Starting phenix.real_space_refine on Thu Oct 29 14:59:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bog_12242/10_2026/7bog_12242.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 1071 5.49 5 Mg 105 5.21 5 S 45 5.16 5 C 16807 2.51 5 N 6235 2.21 5 O 9326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33589 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 23015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 23015 Classifications: {'RNA': 6, 'RNAv2': 1065} Modifications used: {'rna2p': 1, 'rna2p_pur': 74, 'rna2p_pyr': 53, 'rna3p': 6, 'rna3p_pur': 541, 'rna3p_pyr': 396} Link IDs: {'rna2p': 128, 'rna3p': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Unusual residues: {' MG': 103} Classifications: {'undetermined': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.17 Number of scatterers: 33589 At special positions: 0 Unit cell: (186.9, 150.15, 175.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 P 1071 15.00 Mg 105 11.99 O 9326 8.00 N 6235 7.00 C 16807 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 539.0 milliseconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 42.0% alpha, 21.9% beta 363 base pairs and 637 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 152 through 163 removed outlier: 3.736A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.926A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.577A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 17 through 32 Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.510A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.742A pdb=" N ALA F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.903A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 72 Processing helix chain 'K' and resid 73 through 78 removed outlier: 5.445A pdb=" N GLU K 76 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 102 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.059A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 4.078A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.580A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 33 No H-bonds generated for 'chain 'R' and resid 31 through 33' Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.523A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.789A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.525A pdb=" N LYS T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU T 86 " --> pdb=" O GLN T 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 25 Processing helix chain 'V' and resid 61 through 88 removed outlier: 3.914A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY V 77 " --> pdb=" O GLN V 73 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE V 78 " --> pdb=" O GLU V 74 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG V 88 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.323A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AA4, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 44 removed outlier: 5.389A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=AA7, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.815A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 41 through 46 removed outlier: 7.087A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY K 19 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N MET K 85 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LYS K 87 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE K 23 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE K 110 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL K 86 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP K 112 " --> pdb=" O VAL K 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 40 removed outlier: 6.843A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.311A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 8 through 17 removed outlier: 7.618A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL Q 76 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG Q 62 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 37 through 43 removed outlier: 5.256A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY V 40 " --> pdb=" O TYR V 53 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 903 hydrogen bonds 1406 hydrogen bond angles 0 basepair planarities 363 basepair parallelities 637 stacking parallelities Total time for adding SS restraints: 13.67 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5879 1.33 - 1.45: 14797 1.45 - 1.58: 13493 1.58 - 1.70: 2138 1.70 - 1.82: 79 Bond restraints: 36386 Sorted by residual: bond pdb=" C1' C A1536 " pdb=" N1 C A1536 " ideal model delta sigma weight residual 1.478 1.569 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C1' U A1506 " pdb=" N1 U A1506 " ideal model delta sigma weight residual 1.478 1.564 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C4 PSU A 516 " pdb=" C5 PSU A 516 " ideal model delta sigma weight residual 1.390 1.474 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.463 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.394 1.469 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 36381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 52520 2.77 - 5.53: 1849 5.53 - 8.30: 38 8.30 - 11.07: 11 11.07 - 13.83: 4 Bond angle restraints: 54422 Sorted by residual: angle pdb=" N LYS P 46 " pdb=" CA LYS P 46 " pdb=" C LYS P 46 " ideal model delta sigma weight residual 113.17 106.03 7.14 1.26e+00 6.30e-01 3.21e+01 angle pdb=" C4' G7M A 527 " pdb=" C3' G7M A 527 " pdb=" C2' G7M A 527 " ideal model delta sigma weight residual 102.60 97.03 5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" N ARG V 45 " pdb=" CA ARG V 45 " pdb=" C ARG V 45 " ideal model delta sigma weight residual 111.28 105.50 5.78 1.09e+00 8.42e-01 2.81e+01 angle pdb=" C6 MA6 A1519 " pdb=" N6 MA6 A1519 " pdb=" C9 MA6 A1519 " ideal model delta sigma weight residual 122.78 108.95 13.83 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O3' U A1532 " pdb=" P C A1533 " pdb=" OP2 C A1533 " ideal model delta sigma weight residual 108.00 121.72 -13.72 3.00e+00 1.11e-01 2.09e+01 ... (remaining 54417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15771 17.58 - 35.15: 1808 35.15 - 52.73: 1152 52.73 - 70.30: 596 70.30 - 87.88: 131 Dihedral angle restraints: 19458 sinusoidal: 15625 harmonic: 3833 Sorted by residual: dihedral pdb=" C4' C A 90 " pdb=" C3' C A 90 " pdb=" C2' C A 90 " pdb=" C1' C A 90 " ideal model delta sinusoidal sigma weight residual 36.34 -39.28 75.62 1 3.10e+00 1.04e-01 7.51e+02 dihedral pdb=" C4' A A 889 " pdb=" C3' A A 889 " pdb=" C2' A A 889 " pdb=" C1' A A 889 " ideal model delta sinusoidal sigma weight residual 36.34 -39.22 75.57 1 3.10e+00 1.04e-01 7.50e+02 dihedral pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" C2' A A 246 " pdb=" C1' A A 246 " ideal model delta sinusoidal sigma weight residual 36.35 -39.03 75.37 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 19455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5163 0.066 - 0.133: 377 0.133 - 0.199: 226 0.199 - 0.266: 1029 0.266 - 0.332: 152 Chirality restraints: 6947 Sorted by residual: chirality pdb=" C3' A A 889 " pdb=" C4' A A 889 " pdb=" O3' A A 889 " pdb=" C2' A A 889 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3' A A 499 " pdb=" C4' A A 499 " pdb=" O3' A A 499 " pdb=" C2' A A 499 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' C A 73 " pdb=" C3' C A 73 " pdb=" O2' C A 73 " pdb=" C1' C A 73 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 6944 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.131 2.00e-02 2.50e+03 2.15e-01 4.63e+02 pdb=" N6 MA6 A1519 " -0.373 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.122 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.127 2.00e-02 2.50e+03 2.11e-01 4.46e+02 pdb=" N6 MA6 A1518 " -0.366 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.118 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.038 2.00e-02 2.50e+03 8.03e-02 2.10e+02 pdb=" N9 2MG A1516 " 0.011 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.039 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.055 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.017 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.008 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.042 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.036 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.077 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.117 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.070 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.032 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.221 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 213 2.53 - 3.12: 23448 3.12 - 3.71: 65221 3.71 - 4.31: 96256 4.31 - 4.90: 126311 Nonbonded interactions: 311449 Sorted by model distance: nonbonded pdb=" O4 U A 180 " pdb="MG MG A1643 " model vdw 1.937 2.170 nonbonded pdb=" OP2 G A 760 " pdb="MG MG A1660 " model vdw 1.971 2.170 nonbonded pdb=" OP1 G A 450 " pdb="MG MG A1637 " model vdw 1.974 2.170 nonbonded pdb=" OP2 A A 441 " pdb="MG MG A1626 " model vdw 1.993 2.170 nonbonded pdb=" O6 G A 299 " pdb="MG MG A1619 " model vdw 2.005 2.170 ... (remaining 311444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.090 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.090 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 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 : 0.006 0.091 36386 Z= 0.321 Angle : 0.936 13.831 54422 Z= 0.410 Chirality : 0.106 0.332 6947 Planarity : 0.007 0.215 2919 Dihedral : 19.712 87.879 16984 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.21), residues: 1309 helix: -0.64 (0.20), residues: 502 sheet: -1.89 (0.31), residues: 226 loop : -1.47 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 77 TYR 0.011 0.001 TYR Q 34 PHE 0.016 0.001 PHE F 8 TRP 0.008 0.001 TRP D 170 HIS 0.012 0.001 HIS R 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.32 (36386) covalent geometry : angle 0.93603 / 0.41 (54422) hydrogen bonds : bond 0.16162 / 8.42 ( 1417) hydrogen bonds : angle 6.16484 / 2.57 ( 2867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 149 SER cc_start: 0.9047 (p) cc_final: 0.8543 (p) REVERT: F 68 GLN cc_start: 0.8602 (mt0) cc_final: 0.8347 (mt0) REVERT: F 72 ASP cc_start: 0.7809 (p0) cc_final: 0.7341 (p0) REVERT: F 97 THR cc_start: 0.7994 (p) cc_final: 0.7381 (p) REVERT: K 27 PHE cc_start: 0.8968 (m-80) cc_final: 0.8666 (m-80) REVERT: K 40 ASN cc_start: 0.9010 (m-40) cc_final: 0.7876 (m110) REVERT: K 68 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8207 (mm-30) REVERT: K 85 MET cc_start: 0.8328 (mtm) cc_final: 0.8017 (mtm) REVERT: L 47 SER cc_start: 0.8695 (t) cc_final: 0.8468 (t) REVERT: L 112 GLN cc_start: 0.9018 (mt0) cc_final: 0.8752 (mt0) REVERT: O 21 ASP cc_start: 0.8576 (t0) cc_final: 0.8307 (t0) REVERT: O 47 LYS cc_start: 0.8587 (ptpp) cc_final: 0.8331 (pttt) REVERT: R 25 ASP cc_start: 0.8636 (t0) cc_final: 0.8372 (t70) REVERT: R 43 ARG cc_start: 0.8641 (ttt-90) cc_final: 0.7840 (ttt-90) REVERT: V 17 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8817 (mtpp) REVERT: V 49 TYR cc_start: 0.8117 (m-80) cc_final: 0.7675 (m-80) REVERT: V 51 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8398 (mtpp) outliers start: 0 outliers final: 1 residues processed: 441 average time/residue: 0.7188 time to fit residues: 373.3862 Evaluate side-chains 383 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 GLN D 41 HIS D 54 GLN D 126 ASN D 152 GLN D 164 GLN E 12 GLN E 83 HIS E 122 ASN E 135 ASN E 146 ASN E 148 ASN F 3 HIS F 17 GLN F 37 HIS K 15 GLN K 28 ASN K 109 ASN L 73 ASN L 112 GLN O 28 GLN O 35 GLN O 46 HIS P 18 GLN P 29 ASN P 40 ASN Q 9 GLN R 54 GLN T 70 ASN T 84 ASN V 58 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.050154 restraints weight = 85457.389| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.11 r_work: 0.2624 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36386 Z= 0.251 Angle : 1.258 18.456 54422 Z= 0.500 Chirality : 0.108 1.190 6947 Planarity : 0.005 0.040 2919 Dihedral : 18.543 160.569 14360 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.73 % Allowed : 16.74 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1309 helix: 0.50 (0.21), residues: 515 sheet: -1.49 (0.31), residues: 239 loop : -1.01 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 73 TYR 0.010 0.001 TYR D 65 PHE 0.017 0.001 PHE F 8 TRP 0.009 0.002 TRP K 44 HIS 0.007 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.25 (36386) covalent geometry : angle 1.25821 / 0.50 (54422) hydrogen bonds : bond 0.06530 / 3.40 ( 1417) hydrogen bonds : angle 3.52786 / 1.43 ( 2867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 406 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: E 61 GLN cc_start: 0.8217 (pp30) cc_final: 0.8006 (tm-30) REVERT: F 22 ILE cc_start: 0.9150 (mt) cc_final: 0.8863 (mp) REVERT: F 24 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7946 (ptp-110) REVERT: F 68 GLN cc_start: 0.8464 (mt0) cc_final: 0.8093 (mt0) REVERT: F 72 ASP cc_start: 0.8112 (p0) cc_final: 0.7793 (p0) REVERT: H 60 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8257 (tm-30) REVERT: K 85 MET cc_start: 0.8839 (mtm) cc_final: 0.8387 (mtm) REVERT: O 17 ARG cc_start: 0.7813 (tmm-80) cc_final: 0.7557 (tmm-80) REVERT: O 21 ASP cc_start: 0.8778 (t0) cc_final: 0.8304 (t0) REVERT: O 47 LYS cc_start: 0.8896 (ptpp) cc_final: 0.8624 (pttt) REVERT: O 88 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8254 (mmm160) REVERT: R 25 ASP cc_start: 0.8943 (t0) cc_final: 0.8613 (t0) REVERT: R 38 LYS cc_start: 0.9111 (ptmt) cc_final: 0.8862 (ptmm) REVERT: V 49 TYR cc_start: 0.8337 (m-80) cc_final: 0.7874 (m-80) REVERT: V 51 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8736 (mtpt) outliers start: 41 outliers final: 18 residues processed: 414 average time/residue: 0.7470 time to fit residues: 363.9636 Evaluate side-chains 392 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 372 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [211, 66, 84, 199, 187, 77, 137, 72, 67, 39, 203] chunk 211 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 199 optimal weight: 0.0980 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN E 146 ASN H 38 ASN H 76 GLN K 101 ASN K 109 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.050654 restraints weight = 85829.512| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.14 r_work: 0.2644 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36386 Z= 0.237 Angle : 1.066 15.298 54422 Z= 0.433 Chirality : 0.088 1.000 6947 Planarity : 0.004 0.043 2919 Dihedral : 18.617 176.629 14357 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.73 % Allowed : 18.93 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.23), residues: 1309 helix: 0.99 (0.22), residues: 518 sheet: -1.05 (0.33), residues: 239 loop : -0.78 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 10 TYR 0.011 0.001 TYR F 59 PHE 0.017 0.001 PHE F 8 TRP 0.016 0.002 TRP F 42 HIS 0.006 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 (36386) covalent geometry : angle 1.06583 / 0.43 (54422) hydrogen bonds : bond 0.05869 / 3.07 ( 1417) hydrogen bonds : angle 3.37087 / 1.36 ( 2867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 393 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 GLN cc_start: 0.8378 (pp30) cc_final: 0.8081 (tm-30) REVERT: F 14 GLN cc_start: 0.8643 (mp10) cc_final: 0.8424 (mp10) REVERT: F 24 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8048 (ptp-110) REVERT: F 68 GLN cc_start: 0.8477 (mt0) cc_final: 0.8196 (mt0) REVERT: F 69 GLU cc_start: 0.9021 (mp0) cc_final: 0.8683 (mp0) REVERT: F 72 ASP cc_start: 0.8213 (p0) cc_final: 0.7828 (p0) REVERT: F 80 PHE cc_start: 0.8752 (m-80) cc_final: 0.8468 (m-80) REVERT: H 52 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8075 (mt-10) REVERT: H 60 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8332 (tm-30) REVERT: K 34 ILE cc_start: 0.9018 (mm) cc_final: 0.8678 (tp) REVERT: L 43 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8312 (mttp) REVERT: L 94 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8763 (mtp85) REVERT: O 17 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7691 (tmm-80) REVERT: O 21 ASP cc_start: 0.8795 (t0) cc_final: 0.8237 (t0) REVERT: O 47 LYS cc_start: 0.8958 (ptpp) cc_final: 0.8713 (pttt) REVERT: O 88 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8331 (mmm160) REVERT: Q 60 GLU cc_start: 0.8921 (tt0) cc_final: 0.8511 (tt0) REVERT: R 25 ASP cc_start: 0.8931 (t0) cc_final: 0.8696 (t0) REVERT: R 38 LYS cc_start: 0.9089 (ptmt) cc_final: 0.8822 (ptmm) REVERT: R 43 ARG cc_start: 0.9074 (ttt-90) cc_final: 0.8683 (ttt90) REVERT: V 18 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8585 (mm-30) REVERT: V 49 TYR cc_start: 0.8462 (m-80) cc_final: 0.7969 (m-80) REVERT: V 98 PHE cc_start: 0.8507 (m-80) cc_final: 0.8272 (m-10) outliers start: 52 outliers final: 28 residues processed: 408 average time/residue: 0.7591 time to fit residues: 363.2975 Evaluate side-chains 401 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 370 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 43 MET Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [196, 227, 181, 58, 146, 12, 232, 139, 94, 207, 171] chunk 196 optimal weight: 0.5980 chunk 227 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN F 11 HIS F 46 GLN H 38 ASN K 109 ASN L 73 ASN O 35 GLN O 80 GLN Q 9 GLN R 54 GLN T 13 GLN V 13 GLN V 16 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.048744 restraints weight = 84760.209| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.12 r_work: 0.2570 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 36386 Z= 0.316 Angle : 1.116 17.510 54422 Z= 0.454 Chirality : 0.093 1.043 6947 Planarity : 0.005 0.036 2919 Dihedral : 18.624 179.616 14357 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.19 % Allowed : 20.38 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1309 helix: 1.09 (0.23), residues: 516 sheet: -0.82 (0.34), residues: 233 loop : -0.72 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 11 TYR 0.011 0.001 TYR Q 34 PHE 0.016 0.001 PHE F 8 TRP 0.018 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.32 (36386) covalent geometry : angle 1.11573 / 0.45 (54422) hydrogen bonds : bond 0.05910 / 3.09 ( 1417) hydrogen bonds : angle 3.41382 / 1.37 ( 2867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8898 (m-30) cc_final: 0.8670 (m-30) REVERT: E 61 GLN cc_start: 0.8380 (pp30) cc_final: 0.7993 (tm-30) REVERT: E 65 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8539 (mm-30) REVERT: F 22 ILE cc_start: 0.9171 (mt) cc_final: 0.8958 (mp) REVERT: F 24 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7933 (ptp-110) REVERT: F 68 GLN cc_start: 0.8456 (mt0) cc_final: 0.8094 (mt0) REVERT: F 72 ASP cc_start: 0.8085 (p0) cc_final: 0.7807 (p0) REVERT: F 80 PHE cc_start: 0.8698 (m-80) cc_final: 0.8438 (m-80) REVERT: H 52 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7994 (mt-10) REVERT: H 60 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8350 (tm-30) REVERT: K 79 ILE cc_start: 0.8467 (mp) cc_final: 0.7821 (tp) REVERT: L 94 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8770 (mtp85) REVERT: O 21 ASP cc_start: 0.8812 (t0) cc_final: 0.8343 (t0) REVERT: O 47 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8770 (pttt) REVERT: O 88 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8319 (mmm160) REVERT: Q 40 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8303 (mmp-170) REVERT: R 25 ASP cc_start: 0.8968 (t0) cc_final: 0.8596 (t0) REVERT: R 38 LYS cc_start: 0.9122 (ptmt) cc_final: 0.8864 (ptmm) REVERT: T 40 GLU cc_start: 0.8083 (mp0) cc_final: 0.7858 (mm-30) REVERT: T 43 ASP cc_start: 0.8388 (t0) cc_final: 0.8167 (t0) REVERT: V 17 LYS cc_start: 0.9007 (mtpm) cc_final: 0.8710 (mtpp) REVERT: V 18 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8184 (mm-30) REVERT: V 31 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6904 (mtt-85) REVERT: V 49 TYR cc_start: 0.8579 (m-80) cc_final: 0.8191 (m-80) REVERT: V 51 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8241 (mtpt) REVERT: V 87 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8107 (tpt) outliers start: 57 outliers final: 27 residues processed: 393 average time/residue: 0.7534 time to fit residues: 348.2812 Evaluate side-chains 388 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [82, 168, 147, 158, 204, 98, 80, 165, 232, 142, 8] chunk 82 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN E 70 ASN F 11 HIS H 38 ASN K 101 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN T 13 GLN T 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.049360 restraints weight = 85065.612| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.13 r_work: 0.2589 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 36386 Z= 0.271 Angle : 1.090 17.274 54422 Z= 0.445 Chirality : 0.090 0.994 6947 Planarity : 0.005 0.046 2919 Dihedral : 18.653 178.063 14357 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.55 % Allowed : 22.66 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1309 helix: 1.13 (0.23), residues: 518 sheet: -0.72 (0.34), residues: 234 loop : -0.63 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 11 TYR 0.011 0.001 TYR Q 34 PHE 0.021 0.002 PHE K 61 TRP 0.015 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.27 (36386) covalent geometry : angle 1.08988 / 0.44 (54422) hydrogen bonds : bond 0.05834 / 3.06 ( 1417) hydrogen bonds : angle 3.39434 / 1.37 ( 2867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 368 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8048 (mtt) REVERT: D 190 ASP cc_start: 0.8921 (m-30) cc_final: 0.8677 (m-30) REVERT: E 61 GLN cc_start: 0.8384 (pp30) cc_final: 0.8126 (tm-30) REVERT: F 22 ILE cc_start: 0.9180 (mt) cc_final: 0.8948 (mp) REVERT: F 24 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7934 (ptp-110) REVERT: F 68 GLN cc_start: 0.8376 (mt0) cc_final: 0.8036 (mt0) REVERT: F 69 GLU cc_start: 0.8927 (mp0) cc_final: 0.8694 (mp0) REVERT: F 72 ASP cc_start: 0.8108 (p0) cc_final: 0.7886 (p0) REVERT: F 80 PHE cc_start: 0.8677 (m-80) cc_final: 0.8409 (m-80) REVERT: H 52 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8004 (mt-10) REVERT: H 60 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8335 (tm-30) REVERT: K 58 SER cc_start: 0.8886 (p) cc_final: 0.8574 (m) REVERT: K 79 ILE cc_start: 0.8480 (mp) cc_final: 0.7847 (tp) REVERT: L 94 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8799 (mtp85) REVERT: O 21 ASP cc_start: 0.8778 (t0) cc_final: 0.8273 (t0) REVERT: O 47 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8745 (pttt) REVERT: O 88 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8318 (mmm160) REVERT: P 53 ASP cc_start: 0.8661 (t0) cc_final: 0.8427 (t0) REVERT: Q 77 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8481 (ptt-90) REVERT: R 25 ASP cc_start: 0.8946 (t0) cc_final: 0.8660 (t0) REVERT: R 38 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8856 (ptmm) REVERT: R 43 ARG cc_start: 0.9164 (ttt-90) cc_final: 0.8674 (ttt90) REVERT: V 18 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8095 (mm-30) REVERT: V 31 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6906 (mtt-85) REVERT: V 49 TYR cc_start: 0.8562 (m-80) cc_final: 0.8112 (m-80) REVERT: V 51 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8447 (mtpt) REVERT: V 87 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8068 (tpt) REVERT: V 98 PHE cc_start: 0.8461 (m-10) cc_final: 0.8194 (m-10) outliers start: 61 outliers final: 29 residues processed: 391 average time/residue: 0.7256 time to fit residues: 334.0665 Evaluate side-chains 391 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 87 MET Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [95, 231, 40, 99, 154, 163, 211, 187, 124, 214, 182] chunk 95 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN F 11 HIS H 38 ASN K 101 ASN K 109 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN T 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.046981 restraints weight = 85042.647| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 1.13 r_work: 0.2521 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 36386 Z= 0.437 Angle : 1.210 18.219 54422 Z= 0.494 Chirality : 0.100 1.121 6947 Planarity : 0.005 0.049 2919 Dihedral : 18.716 177.563 14357 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.73 % Allowed : 23.11 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1309 helix: 0.98 (0.23), residues: 521 sheet: -0.71 (0.33), residues: 233 loop : -0.66 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 11 TYR 0.012 0.002 TYR R 51 PHE 0.015 0.002 PHE F 8 TRP 0.023 0.002 TRP F 42 HIS 0.006 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00895 / 0.44 (36386) covalent geometry : angle 1.20963 / 0.49 (54422) hydrogen bonds : bond 0.06325 / 3.29 ( 1417) hydrogen bonds : angle 3.53436 / 1.42 ( 2867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 367 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8951 (m-30) cc_final: 0.8696 (m-30) REVERT: E 61 GLN cc_start: 0.8371 (pp30) cc_final: 0.7871 (tm-30) REVERT: E 65 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8467 (mm-30) REVERT: F 22 ILE cc_start: 0.9220 (mt) cc_final: 0.8975 (mp) REVERT: F 24 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8012 (ptp-110) REVERT: F 44 ARG cc_start: 0.8585 (mtp85) cc_final: 0.7877 (mtp85) REVERT: F 68 GLN cc_start: 0.8493 (mt0) cc_final: 0.8089 (mt0) REVERT: F 72 ASP cc_start: 0.8140 (p0) cc_final: 0.7883 (p0) REVERT: F 80 PHE cc_start: 0.8773 (m-80) cc_final: 0.8547 (m-80) REVERT: H 47 GLU cc_start: 0.8638 (tp30) cc_final: 0.8414 (tt0) REVERT: H 52 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8034 (mt-10) REVERT: H 60 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8407 (tm-30) REVERT: K 79 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.7899 (tp) REVERT: L 94 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8643 (mtp85) REVERT: O 21 ASP cc_start: 0.8782 (t0) cc_final: 0.8323 (t0) REVERT: O 47 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8791 (pttt) REVERT: O 77 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8465 (ttp80) REVERT: O 88 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8410 (mmm160) REVERT: P 53 ASP cc_start: 0.8795 (t0) cc_final: 0.8531 (t0) REVERT: Q 40 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8311 (mmp-170) REVERT: R 25 ASP cc_start: 0.8929 (t0) cc_final: 0.8484 (t0) REVERT: R 29 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9199 (mp) REVERT: R 73 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8133 (mmm160) REVERT: V 25 ARG cc_start: 0.8725 (ttm170) cc_final: 0.8491 (tpp80) REVERT: V 31 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6950 (mtt-85) REVERT: V 49 TYR cc_start: 0.8629 (m-80) cc_final: 0.8158 (m-80) REVERT: V 51 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8570 (mtpt) outliers start: 63 outliers final: 37 residues processed: 385 average time/residue: 0.7545 time to fit residues: 340.8317 Evaluate side-chains 399 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 356 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [111, 195, 95, 143, 18, 89, 57, 229, 157, 45, 117] chunk 111 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 ASN D 140 ASN D 196 ASN F 68 GLN H 38 ASN K 40 ASN K 101 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN T 13 GLN T 48 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.070186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.048774 restraints weight = 85073.748| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 1.13 r_work: 0.2575 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36386 Z= 0.267 Angle : 1.119 15.882 54422 Z= 0.458 Chirality : 0.092 1.039 6947 Planarity : 0.005 0.065 2919 Dihedral : 18.749 176.863 14357 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.19 % Allowed : 24.75 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1309 helix: 1.05 (0.23), residues: 519 sheet: -0.75 (0.34), residues: 233 loop : -0.58 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 11 TYR 0.011 0.001 TYR E 128 PHE 0.025 0.002 PHE K 61 TRP 0.022 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.27 (36386) covalent geometry : angle 1.11923 / 0.46 (54422) hydrogen bonds : bond 0.06040 / 3.15 ( 1417) hydrogen bonds : angle 3.45515 / 1.39 ( 2867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8927 (m-30) cc_final: 0.8654 (m-30) REVERT: E 61 GLN cc_start: 0.8441 (pp30) cc_final: 0.7950 (tm-30) REVERT: E 65 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8534 (mm-30) REVERT: F 22 ILE cc_start: 0.9175 (mt) cc_final: 0.8945 (mp) REVERT: F 24 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7994 (ptp-110) REVERT: F 44 ARG cc_start: 0.8553 (mtp85) cc_final: 0.7798 (mtp85) REVERT: F 68 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: F 69 GLU cc_start: 0.8935 (mp0) cc_final: 0.8659 (mp0) REVERT: F 72 ASP cc_start: 0.8112 (p0) cc_final: 0.7901 (p0) REVERT: F 80 PHE cc_start: 0.8717 (m-80) cc_final: 0.8491 (m-80) REVERT: H 47 GLU cc_start: 0.8590 (tp30) cc_final: 0.8367 (tt0) REVERT: H 52 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8036 (mt-10) REVERT: H 60 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8325 (tm-30) REVERT: K 58 SER cc_start: 0.8863 (p) cc_final: 0.8576 (m) REVERT: K 79 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.7904 (tp) REVERT: L 94 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8640 (mtp85) REVERT: O 21 ASP cc_start: 0.8725 (t0) cc_final: 0.8282 (t0) REVERT: O 47 LYS cc_start: 0.9019 (ptpp) cc_final: 0.8749 (pttt) REVERT: O 88 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8343 (mmm160) REVERT: R 25 ASP cc_start: 0.8887 (t0) cc_final: 0.8655 (t0) REVERT: R 38 LYS cc_start: 0.9109 (ptmt) cc_final: 0.8878 (ptmm) REVERT: V 17 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8585 (mtpp) REVERT: V 25 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8452 (tpp80) REVERT: V 31 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6813 (mtt-85) REVERT: V 49 TYR cc_start: 0.8628 (m-80) cc_final: 0.8149 (m-80) REVERT: V 51 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8405 (mtpt) outliers start: 57 outliers final: 31 residues processed: 385 average time/residue: 0.7561 time to fit residues: 341.7518 Evaluate side-chains 392 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 356 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [89, 1, 200, 35, 25, 15, 70, 31, 116, 113, 187] chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 ASN F 11 HIS H 38 ASN K 109 ASN L 73 ASN O 35 GLN P 26 ASN Q 9 GLN R 54 GLN T 13 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.047879 restraints weight = 84727.815| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.13 r_work: 0.2550 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 36386 Z= 0.357 Angle : 1.148 16.957 54422 Z= 0.470 Chirality : 0.094 1.064 6947 Planarity : 0.005 0.063 2919 Dihedral : 18.749 178.006 14357 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.28 % Allowed : 26.21 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.23), residues: 1309 helix: 1.04 (0.23), residues: 518 sheet: -0.68 (0.33), residues: 233 loop : -0.59 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 11 TYR 0.011 0.002 TYR E 128 PHE 0.015 0.002 PHE F 8 TRP 0.026 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.36 (36386) covalent geometry : angle 1.14819 / 0.47 (54422) hydrogen bonds : bond 0.06121 / 3.19 ( 1417) hydrogen bonds : angle 3.50069 / 1.41 ( 2867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8963 (m-30) cc_final: 0.8684 (m-30) REVERT: E 61 GLN cc_start: 0.8387 (pp30) cc_final: 0.8126 (tm-30) REVERT: F 22 ILE cc_start: 0.9184 (mt) cc_final: 0.8943 (mp) REVERT: F 24 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8019 (ptp-110) REVERT: F 44 ARG cc_start: 0.8572 (mtp85) cc_final: 0.7864 (mtp85) REVERT: F 68 GLN cc_start: 0.8445 (mt0) cc_final: 0.8104 (mt0) REVERT: F 80 PHE cc_start: 0.8741 (m-80) cc_final: 0.8533 (m-80) REVERT: H 47 GLU cc_start: 0.8558 (tp30) cc_final: 0.8336 (tt0) REVERT: H 52 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8039 (mt-10) REVERT: H 60 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8367 (tm-30) REVERT: K 79 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.7913 (tp) REVERT: L 94 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8607 (mtp85) REVERT: O 21 ASP cc_start: 0.8746 (t0) cc_final: 0.8313 (t0) REVERT: O 47 LYS cc_start: 0.9017 (ptpp) cc_final: 0.8756 (pttt) REVERT: O 88 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8358 (mmm160) REVERT: R 25 ASP cc_start: 0.8889 (t0) cc_final: 0.8546 (t0) REVERT: V 25 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8376 (tpp80) REVERT: V 31 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6954 (mtt-85) REVERT: V 49 TYR cc_start: 0.8645 (m-80) cc_final: 0.8174 (m-80) REVERT: V 51 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8473 (mtpt) outliers start: 58 outliers final: 34 residues processed: 383 average time/residue: 0.7570 time to fit residues: 340.4266 Evaluate side-chains 397 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 359 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 69 ILE Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [220, 34, 137, 227, 211, 142, 76, 92, 123, 151, 64] chunk 220 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 ASN D 196 ASN F 11 HIS H 38 ASN K 101 ASN L 73 ASN Q 9 GLN R 54 GLN T 13 GLN T 48 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.069593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.048181 restraints weight = 84655.563| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.12 r_work: 0.2556 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 36386 Z= 0.341 Angle : 1.142 16.692 54422 Z= 0.470 Chirality : 0.093 1.061 6947 Planarity : 0.005 0.070 2919 Dihedral : 18.763 178.272 14357 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.19 % Allowed : 28.30 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1309 helix: 1.01 (0.23), residues: 519 sheet: -0.72 (0.33), residues: 237 loop : -0.61 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 11 TYR 0.013 0.002 TYR E 128 PHE 0.028 0.002 PHE K 61 TRP 0.030 0.002 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.34 (36386) covalent geometry : angle 1.14216 / 0.47 (54422) hydrogen bonds : bond 0.06115 / 3.19 ( 1417) hydrogen bonds : angle 3.48999 / 1.40 ( 2867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 361 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8960 (m-30) cc_final: 0.8679 (m-30) REVERT: E 61 GLN cc_start: 0.8377 (pp30) cc_final: 0.8141 (tm-30) REVERT: F 22 ILE cc_start: 0.9181 (mt) cc_final: 0.8939 (mp) REVERT: F 24 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8020 (ptp-110) REVERT: F 44 ARG cc_start: 0.8544 (mtp85) cc_final: 0.7837 (mtp85) REVERT: F 68 GLN cc_start: 0.8429 (mt0) cc_final: 0.8128 (mt0) REVERT: F 80 PHE cc_start: 0.8728 (m-80) cc_final: 0.8518 (m-80) REVERT: H 47 GLU cc_start: 0.8546 (tp30) cc_final: 0.8327 (tt0) REVERT: H 52 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8007 (mt-10) REVERT: H 60 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8354 (tm-30) REVERT: K 58 SER cc_start: 0.8854 (p) cc_final: 0.8583 (m) REVERT: K 79 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.7920 (tp) REVERT: L 94 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8633 (mtp85) REVERT: O 21 ASP cc_start: 0.8787 (t0) cc_final: 0.8341 (t0) REVERT: O 47 LYS cc_start: 0.9009 (ptpp) cc_final: 0.8740 (pttt) REVERT: O 48 LYS cc_start: 0.9094 (ptpp) cc_final: 0.8868 (ptpp) REVERT: O 88 ARG cc_start: 0.8647 (mmm160) cc_final: 0.8355 (mmm160) REVERT: R 25 ASP cc_start: 0.8889 (t0) cc_final: 0.8670 (t70) REVERT: V 25 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8464 (tpp80) REVERT: V 31 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6882 (mtt-85) REVERT: V 49 TYR cc_start: 0.8639 (m-80) cc_final: 0.8145 (m-80) REVERT: V 51 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8321 (mtpt) outliers start: 46 outliers final: 33 residues processed: 375 average time/residue: 0.7393 time to fit residues: 326.1076 Evaluate side-chains 394 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [83, 71, 13, 182, 33, 67, 44, 122, 152, 6, 210] chunk 83 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 ASN F 11 HIS H 38 ASN K 109 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN T 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.048460 restraints weight = 85169.482| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.13 r_work: 0.2565 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 36386 Z= 0.309 Angle : 1.130 16.156 54422 Z= 0.465 Chirality : 0.092 1.060 6947 Planarity : 0.005 0.072 2919 Dihedral : 18.772 178.457 14357 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.73 % Allowed : 28.57 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1309 helix: 1.05 (0.23), residues: 517 sheet: -0.66 (0.33), residues: 233 loop : -0.57 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 11 TYR 0.015 0.002 TYR E 128 PHE 0.015 0.002 PHE F 8 TRP 0.036 0.003 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.31 (36386) covalent geometry : angle 1.12963 / 0.47 (54422) hydrogen bonds : bond 0.06087 / 3.17 ( 1417) hydrogen bonds : angle 3.46202 / 1.39 ( 2867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 ASP cc_start: 0.8960 (m-30) cc_final: 0.8676 (m-30) REVERT: E 61 GLN cc_start: 0.8419 (pp30) cc_final: 0.8142 (tm-30) REVERT: F 22 ILE cc_start: 0.9179 (mt) cc_final: 0.8938 (mp) REVERT: F 24 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8022 (ptp-110) REVERT: F 44 ARG cc_start: 0.8546 (mtp85) cc_final: 0.7858 (mtp85) REVERT: F 68 GLN cc_start: 0.8400 (mt0) cc_final: 0.8054 (mt0) REVERT: F 80 PHE cc_start: 0.8725 (m-80) cc_final: 0.8509 (m-80) REVERT: H 47 GLU cc_start: 0.8557 (tp30) cc_final: 0.8334 (tt0) REVERT: H 52 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8013 (mt-10) REVERT: H 60 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8349 (tm-30) REVERT: K 58 SER cc_start: 0.8816 (p) cc_final: 0.8561 (m) REVERT: K 79 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.7924 (tp) REVERT: L 94 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8614 (mtp85) REVERT: O 21 ASP cc_start: 0.8775 (t0) cc_final: 0.8321 (t0) REVERT: O 47 LYS cc_start: 0.9000 (ptpp) cc_final: 0.8736 (pttt) REVERT: O 88 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8350 (mmm160) REVERT: R 25 ASP cc_start: 0.8890 (t0) cc_final: 0.8656 (t70) REVERT: V 17 LYS cc_start: 0.8990 (mtpm) cc_final: 0.8573 (mtpp) REVERT: V 25 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8453 (tpp80) REVERT: V 31 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6881 (mtt-85) REVERT: V 49 TYR cc_start: 0.8651 (m-80) cc_final: 0.8163 (m-80) REVERT: V 51 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8377 (mtpt) outliers start: 41 outliers final: 32 residues processed: 374 average time/residue: 0.7548 time to fit residues: 331.7948 Evaluate side-chains 391 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain V residue 31 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain V residue 96 THR Chi-restraints excluded: chain V residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: [112, 214, 162, 24, 71, 52, 130, 133, 45, 12, 18] chunk 112 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 140 ASN F 11 HIS H 38 ASN K 101 ASN L 73 ASN O 35 GLN Q 9 GLN R 54 GLN T 13 GLN T 48 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.048695 restraints weight = 85022.265| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.12 r_work: 0.2572 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 36386 Z= 0.309 Angle : 1.119 15.867 54422 Z= 0.460 Chirality : 0.091 1.046 6947 Planarity : 0.005 0.067 2919 Dihedral : 18.764 178.523 14357 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.64 % Allowed : 28.75 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1309 helix: 1.04 (0.23), residues: 519 sheet: -0.63 (0.33), residues: 233 loop : -0.57 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 11 TYR 0.014 0.002 TYR E 128 PHE 0.032 0.002 PHE K 61 TRP 0.031 0.003 TRP F 42 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.31 (36386) covalent geometry : angle 1.11913 / 0.46 (54422) hydrogen bonds : bond 0.06053 / 3.16 ( 1417) hydrogen bonds : angle 3.46039 / 1.39 ( 2867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12212.01 seconds wall clock time: 208 minutes 13.71 seconds (12493.71 seconds total)