Starting phenix.real_space_refine on Sun Apr 7 03:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8v_36081/04_2024/8j8v_36081_updated.pdb" } resolution = 3.22 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= 0.000 sd= 0.029 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 14 5.49 5 S 20 5.16 5 C 5963 2.51 5 N 1616 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "F ASP 30": "OD1" <-> "OD2" Residue "F ASP 36": "OD1" <-> "OD2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 260": "OD1" <-> "OD2" Residue "F ASP 351": "OD1" <-> "OD2" Residue "F GLU 400": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9437 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.47, per 1000 atoms: 0.58 Number of scatterers: 9437 At special positions: 0 Unit cell: (135.569, 86.3707, 104.957, 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 20 16.00 P 14 15.00 O 1824 8.00 N 1616 7.00 C 5963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 24 sheets defined 4.7% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 100 through 112 removed outlier: 6.755A pdb=" N GLN A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N HIS A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 394 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.636A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 165 through 169 removed outlier: 4.003A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 88 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.655A pdb=" N SER A 203 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 223 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.600A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 342 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 259 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= H, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.528A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.573A pdb=" N TYR B 112 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 5 through 8 Processing sheet with id= K, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.216A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.611A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 86 through 91 removed outlier: 6.126A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.544A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.574A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.603A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.252A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 86 through 91 removed outlier: 6.054A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 10 through 13 Processing sheet with id= T, first strand: chain 'F' and resid 27 through 29 removed outlier: 6.573A pdb=" N ARG F 170 " --> pdb=" O PHE F 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 165 through 169 removed outlier: 4.019A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 144 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE F 88 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL F 56 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN F 86 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU F 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN F 84 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL F 60 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE F 82 " --> pdb=" O VAL F 60 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 128 through 130 Processing sheet with id= W, first strand: chain 'F' and resid 184 through 190 removed outlier: 3.880A pdb=" N SER F 203 " --> pdb=" O ASN F 218 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN F 223 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 336 through 342 removed outlier: 3.637A pdb=" N VAL F 336 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE F 342 " --> pdb=" O TYR F 322 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR F 322 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 232 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN F 259 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 255 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN F 238 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA F 240 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS F 251 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE F 242 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN F 249 " --> pdb=" O ILE F 242 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3026 1.34 - 1.46: 1903 1.46 - 1.58: 4652 1.58 - 1.69: 42 1.69 - 1.81: 28 Bond restraints: 9651 Sorted by residual: bond pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O1P SEP H 345 " pdb=" P SEP H 345 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O1P SEP G 343 " pdb=" P SEP G 343 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" O2P SEP H 345 " pdb=" P SEP H 345 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 9646 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.08: 232 105.08 - 112.30: 5021 112.30 - 119.52: 2931 119.52 - 126.73: 4812 126.73 - 133.95: 126 Bond angle restraints: 13122 Sorted by residual: angle pdb=" N LEU F 49 " pdb=" CA LEU F 49 " pdb=" C LEU F 49 " ideal model delta sigma weight residual 110.55 97.86 12.69 1.35e+00 5.49e-01 8.83e+01 angle pdb=" N LYS F 50 " pdb=" CA LYS F 50 " pdb=" C LYS F 50 " ideal model delta sigma weight residual 112.12 103.01 9.11 1.34e+00 5.57e-01 4.62e+01 angle pdb=" N VAL A 315 " pdb=" CA VAL A 315 " pdb=" C VAL A 315 " ideal model delta sigma weight residual 106.21 112.51 -6.30 1.07e+00 8.73e-01 3.47e+01 angle pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 120.72 111.56 9.16 1.67e+00 3.59e-01 3.01e+01 angle pdb=" N PHE A 245 " pdb=" CA PHE A 245 " pdb=" C PHE A 245 " ideal model delta sigma weight residual 114.75 108.37 6.38 1.26e+00 6.30e-01 2.56e+01 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5348 17.67 - 35.33: 363 35.33 - 53.00: 67 53.00 - 70.66: 13 70.66 - 88.33: 15 Dihedral angle restraints: 5806 sinusoidal: 2297 harmonic: 3509 Sorted by residual: dihedral pdb=" CA SER F 75 " pdb=" C SER F 75 " pdb=" N PHE F 76 " pdb=" CA PHE F 76 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU F 244 " pdb=" C LEU F 244 " pdb=" N PHE F 245 " pdb=" CA PHE F 245 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 75 " pdb=" C SER A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1284 0.070 - 0.140: 173 0.140 - 0.210: 7 0.210 - 0.279: 1 0.279 - 0.349: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CA LEU A 49 " pdb=" N LEU A 49 " pdb=" C LEU A 49 " pdb=" CB LEU A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LEU F 49 " pdb=" N LEU F 49 " pdb=" C LEU F 49 " pdb=" CB LEU F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LYS F 50 " pdb=" N LYS F 50 " pdb=" C LYS F 50 " pdb=" CB LYS F 50 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1464 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 48 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C TYR F 48 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR F 48 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU F 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 350 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C HIS F 350 " 0.035 2.00e-02 2.50e+03 pdb=" O HIS F 350 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP F 351 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 48 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C TYR A 48 " -0.032 2.00e-02 2.50e+03 pdb=" O TYR A 48 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 49 " 0.011 2.00e-02 2.50e+03 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1318 2.76 - 3.30: 8450 3.30 - 3.83: 14816 3.83 - 4.37: 17110 4.37 - 4.90: 31721 Nonbonded interactions: 73415 Sorted by model distance: nonbonded pdb=" OD1 ASP A 205 " pdb=" OH TYR A 209 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASP F 205 " pdb=" OH TYR F 209 " model vdw 2.230 2.440 nonbonded pdb=" OD2 ASP F 261 " pdb=" OH TYR F 273 " model vdw 2.267 2.440 nonbonded pdb=" OD2 ASP A 261 " pdb=" OH TYR A 273 " model vdw 2.270 2.440 nonbonded pdb=" NZ LYS F 293 " pdb=" OG1 THR F 299 " model vdw 2.277 2.520 ... (remaining 73410 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' selection = chain 'F' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 5 through 121) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 65 or (resid 66 and (name N or name CA \ or name C or name O or name CB )) or resid 67 through 107)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.720 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: 10.370 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.580 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.005 0.109 9651 Z= 0.339 Angle : 0.718 12.689 13122 Z= 0.399 Chirality : 0.046 0.349 1467 Planarity : 0.004 0.045 1672 Dihedral : 13.272 88.326 3536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.98 % Allowed : 0.59 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.23 (0.25), residues: 1163 helix: 2.76 (0.69), residues: 52 sheet: 0.66 (0.23), residues: 521 loop : -0.54 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 50 HIS 0.003 0.001 HIS A 346 PHE 0.009 0.001 PHE A 116 TYR 0.010 0.001 TYR E 50 ARG 0.005 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.064 Fit side-chains REVERT: A 350 HIS cc_start: 0.5562 (m90) cc_final: 0.5345 (m170) REVERT: B 76 ASP cc_start: 0.7148 (t0) cc_final: 0.6899 (t0) REVERT: D 76 ASP cc_start: 0.7074 (t0) cc_final: 0.6860 (t0) REVERT: F 52 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4918 (mtp180) REVERT: F 351 ASP cc_start: 0.4956 (OUTLIER) cc_final: 0.4301 (t0) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.2434 time to fit residues: 43.5292 Evaluate side-chains 106 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS B 87 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9651 Z= 0.170 Angle : 0.530 8.955 13122 Z= 0.273 Chirality : 0.043 0.132 1467 Planarity : 0.004 0.046 1672 Dihedral : 8.222 80.950 1377 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.56 % Allowed : 6.34 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.25 (0.25), residues: 1163 helix: 2.64 (0.70), residues: 54 sheet: 0.77 (0.23), residues: 512 loop : -0.59 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 50 HIS 0.006 0.001 HIS F 199 PHE 0.011 0.001 PHE A 116 TYR 0.009 0.001 TYR A 273 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.047 Fit side-chains REVERT: A 351 ASP cc_start: 0.5336 (OUTLIER) cc_final: 0.5022 (t70) REVERT: E 25 ARG cc_start: 0.7958 (tpt170) cc_final: 0.7645 (tpp-160) REVERT: F 351 ASP cc_start: 0.5097 (OUTLIER) cc_final: 0.4317 (t0) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.2333 time to fit residues: 35.3088 Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 0.0970 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9651 Z= 0.180 Angle : 0.513 11.341 13122 Z= 0.261 Chirality : 0.043 0.145 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.813 81.637 1367 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.05 % Allowed : 8.00 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.34 (0.25), residues: 1163 helix: 2.68 (0.70), residues: 54 sheet: 0.77 (0.22), residues: 530 loop : -0.50 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.005 0.001 HIS F 199 PHE 0.011 0.001 PHE A 116 TYR 0.009 0.001 TYR A 48 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.192 Fit side-chains REVERT: A 351 ASP cc_start: 0.5462 (OUTLIER) cc_final: 0.5096 (t70) REVERT: F 351 ASP cc_start: 0.5294 (OUTLIER) cc_final: 0.4412 (t0) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.2233 time to fit residues: 34.5999 Evaluate side-chains 113 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 112 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9651 Z= 0.189 Angle : 0.512 10.894 13122 Z= 0.259 Chirality : 0.043 0.137 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.718 81.811 1367 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.73 % Allowed : 9.07 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.32 (0.25), residues: 1163 helix: 2.69 (0.70), residues: 54 sheet: 0.70 (0.22), residues: 548 loop : -0.49 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.005 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.010 0.001 TYR B 98 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.122 Fit side-chains REVERT: A 296 HIS cc_start: 0.7814 (m-70) cc_final: 0.7612 (m-70) REVERT: A 351 ASP cc_start: 0.5433 (OUTLIER) cc_final: 0.4769 (t70) REVERT: F 351 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4580 (t0) outliers start: 28 outliers final: 18 residues processed: 112 average time/residue: 0.2180 time to fit residues: 34.5484 Evaluate side-chains 111 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 112 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9651 Z= 0.171 Angle : 0.503 10.081 13122 Z= 0.253 Chirality : 0.042 0.136 1467 Planarity : 0.004 0.045 1672 Dihedral : 7.614 81.622 1367 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.95 % Allowed : 10.73 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.35 (0.25), residues: 1163 helix: 2.73 (0.70), residues: 54 sheet: 0.75 (0.22), residues: 550 loop : -0.52 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.005 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.009 0.001 TYR B 98 ARG 0.002 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.087 Fit side-chains REVERT: A 351 ASP cc_start: 0.5511 (OUTLIER) cc_final: 0.5161 (t70) REVERT: F 351 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4690 (t0) outliers start: 20 outliers final: 17 residues processed: 104 average time/residue: 0.2158 time to fit residues: 31.9486 Evaluate side-chains 109 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 351 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 101 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9651 Z= 0.158 Angle : 0.493 9.497 13122 Z= 0.248 Chirality : 0.042 0.134 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.485 81.264 1367 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.95 % Allowed : 11.32 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.41 (0.25), residues: 1163 helix: 2.77 (0.70), residues: 54 sheet: 0.79 (0.22), residues: 550 loop : -0.48 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.005 0.001 HIS A 350 PHE 0.011 0.001 PHE A 116 TYR 0.008 0.001 TYR B 98 ARG 0.003 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.131 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.2133 time to fit residues: 31.3092 Evaluate side-chains 106 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9651 Z= 0.222 Angle : 0.523 9.628 13122 Z= 0.264 Chirality : 0.043 0.145 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.235 81.106 1360 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.24 % Allowed : 11.80 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.36 (0.25), residues: 1163 helix: 2.77 (0.70), residues: 54 sheet: 0.72 (0.22), residues: 548 loop : -0.46 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.005 0.001 HIS A 199 PHE 0.012 0.001 PHE A 116 TYR 0.011 0.001 TYR B 98 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.045 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 104 average time/residue: 0.2048 time to fit residues: 30.7340 Evaluate side-chains 108 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 101 GLN F 112 HIS F 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9651 Z= 0.240 Angle : 0.533 9.564 13122 Z= 0.270 Chirality : 0.043 0.148 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.150 81.035 1357 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.85 % Allowed : 11.80 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.31 (0.25), residues: 1163 helix: 2.80 (0.70), residues: 54 sheet: 0.67 (0.22), residues: 548 loop : -0.48 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.006 0.001 HIS A 199 PHE 0.012 0.001 PHE A 117 TYR 0.013 0.001 TYR F 48 ARG 0.001 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.152 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 103 average time/residue: 0.2104 time to fit residues: 31.0778 Evaluate side-chains 108 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 4 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9651 Z= 0.218 Angle : 0.527 9.413 13122 Z= 0.267 Chirality : 0.043 0.145 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.131 80.806 1357 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.66 % Allowed : 12.00 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.32 (0.25), residues: 1163 helix: 2.79 (0.70), residues: 54 sheet: 0.68 (0.22), residues: 548 loop : -0.48 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.005 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.012 0.001 TYR F 48 ARG 0.001 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.113 Fit side-chains REVERT: B 5 VAL cc_start: 0.8029 (t) cc_final: 0.7689 (p) outliers start: 17 outliers final: 15 residues processed: 102 average time/residue: 0.2079 time to fit residues: 30.4814 Evaluate side-chains 107 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9651 Z= 0.173 Angle : 0.505 8.931 13122 Z= 0.256 Chirality : 0.042 0.136 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.041 80.126 1357 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.56 % Allowed : 12.20 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.33 (0.25), residues: 1163 helix: 2.80 (0.70), residues: 54 sheet: 0.71 (0.22), residues: 550 loop : -0.50 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS F 199 PHE 0.012 0.001 PHE A 116 TYR 0.009 0.001 TYR B 98 ARG 0.002 0.000 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.121 Fit side-chains REVERT: B 5 VAL cc_start: 0.8050 (t) cc_final: 0.7731 (p) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.2139 time to fit residues: 30.8553 Evaluate side-chains 106 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.0270 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.153039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121971 restraints weight = 12527.737| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.26 r_work: 0.3249 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9651 Z= 0.212 Angle : 0.874 59.159 13122 Z= 0.505 Chirality : 0.047 0.847 1467 Planarity : 0.004 0.044 1672 Dihedral : 7.048 80.120 1357 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.37 % Allowed : 12.39 % Favored : 86.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.18 % 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: 0.32 (0.25), residues: 1163 helix: 2.79 (0.70), residues: 54 sheet: 0.71 (0.22), residues: 550 loop : -0.52 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS F 199 PHE 0.011 0.001 PHE A 116 TYR 0.009 0.001 TYR B 98 ARG 0.001 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.47 seconds wall clock time: 41 minutes 33.34 seconds (2493.34 seconds total)