERT: D 200 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7668 (mt-10) REVERT: D 219 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7000 (mt-10) REVERT: D 303 GLU cc_start: 0.7467 (tt0) cc_final: 0.7162 (pt0) REVERT: D 378 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7275 (ttt180) outliers start: 27 outliers final: 13 residues processed: 154 average time/residue: 1.6526 time to fit residues: 271.8986 Evaluate side-chains 150 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 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 362 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7721 moved from start: 0.2524 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= 0.210 Angle : 0.501 6.000 18004 Z= 0.252 Chirality : 0.036 0.142 2140 Planarity : 0.004 0.039 2088 Dihedral : 13.867 116.967 2728 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.82 % Allowed : 9.12 % Favored : 88.06 % 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: 3.38 (0.21), residues: 1548 helix: 2.77 (0.14), residues: 1260 sheet: 0.15 (1.03), residues: 40 loop : -0.41 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS B 307 PHE 0.017 0.002 PHE D 205 TYR 0.017 0.001 TYR D 124 ARG 0.004 0.000 ARG B 38 *********************** 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 180 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.8112 (m100) REVERT: A 200 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 303 GLU cc_start: 0.7421 (tt0) cc_final: 0.7119 (pt0) REVERT: A 378 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7228 (ttt180) REVERT: B 87 MET cc_start: 0.4504 (OUTLIER) cc_final: 0.3882 (mmm) REVERT: B 193 TRP cc_start: 0.8471 (OUTLIER) cc_final: 0.8114 (m100) REVERT: B 200 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 303 GLU cc_start: 0.7398 (tt0) cc_final: 0.7100 (pt0) REVERT: B 378 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7229 (ttt180) REVERT: C 193 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.8114 (m100) REVERT: C 200 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 219 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6936 (mt-10) REVERT: C 303 GLU cc_start: 0.7410 (tt0) cc_final: 0.7111 (pt0) REVERT: C 378 ARG cc_start: 0.7463 (mtt180) cc_final: 0.7223 (ttt180) REVERT: D 193 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.8114 (m100) REVERT: D 200 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7613 (mt-10) REVERT: D 303 GLU cc_start: 0.7396 (tt0) cc_final: 0.7094 (pt0) REVERT: D 378 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7257 (ttt180) outliers start: 38 outliers final: 15 residues processed: 161 average time/residue: 1.6533 time to fit residues: 284.7198 Evaluate side-chains 157 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 273 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 87 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 91 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 273 MET Chi-restraints excluded: chain C residue 362 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 362 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.2656 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= 0.215 Angle : 0.498 6.201 18004 Z= 0.251 Chirality : 0.036 0.143 2140 Planarity : 0.004 0.039 2088 Dihedral : 12.973 96.472 2728 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.52 % Allowed : 9.94 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.43 (0.21), residues: 1548 helix: 2.83 (0.14), residues: 1260 sheet: -0.59 (0.61), residues: 88 loop : -0.24 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS C 392 PHE 0.018 0.002 PHE D 205 TYR 0.019 0.001 TYR B 124 ARG 0.004 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.8130 (m100) REVERT: A 219 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6885 (mt-10) REVERT: A 303 GLU cc_start: 0.7400 (tt0) cc_final: 0.7095 (pt0) REVERT: A 378 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7211 (ttt180) REVERT: B 87 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.3883 (mmm) REVERT: B 193 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8127 (m100) REVERT: B 219 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6894 (mt-10) REVERT: B 303 GLU cc_start: 0.7388 (tt0) cc_final: 0.7087 (pt0) REVERT: B 378 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7227 (ttt180) REVERT: C 193 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.8123 (m100) REVERT: C 200 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 219 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6884 (mt-10) REVERT: C 303 GLU cc_start: 0.7397 (tt0) cc_final: 0.7089 (pt0) REVERT: C 378 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7206 (ttt180) REVERT: D 193 TRP cc_start: 0.8489 (OUTLIER) cc_final: 0.8137 (m100) REVERT: D 200 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7639 (mt-10) REVERT: D 219 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6905 (mt-10) REVERT: D 303 GLU cc_start: 0.7405 (tt0) cc_final: 0.7101 (pt0) REVERT: D 378 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7242 (ttt180) outliers start: 34 outliers final: 15 residues processed: 156 average time/residue: 1.6825 time to fit residues: 280.9165 Evaluate side-chains 157 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 87 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 273 MET Chi-restraints excluded: chain C residue 362 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 362 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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: 0.7695 moved from start: 0.2791 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= 0.170 Angle : 0.464 5.114 18004 Z= 0.235 Chirality : 0.035 0.137 2140 Planarity : 0.004 0.038 2088 Dihedral : 12.297 76.914 2728 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.15 % Allowed : 10.31 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.72 (0.21), residues: 1548 helix: 3.04 (0.14), residues: 1260 sheet: -0.26 (0.61), residues: 84 loop : -0.36 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.001 0.000 HIS A 392 PHE 0.019 0.002 PHE B 205 TYR 0.017 0.001 TYR A 124 ARG 0.009 0.000 ARG A 213 *********************** 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 171 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.3991 (mmm) REVERT: A 219 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6857 (mt-10) REVERT: A 303 GLU cc_start: 0.7379 (tt0) cc_final: 0.7088 (pt0) REVERT: A 378 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7212 (ttt180) REVERT: A 419 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: B 87 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.3834 (mmm) REVERT: B 219 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6871 (mt-10) REVERT: B 303 GLU cc_start: 0.7375 (tt0) cc_final: 0.7091 (pt0) REVERT: B 378 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7210 (ttt180) REVERT: B 419 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8211 (mtt) REVERT: C 219 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6855 (mt-10) REVERT: C 303 GLU cc_start: 0.7379 (tt0) cc_final: 0.7088 (pt0) REVERT: C 378 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7208 (ttt180) REVERT: C 419 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8263 (mtt) REVERT: D 87 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.3776 (mmm) REVERT: D 219 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6850 (mt-10) REVERT: D 303 GLU cc_start: 0.7368 (tt0) cc_final: 0.7086 (pt0) REVERT: D 378 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7214 (ttt180) REVERT: D 419 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8213 (mtt) outliers start: 29 outliers final: 12 residues processed: 147 average time/residue: 1.6674 time to fit residues: 262.4870 Evaluate side-chains 158 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 123 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 87 MET 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 419 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 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: 0.7739 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13360 Z= 0.243 Angle : 0.511 6.793 18004 Z= 0.256 Chirality : 0.037 0.145 2140 Planarity : 0.004 0.040 2088 Dihedral : 12.178 72.349 2728 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.82 % Allowed : 10.01 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.21), residues: 1548 helix: 2.90 (0.14), residues: 1260 sheet: -0.21 (0.62), residues: 84 loop : -0.39 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 193 HIS 0.002 0.001 HIS D 370 PHE 0.021 0.002 PHE A 205 TYR 0.019 0.001 TYR C 124 ARG 0.007 0.000 ARG A 213 *********************** 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 179 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.3917 (mmm) REVERT: A 193 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.8085 (m100) REVERT: A 219 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6896 (mt-10) REVERT: A 303 GLU cc_start: 0.7415 (tt0) cc_final: 0.7089 (pt0) REVERT: A 419 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: B 193 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.8076 (m100) REVERT: B 219 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6902 (mt-10) REVERT: B 303 GLU cc_start: 0.7404 (tt0) cc_final: 0.7084 (pt0) REVERT: B 378 ARG cc_start: 0.7416 (mtt180) cc_final: 0.7212 (ttt180) REVERT: B 419 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: C 193 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.8075 (m100) REVERT: C 219 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6892 (mt-10) REVERT: C 303 GLU cc_start: 0.7420 (tt0) cc_final: 0.7101 (pt0) REVERT: C 378 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7210 (ttt180) REVERT: C 419 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8260 (mtt) REVERT: D 193 TRP cc_start: 0.8485 (OUTLIER) cc_final: 0.8076 (m100) REVERT: D 219 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6869 (mt-10) REVERT: D 303 GLU cc_start: 0.7403 (tt0) cc_final: 0.7089 (pt0) REVERT: D 378 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7215 (ttt180) REVERT: D 419 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8290 (mtt) outliers start: 38 outliers final: 17 residues processed: 151 average time/residue: 1.6704 time to fit residues: 269.6883 Evaluate side-chains 166 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 193 TRP Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 419 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 419 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 419 MET 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 419 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 0.0010 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13360 Z= 0.150 Angle : 0.444 4.794 18004 Z= 0.226 Chirality : 0.035 0.138 2140 Planarity : 0.004 0.040 2088 Dihedral : 11.768 59.846 2728 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.71 % Allowed : 11.35 % Favored : 86.94 % 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: 3.94 (0.21), residues: 1548 helix: 3.21 (0.14), residues: 1260 sheet: -0.18 (0.62), residues: 84 loop : -0.37 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 193 HIS 0.001 0.000 HIS D 22 PHE 0.017 0.001 PHE A 205 TYR 0.017 0.001 TYR D 124 ARG 0.007 0.000 ARG A 213 *********************** 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 151 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7351 (tt0) cc_final: 0.7070 (pt0) REVERT: A 336 MET cc_start: 0.7531 (mmp) cc_final: 0.7254 (mmp) REVERT: B 303 GLU cc_start: 0.7339 (tt0) cc_final: 0.7094 (pt0) REVERT: B 378 ARG cc_start: 0.7406 (mtt180) cc_final: 0.7200 (ttt180) REVERT: C 303 GLU cc_start: 0.7342 (tt0) cc_final: 0.7092 (pt0) REVERT: C 378 ARG cc_start: 0.7403 (mtt180) cc_final: 0.7198 (ttt180) REVERT: D 303 GLU cc_start: 0.7350 (tt0) cc_final: 0.7105 (pt0) REVERT: D 378 ARG cc_start: 0.7410 (mtt180) cc_final: 0.7208 (ttt180) outliers start: 23 outliers final: 12 residues processed: 137 average time/residue: 1.6264 time to fit residues: 239.0586 Evaluate side-chains 137 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 91 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 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3000 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= 0.176 Angle : 0.471 5.621 18004 Z= 0.237 Chirality : 0.035 0.141 2140 Planarity : 0.004 0.040 2088 Dihedral : 11.713 59.088 2728 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 12.09 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.21), residues: 1548 helix: 3.21 (0.14), residues: 1260 sheet: -0.14 (0.63), residues: 84 loop : -0.41 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 193 HIS 0.002 0.001 HIS B 392 PHE 0.019 0.002 PHE A 205 TYR 0.018 0.001 TYR A 124 ARG 0.007 0.000 ARG A 213 ********************** 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 155 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6791 (mt-10) REVERT: A 303 GLU cc_start: 0.7393 (tt0) cc_final: 0.7099 (pt0) REVERT: A 336 MET cc_start: 0.7478 (mmp) cc_final: 0.7229 (mmp) REVERT: B 219 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6855 (mt-10) REVERT: B 303 GLU cc_start: 0.7355 (tt0) cc_final: 0.7077 (pt0) REVERT: C 219 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6853 (mt-10) REVERT: C 303 GLU cc_start: 0.7359 (tt0) cc_final: 0.7079 (pt0) REVERT: C 378 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7212 (ttt180) REVERT: D 219 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6842 (mt-10) REVERT: D 303 GLU cc_start: 0.7357 (tt0) cc_final: 0.7088 (pt0) outliers start: 15 outliers final: 13 residues processed: 145 average time/residue: 1.6561 time to fit residues: 257.8282 Evaluate side-chains 152 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 362 MET Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 91 MET Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 362 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 0.0030 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151524 restraints weight = 11812.219| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.92 r_work: 0.3569 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13360 Z= 0.158 Angle : 0.454 4.997 18004 Z= 0.230 Chirality : 0.035 0.139 2140 Planarity : 0.004 0.039 2088 Dihedral : 11.561 59.954 2728 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.19 % Allowed : 12.76 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.21), residues: 1548 helix: 3.30 (0.14), residues: 1260 sheet: -0.08 (0.63), residues: 84 loop : -0.43 (0.49), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.001 0.000 HIS C 392 PHE 0.018 0.001 PHE C 205 TYR 0.017 0.001 TYR D 124 ARG 0.007 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.20 seconds wall clock time: 78 minutes 39.37 seconds (4719.37 seconds total)