Starting phenix.real_space_refine on Thu Jul 31 07:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.map" model { file = "/net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kgf_8246/07_2025/5kgf_8246.cif" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 16 5.16 5 C 7741 2.51 5 N 2597 2.21 5 O 3140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13782 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 832 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 788 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 9 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N GLU C 121 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU C 121 " occ=0.00 residue: pdb=" N LYS G 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS G 9 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 7.38, per 1000 atoms: 0.54 Number of scatterers: 13782 At special positions: 0 Unit cell: (120.35, 124.7, 116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 288 15.00 O 3140 8.00 N 2597 7.00 C 7741 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 Atom "ATOM 8125 O4' DA I 17 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 62.5% alpha, 4.1% beta 118 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 5.81 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.656A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.710A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.977A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.970A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.690A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.504A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.741A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.551A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.597A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.216A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.517A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 82 removed outlier: 3.797A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.553A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.559A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.912A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.712A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.976A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.971A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.689A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.505A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.546A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.742A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.550A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 4.218A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.518A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.796A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.556A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.560A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 1623 through 1630 removed outlier: 3.535A pdb=" N ARG L1627 " --> pdb=" O VAL L1623 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'K' and resid 1623 through 1630 removed outlier: 3.536A pdb=" N ARG K1627 " --> pdb=" O VAL K1623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.562A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.061A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.771A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 15 through 16 removed outlier: 3.551A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 15 through 16 removed outlier: 3.548A pdb=" N PHE M 45 " --> pdb=" O LYS M 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 3.77 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: 2701 1.33 - 1.45: 4263 1.45 - 1.57: 7028 1.57 - 1.68: 577 1.68 - 1.80: 26 Bond restraints: 14595 Sorted by residual: bond pdb=" SG M2L F 20 " pdb=" CD M2L F 20 " ideal model delta sigma weight residual 1.822 1.524 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" SG M2L B 20 " pdb=" CD M2L B 20 " ideal model delta sigma weight residual 1.822 1.525 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" CB M2L B 20 " pdb=" SG M2L B 20 " ideal model delta sigma weight residual 1.815 1.523 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" CB M2L F 20 " pdb=" SG M2L F 20 " ideal model delta sigma weight residual 1.815 1.525 0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" O5' DA I -72 " pdb=" C5' DA I -72 " ideal model delta sigma weight residual 1.423 1.649 -0.226 3.00e-02 1.11e+03 5.70e+01 ... (remaining 14590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 20710 4.97 - 9.95: 194 9.95 - 14.92: 9 14.92 - 19.89: 3 19.89 - 24.86: 2 Bond angle restraints: 20918 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 81.26 22.74 1.50e+00 4.44e-01 2.30e+02 angle pdb=" N ARG G 11 " pdb=" CA ARG G 11 " pdb=" C ARG G 11 " ideal model delta sigma weight residual 111.33 121.82 -10.49 1.21e+00 6.83e-01 7.51e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 83.14 24.86 3.00e+00 1.11e-01 6.87e+01 angle pdb=" C ASN K1621 " pdb=" CA ASN K1621 " pdb=" CB ASN K1621 " ideal model delta sigma weight residual 110.42 125.96 -15.54 1.99e+00 2.53e-01 6.10e+01 angle pdb=" C ASN L1621 " pdb=" CA ASN L1621 " pdb=" CB ASN L1621 " ideal model delta sigma weight residual 110.42 125.91 -15.49 1.99e+00 2.53e-01 6.06e+01 ... (remaining 20913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 6394 31.73 - 63.46: 1621 63.46 - 95.19: 83 95.19 - 126.92: 14 126.92 - 158.65: 3 Dihedral angle restraints: 8115 sinusoidal: 5271 harmonic: 2844 Sorted by residual: dihedral pdb=" CA ARG H 28 " pdb=" C ARG H 28 " pdb=" N SER H 29 " pdb=" CA SER H 29 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA GLY D 23 " pdb=" C GLY D 23 " pdb=" N LYS D 24 " pdb=" CA LYS D 24 " ideal model delta harmonic sigma weight residual 180.00 117.45 62.55 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASP L1620 " pdb=" C ASP L1620 " pdb=" N ASN L1621 " pdb=" CA ASN L1621 " ideal model delta harmonic sigma weight residual 180.00 118.72 61.28 0 5.00e+00 4.00e-02 1.50e+02 ... (remaining 8112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 2377 0.327 - 0.655: 2 0.655 - 0.982: 0 0.982 - 1.310: 0 1.310 - 1.637: 1 Chirality restraints: 2380 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.71 1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" CA ASN L1621 " pdb=" N ASN L1621 " pdb=" C ASN L1621 " pdb=" CB ASN L1621 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA ASN K1621 " pdb=" N ASN K1621 " pdb=" C ASN K1621 " pdb=" CB ASN K1621 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 2377 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 26 " 0.045 2.00e-02 2.50e+03 9.76e-02 9.52e+01 pdb=" C ARG D 26 " -0.168 2.00e-02 2.50e+03 pdb=" O ARG D 26 " 0.068 2.00e-02 2.50e+03 pdb=" N LYS D 27 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 26 " -0.027 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C ARG H 26 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG H 26 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS H 27 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 23 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C GLY D 23 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY D 23 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS D 24 " -0.028 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 9 1.97 - 2.71: 915 2.71 - 3.44: 20298 3.44 - 4.17: 39352 4.17 - 4.90: 58510 Nonbonded interactions: 119084 Sorted by model distance: nonbonded pdb=" O ARG H 26 " pdb=" O3' DC J 30 " model vdw 1.243 3.040 nonbonded pdb=" CG1 VAL A 46 " pdb=" OP2 DT J 9 " model vdw 1.353 3.460 nonbonded pdb=" NH2 ARG E 63 " pdb=" C4' DA I 17 " model vdw 1.534 3.550 nonbonded pdb=" NH2 ARG E 63 " pdb=" O4' DA I 17 " model vdw 1.554 3.120 nonbonded pdb=" CD1 ILE L1617 " pdb=" CD2 HIS M 68 " model vdw 1.561 3.680 ... (remaining 119079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 122) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.010 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.009 0.298 14595 Z= 0.447 Angle : 1.372 24.863 20918 Z= 0.819 Chirality : 0.069 1.637 2380 Planarity : 0.006 0.098 1650 Dihedral : 27.921 158.653 6277 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.47 % Favored : 93.11 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.19), residues: 958 helix: -3.93 (0.13), residues: 498 sheet: -2.89 (0.53), residues: 38 loop : -2.12 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS O 68 PHE 0.014 0.002 PHE C 25 TYR 0.031 0.004 TYR H 37 ARG 0.011 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.28533 ( 697) hydrogen bonds : angle 11.50447 ( 1766) covalent geometry : bond 0.00931 (14595) covalent geometry : angle 1.37168 (20918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8571 (m-80) cc_final: 0.7127 (m-10) REVERT: A 55 GLN cc_start: 0.8695 (mt0) cc_final: 0.8442 (mt0) REVERT: A 60 LEU cc_start: 0.9132 (mt) cc_final: 0.7937 (mp) REVERT: A 112 ILE cc_start: 0.9268 (mt) cc_final: 0.8808 (mm) REVERT: B 58 LEU cc_start: 0.9354 (tp) cc_final: 0.9125 (tp) REVERT: B 64 ASN cc_start: 0.9159 (m-40) cc_final: 0.8905 (p0) REVERT: C 39 TYR cc_start: 0.8169 (m-80) cc_final: 0.7891 (m-80) REVERT: C 56 GLU cc_start: 0.8622 (tt0) cc_final: 0.8354 (tt0) REVERT: C 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.8198 (tp30) REVERT: C 92 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6335 (tt0) REVERT: D 38 VAL cc_start: 0.9409 (t) cc_final: 0.9116 (t) REVERT: D 58 ILE cc_start: 0.8845 (mm) cc_final: 0.8636 (mt) REVERT: D 103 LEU cc_start: 0.9075 (tt) cc_final: 0.8487 (tp) REVERT: D 106 HIS cc_start: 0.8648 (m-70) cc_final: 0.7346 (m-70) REVERT: E 56 LYS cc_start: 0.9254 (tttt) cc_final: 0.8968 (tptm) REVERT: E 90 MET cc_start: 0.8530 (mmm) cc_final: 0.8183 (mmp) REVERT: E 94 GLU cc_start: 0.7782 (tp30) cc_final: 0.7561 (tp30) REVERT: E 112 ILE cc_start: 0.9266 (mt) cc_final: 0.8843 (mm) REVERT: E 119 ILE cc_start: 0.9248 (pt) cc_final: 0.8949 (pt) REVERT: E 125 GLN cc_start: 0.9201 (mt0) cc_final: 0.8958 (mm-40) REVERT: E 130 ILE cc_start: 0.9205 (mt) cc_final: 0.8915 (mt) REVERT: F 29 ILE cc_start: 0.9472 (mm) cc_final: 0.9217 (mm) REVERT: F 43 VAL cc_start: 0.9713 (t) cc_final: 0.9166 (p) REVERT: F 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.9197 (ttpt) REVERT: F 84 MET cc_start: 0.8306 (mmm) cc_final: 0.8029 (tpp) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8675 (m-80) REVERT: G 64 GLU cc_start: 0.8440 (tp30) cc_final: 0.8119 (tp30) REVERT: G 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8376 (m-30) REVERT: G 74 LYS cc_start: 0.8981 (mttp) cc_final: 0.8470 (tppt) REVERT: G 92 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7882 (tt0) REVERT: O 17 VAL cc_start: 0.6987 (m) cc_final: 0.5843 (m) REVERT: M 17 VAL cc_start: 0.8074 (m) cc_final: 0.7786 (p) REVERT: M 23 ILE cc_start: 0.7350 (mm) cc_final: 0.6876 (mm) REVERT: M 67 LEU cc_start: 0.8359 (mt) cc_final: 0.8020 (mp) REVERT: M 70 VAL cc_start: 0.4845 (t) cc_final: 0.4554 (t) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.3231 time to fit residues: 182.8154 Evaluate side-chains 281 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 30.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN B 93 GLN C 31 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.050452 restraints weight = 66385.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051847 restraints weight = 39214.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052725 restraints weight = 28183.489| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14595 Z= 0.281 Angle : 0.890 12.531 20918 Z= 0.491 Chirality : 0.046 0.245 2380 Planarity : 0.009 0.172 1650 Dihedral : 32.190 158.272 4276 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.70 % Favored : 94.89 % Rotamer: Outliers : 0.12 % Allowed : 4.10 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.23), residues: 958 helix: -0.74 (0.19), residues: 576 sheet: -2.38 (0.51), residues: 50 loop : -1.48 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 31 PHE 0.014 0.002 PHE G 25 TYR 0.027 0.003 TYR A 54 ARG 0.026 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06898 ( 697) hydrogen bonds : angle 5.27845 ( 1766) covalent geometry : bond 0.00619 (14595) covalent geometry : angle 0.89026 (20918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.6818 (t-90) cc_final: 0.6613 (t-90) REVERT: A 50 GLU cc_start: 0.8101 (tp30) cc_final: 0.7779 (mm-30) REVERT: A 54 TYR cc_start: 0.8368 (m-80) cc_final: 0.7592 (m-10) REVERT: A 57 SER cc_start: 0.9510 (p) cc_final: 0.8653 (m) REVERT: A 93 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 107 THR cc_start: 0.9378 (m) cc_final: 0.8958 (m) REVERT: B 52 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 53 GLU cc_start: 0.8129 (tp30) cc_final: 0.7353 (tp30) REVERT: B 59 LYS cc_start: 0.9382 (ttpt) cc_final: 0.8939 (tppt) REVERT: C 39 TYR cc_start: 0.8471 (m-80) cc_final: 0.8253 (m-80) REVERT: C 56 GLU cc_start: 0.8926 (tt0) cc_final: 0.7957 (tt0) REVERT: C 65 LEU cc_start: 0.9468 (mt) cc_final: 0.9108 (mt) REVERT: C 92 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 94 ASN cc_start: 0.9255 (t0) cc_final: 0.8596 (t0) REVERT: D 58 ILE cc_start: 0.9566 (mm) cc_final: 0.9270 (mt) REVERT: D 65 ASP cc_start: 0.9204 (t0) cc_final: 0.9002 (t0) REVERT: D 66 ILE cc_start: 0.9440 (mt) cc_final: 0.9236 (mt) REVERT: D 83 ARG cc_start: 0.8643 (mmt-90) cc_final: 0.8196 (tpp80) REVERT: D 102 GLU cc_start: 0.8072 (pm20) cc_final: 0.7728 (pm20) REVERT: D 103 LEU cc_start: 0.9547 (tt) cc_final: 0.9203 (mt) REVERT: D 106 HIS cc_start: 0.7219 (m-70) cc_final: 0.6989 (m-70) REVERT: E 56 LYS cc_start: 0.9420 (tttt) cc_final: 0.9182 (tptm) REVERT: E 59 GLU cc_start: 0.7820 (tp30) cc_final: 0.7449 (tp30) REVERT: E 70 LEU cc_start: 0.9617 (tp) cc_final: 0.9137 (tp) REVERT: E 80 THR cc_start: 0.8636 (p) cc_final: 0.8148 (p) REVERT: E 105 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8777 (mm-30) REVERT: E 110 CYS cc_start: 0.9463 (m) cc_final: 0.8939 (t) REVERT: F 25 ASN cc_start: 0.8744 (m-40) cc_final: 0.8467 (t0) REVERT: F 44 LYS cc_start: 0.9523 (tttt) cc_final: 0.8927 (mtmt) REVERT: F 60 VAL cc_start: 0.9404 (t) cc_final: 0.9014 (t) REVERT: F 63 GLU cc_start: 0.8772 (pt0) cc_final: 0.8478 (pt0) REVERT: F 85 ASP cc_start: 0.8702 (m-30) cc_final: 0.8479 (m-30) REVERT: G 56 GLU cc_start: 0.9125 (tt0) cc_final: 0.8188 (tt0) REVERT: G 64 GLU cc_start: 0.8788 (tp30) cc_final: 0.8108 (tp30) REVERT: G 72 ASP cc_start: 0.9358 (m-30) cc_final: 0.9074 (m-30) REVERT: G 74 LYS cc_start: 0.9277 (mttp) cc_final: 0.8761 (tppt) REVERT: G 82 HIS cc_start: 0.9343 (m170) cc_final: 0.9128 (m-70) REVERT: G 83 LEU cc_start: 0.9812 (mt) cc_final: 0.9564 (mm) REVERT: G 92 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8245 (mt-10) REVERT: H 56 MET cc_start: 0.8264 (tpt) cc_final: 0.7587 (tpt) REVERT: H 110 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9104 (mm-30) REVERT: O 17 VAL cc_start: 0.7765 (m) cc_final: 0.7142 (m) REVERT: O 23 ILE cc_start: 0.9059 (mp) cc_final: 0.8754 (mp) REVERT: O 41 GLN cc_start: 0.7679 (mt0) cc_final: 0.7306 (mt0) REVERT: O 43 LEU cc_start: 0.8832 (mm) cc_final: 0.8308 (mm) REVERT: O 44 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6404 (mp) REVERT: O 51 GLU cc_start: 0.5545 (pm20) cc_final: 0.4882 (pm20) REVERT: O 68 HIS cc_start: 0.8481 (m170) cc_final: 0.7577 (m170) REVERT: M 13 ILE cc_start: 0.9121 (tt) cc_final: 0.8894 (tt) REVERT: M 23 ILE cc_start: 0.8753 (mm) cc_final: 0.8208 (mm) REVERT: M 44 ILE cc_start: 0.8638 (mt) cc_final: 0.8355 (mp) REVERT: M 48 LYS cc_start: 0.8803 (mmpt) cc_final: 0.8579 (mmmt) REVERT: M 68 HIS cc_start: 0.8454 (m90) cc_final: 0.7889 (m170) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2754 time to fit residues: 148.1161 Evaluate side-chains 278 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.051133 restraints weight = 62845.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052684 restraints weight = 36646.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.053692 restraints weight = 25929.596| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14595 Z= 0.187 Angle : 0.733 9.235 20918 Z= 0.415 Chirality : 0.041 0.206 2380 Planarity : 0.006 0.133 1650 Dihedral : 31.404 160.219 4276 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.07 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 958 helix: 0.82 (0.20), residues: 576 sheet: -2.71 (0.51), residues: 48 loop : -0.96 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 46 PHE 0.015 0.002 PHE B 61 TYR 0.017 0.002 TYR G 57 ARG 0.017 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 697) hydrogen bonds : angle 4.21386 ( 1766) covalent geometry : bond 0.00413 (14595) covalent geometry : angle 0.73271 (20918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8154 (m-80) cc_final: 0.7738 (m-80) REVERT: A 60 LEU cc_start: 0.8395 (mm) cc_final: 0.8195 (mm) REVERT: A 97 GLU cc_start: 0.8912 (mt-10) cc_final: 0.7920 (mm-30) REVERT: A 110 CYS cc_start: 0.9524 (m) cc_final: 0.9211 (m) REVERT: B 59 LYS cc_start: 0.9275 (ttpp) cc_final: 0.8901 (tptp) REVERT: C 39 TYR cc_start: 0.8588 (m-80) cc_final: 0.8210 (m-80) REVERT: C 56 GLU cc_start: 0.8802 (tt0) cc_final: 0.7883 (tt0) REVERT: C 64 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8722 (tp30) REVERT: C 79 ILE cc_start: 0.9599 (tt) cc_final: 0.9203 (mm) REVERT: C 82 HIS cc_start: 0.9230 (m90) cc_final: 0.8817 (m-70) REVERT: C 94 ASN cc_start: 0.9132 (t0) cc_final: 0.8458 (t0) REVERT: D 58 ILE cc_start: 0.9648 (mm) cc_final: 0.9362 (mt) REVERT: D 83 ARG cc_start: 0.8646 (mmt-90) cc_final: 0.8293 (tpp80) REVERT: D 92 GLN cc_start: 0.9505 (tt0) cc_final: 0.9254 (tt0) REVERT: D 103 LEU cc_start: 0.9551 (tt) cc_final: 0.9234 (mt) REVERT: E 50 GLU cc_start: 0.8177 (tp30) cc_final: 0.7935 (tp30) REVERT: E 54 TYR cc_start: 0.7963 (m-10) cc_final: 0.7609 (m-10) REVERT: E 56 LYS cc_start: 0.9512 (tttt) cc_final: 0.9223 (tptm) REVERT: E 57 SER cc_start: 0.9587 (m) cc_final: 0.9350 (t) REVERT: E 68 GLN cc_start: 0.9332 (tt0) cc_final: 0.9126 (tt0) REVERT: E 80 THR cc_start: 0.8538 (p) cc_final: 0.8192 (p) REVERT: E 82 LEU cc_start: 0.9038 (mt) cc_final: 0.8817 (mp) REVERT: E 97 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 107 THR cc_start: 0.9359 (p) cc_final: 0.8907 (t) REVERT: E 119 ILE cc_start: 0.8787 (pt) cc_final: 0.8559 (pt) REVERT: E 123 ASP cc_start: 0.8507 (t0) cc_final: 0.7675 (t0) REVERT: F 25 ASN cc_start: 0.8812 (m-40) cc_final: 0.8521 (m-40) REVERT: F 26 ILE cc_start: 0.9493 (tt) cc_final: 0.9092 (tt) REVERT: F 44 LYS cc_start: 0.9537 (tttt) cc_final: 0.8953 (mtmt) REVERT: F 52 GLU cc_start: 0.8784 (tp30) cc_final: 0.8552 (tm-30) REVERT: F 59 LYS cc_start: 0.9536 (tttm) cc_final: 0.8697 (tppt) REVERT: F 60 VAL cc_start: 0.9520 (t) cc_final: 0.9036 (t) REVERT: F 63 GLU cc_start: 0.8917 (pt0) cc_final: 0.8715 (mp0) REVERT: F 85 ASP cc_start: 0.8779 (m-30) cc_final: 0.8544 (m-30) REVERT: G 39 TYR cc_start: 0.9254 (m-80) cc_final: 0.9049 (m-80) REVERT: G 50 TYR cc_start: 0.9257 (t80) cc_final: 0.8622 (t80) REVERT: G 56 GLU cc_start: 0.9062 (tt0) cc_final: 0.8214 (tt0) REVERT: G 61 GLU cc_start: 0.8797 (tp30) cc_final: 0.8506 (tp30) REVERT: G 64 GLU cc_start: 0.8830 (tp30) cc_final: 0.8193 (tp30) REVERT: G 72 ASP cc_start: 0.9502 (m-30) cc_final: 0.9125 (m-30) REVERT: G 74 LYS cc_start: 0.9322 (mttp) cc_final: 0.8750 (tppt) REVERT: G 92 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8086 (mt-10) REVERT: G 116 LEU cc_start: 0.9184 (mt) cc_final: 0.8870 (mm) REVERT: H 49 THR cc_start: 0.8794 (m) cc_final: 0.8542 (p) REVERT: H 54 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7837 (mttt) REVERT: H 56 MET cc_start: 0.8355 (tpt) cc_final: 0.7735 (tpt) REVERT: H 91 ILE cc_start: 0.9688 (mm) cc_final: 0.9464 (mm) REVERT: H 92 GLN cc_start: 0.9355 (tt0) cc_final: 0.8970 (tt0) REVERT: H 99 LEU cc_start: 0.9514 (tt) cc_final: 0.9284 (tt) REVERT: H 102 GLU cc_start: 0.8158 (tp30) cc_final: 0.7540 (tp30) REVERT: H 106 HIS cc_start: 0.7847 (m-70) cc_final: 0.7085 (m-70) REVERT: H 110 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9044 (mm-30) REVERT: O 17 VAL cc_start: 0.7948 (m) cc_final: 0.7090 (m) REVERT: O 41 GLN cc_start: 0.7568 (mt0) cc_final: 0.7072 (mt0) REVERT: O 43 LEU cc_start: 0.8855 (mm) cc_final: 0.8513 (mm) REVERT: O 44 ILE cc_start: 0.7481 (mt) cc_final: 0.6492 (mm) REVERT: O 58 ASP cc_start: 0.8714 (t0) cc_final: 0.8327 (m-30) REVERT: O 68 HIS cc_start: 0.7714 (m170) cc_final: 0.6737 (m170) REVERT: M 18 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7130 (mm-30) REVERT: M 23 ILE cc_start: 0.8447 (mm) cc_final: 0.8101 (mm) REVERT: M 44 ILE cc_start: 0.8257 (mt) cc_final: 0.7666 (mm) REVERT: M 48 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8364 (mmmt) REVERT: M 68 HIS cc_start: 0.8435 (m90) cc_final: 0.7717 (m170) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2737 time to fit residues: 146.3418 Evaluate side-chains 285 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050065 restraints weight = 62750.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.051628 restraints weight = 36177.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052667 restraints weight = 25296.447| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14595 Z= 0.184 Angle : 0.699 9.350 20918 Z= 0.395 Chirality : 0.039 0.187 2380 Planarity : 0.005 0.115 1650 Dihedral : 30.978 159.839 4276 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 0.24 % Allowed : 3.50 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 958 helix: 1.12 (0.21), residues: 577 sheet: -2.43 (0.58), residues: 48 loop : -0.94 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.017 0.002 PHE G 25 TYR 0.016 0.002 TYR D 37 ARG 0.012 0.001 ARG O 42 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 697) hydrogen bonds : angle 4.02166 ( 1766) covalent geometry : bond 0.00402 (14595) covalent geometry : angle 0.69861 (20918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8208 (m-80) cc_final: 0.7806 (m-10) REVERT: A 80 THR cc_start: 0.8508 (p) cc_final: 0.8017 (p) REVERT: A 97 GLU cc_start: 0.8996 (mt-10) cc_final: 0.7868 (mm-30) REVERT: B 22 LEU cc_start: -0.0195 (tp) cc_final: -0.0480 (mp) REVERT: B 44 LYS cc_start: 0.9523 (mtpp) cc_final: 0.9256 (mttt) REVERT: B 59 LYS cc_start: 0.9254 (ttpp) cc_final: 0.8865 (tppt) REVERT: B 63 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 56 GLU cc_start: 0.8893 (tt0) cc_final: 0.8005 (tt0) REVERT: C 64 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8612 (tp30) REVERT: C 72 ASP cc_start: 0.9412 (m-30) cc_final: 0.9115 (m-30) REVERT: C 92 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 94 ASN cc_start: 0.8975 (t0) cc_final: 0.8464 (t0) REVERT: D 92 GLN cc_start: 0.9576 (tt0) cc_final: 0.8597 (tp40) REVERT: D 99 LEU cc_start: 0.9375 (mt) cc_final: 0.8745 (tt) REVERT: D 106 HIS cc_start: 0.7681 (m-70) cc_final: 0.7387 (m-70) REVERT: E 50 GLU cc_start: 0.8364 (tp30) cc_final: 0.7969 (tp30) REVERT: E 57 SER cc_start: 0.9588 (m) cc_final: 0.9315 (t) REVERT: E 68 GLN cc_start: 0.9391 (tt0) cc_final: 0.9144 (tt0) REVERT: E 73 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8757 (tm-30) REVERT: E 80 THR cc_start: 0.8474 (p) cc_final: 0.8094 (p) REVERT: E 105 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8410 (tp30) REVERT: E 107 THR cc_start: 0.9456 (p) cc_final: 0.9241 (t) REVERT: F 26 ILE cc_start: 0.9564 (tt) cc_final: 0.9299 (tt) REVERT: F 44 LYS cc_start: 0.9546 (tttt) cc_final: 0.8883 (mtmt) REVERT: F 52 GLU cc_start: 0.8767 (tp30) cc_final: 0.8493 (tm-30) REVERT: F 53 GLU cc_start: 0.8506 (tp30) cc_final: 0.8268 (tp30) REVERT: F 59 LYS cc_start: 0.9475 (tttm) cc_final: 0.8603 (tppt) REVERT: F 60 VAL cc_start: 0.9545 (t) cc_final: 0.9075 (t) REVERT: F 63 GLU cc_start: 0.8969 (pt0) cc_final: 0.8661 (mp0) REVERT: F 84 MET cc_start: 0.8963 (mmt) cc_final: 0.8665 (mmt) REVERT: F 85 ASP cc_start: 0.8835 (m-30) cc_final: 0.8589 (m-30) REVERT: F 98 TYR cc_start: 0.8866 (m-80) cc_final: 0.8342 (m-80) REVERT: G 39 TYR cc_start: 0.9365 (m-80) cc_final: 0.8451 (m-80) REVERT: G 56 GLU cc_start: 0.9247 (tt0) cc_final: 0.8665 (mt-10) REVERT: G 64 GLU cc_start: 0.8894 (tp30) cc_final: 0.8235 (tp30) REVERT: G 72 ASP cc_start: 0.9507 (m-30) cc_final: 0.9169 (m-30) REVERT: G 74 LYS cc_start: 0.9335 (mttp) cc_final: 0.8684 (tppt) REVERT: G 79 ILE cc_start: 0.9552 (mm) cc_final: 0.9348 (mm) REVERT: G 116 LEU cc_start: 0.9055 (mt) cc_final: 0.8769 (mm) REVERT: H 49 THR cc_start: 0.8900 (m) cc_final: 0.8599 (p) REVERT: H 54 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7687 (mtmt) REVERT: H 56 MET cc_start: 0.8355 (tpp) cc_final: 0.7836 (tpt) REVERT: H 99 LEU cc_start: 0.9514 (tt) cc_final: 0.9192 (tt) REVERT: H 103 LEU cc_start: 0.9339 (tp) cc_final: 0.8972 (tp) REVERT: H 110 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8958 (mm-30) REVERT: L 1621 ASN cc_start: 0.6884 (p0) cc_final: 0.6681 (p0) REVERT: O 13 ILE cc_start: 0.8306 (tt) cc_final: 0.7992 (tt) REVERT: O 17 VAL cc_start: 0.8233 (m) cc_final: 0.7961 (m) REVERT: O 43 LEU cc_start: 0.8750 (mm) cc_final: 0.8051 (mm) REVERT: M 18 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7022 (tm-30) REVERT: M 23 ILE cc_start: 0.8428 (mm) cc_final: 0.8003 (mm) REVERT: M 48 LYS cc_start: 0.8336 (mmpt) cc_final: 0.8120 (mmmt) REVERT: M 68 HIS cc_start: 0.8118 (m90) cc_final: 0.7719 (m170) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.2611 time to fit residues: 132.1411 Evaluate side-chains 279 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048521 restraints weight = 63408.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.050051 restraints weight = 36766.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051036 restraints weight = 25710.246| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14595 Z= 0.212 Angle : 0.701 11.186 20918 Z= 0.395 Chirality : 0.039 0.186 2380 Planarity : 0.005 0.055 1650 Dihedral : 30.539 161.135 4276 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.38 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 958 helix: 1.14 (0.21), residues: 570 sheet: -2.71 (0.56), residues: 48 loop : -0.82 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 79 PHE 0.014 0.002 PHE G 25 TYR 0.020 0.002 TYR C 39 ARG 0.006 0.001 ARG M 42 Details of bonding type rmsd hydrogen bonds : bond 0.04791 ( 697) hydrogen bonds : angle 3.97572 ( 1766) covalent geometry : bond 0.00464 (14595) covalent geometry : angle 0.70119 (20918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7481 (t-90) cc_final: 0.7060 (t70) REVERT: A 54 TYR cc_start: 0.8286 (m-80) cc_final: 0.8045 (m-80) REVERT: A 57 SER cc_start: 0.9474 (m) cc_final: 0.9271 (m) REVERT: A 60 LEU cc_start: 0.8774 (mm) cc_final: 0.8523 (mm) REVERT: A 80 THR cc_start: 0.8469 (p) cc_final: 0.7827 (p) REVERT: A 93 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 94 GLU cc_start: 0.9282 (tt0) cc_final: 0.9036 (tt0) REVERT: A 97 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8138 (mm-30) REVERT: A 110 CYS cc_start: 0.9537 (m) cc_final: 0.9298 (m) REVERT: A 123 ASP cc_start: 0.8629 (m-30) cc_final: 0.8119 (m-30) REVERT: B 30 THR cc_start: 0.9095 (p) cc_final: 0.8569 (t) REVERT: B 53 GLU cc_start: 0.8336 (tp30) cc_final: 0.7886 (tp30) REVERT: B 59 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8848 (tppt) REVERT: B 63 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 56 GLU cc_start: 0.8952 (tt0) cc_final: 0.7971 (tt0) REVERT: C 64 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8626 (tp30) REVERT: C 72 ASP cc_start: 0.9464 (m-30) cc_final: 0.9243 (m-30) REVERT: C 94 ASN cc_start: 0.9145 (t0) cc_final: 0.8514 (t0) REVERT: C 95 LYS cc_start: 0.9267 (tppt) cc_final: 0.8999 (tppt) REVERT: D 92 GLN cc_start: 0.9501 (tt0) cc_final: 0.8301 (tp40) REVERT: E 50 GLU cc_start: 0.8204 (tp30) cc_final: 0.7981 (tp30) REVERT: E 57 SER cc_start: 0.9634 (m) cc_final: 0.9369 (t) REVERT: E 76 GLN cc_start: 0.9266 (tt0) cc_final: 0.8524 (pt0) REVERT: E 80 THR cc_start: 0.8513 (p) cc_final: 0.7924 (p) REVERT: E 105 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8527 (tp30) REVERT: E 123 ASP cc_start: 0.8563 (m-30) cc_final: 0.8355 (m-30) REVERT: F 26 ILE cc_start: 0.9419 (tt) cc_final: 0.9166 (tt) REVERT: F 44 LYS cc_start: 0.9574 (tttt) cc_final: 0.8857 (mtmt) REVERT: F 59 LYS cc_start: 0.9421 (tttm) cc_final: 0.8519 (tppt) REVERT: F 63 GLU cc_start: 0.8944 (pt0) cc_final: 0.8592 (mp0) REVERT: F 84 MET cc_start: 0.8901 (mmt) cc_final: 0.8627 (mmt) REVERT: F 85 ASP cc_start: 0.8861 (m-30) cc_final: 0.8644 (m-30) REVERT: F 98 TYR cc_start: 0.8687 (m-80) cc_final: 0.8484 (m-80) REVERT: G 39 TYR cc_start: 0.9265 (m-80) cc_final: 0.8601 (m-10) REVERT: G 41 GLU cc_start: 0.8667 (tt0) cc_final: 0.8409 (tt0) REVERT: G 42 ARG cc_start: 0.9513 (ttm110) cc_final: 0.9192 (ttp80) REVERT: G 50 TYR cc_start: 0.9418 (t80) cc_final: 0.8293 (t80) REVERT: G 56 GLU cc_start: 0.9256 (tt0) cc_final: 0.8748 (mt-10) REVERT: G 57 TYR cc_start: 0.8916 (t80) cc_final: 0.7049 (t80) REVERT: G 64 GLU cc_start: 0.8912 (tp30) cc_final: 0.8317 (tp30) REVERT: G 72 ASP cc_start: 0.9530 (m-30) cc_final: 0.9101 (m-30) REVERT: G 74 LYS cc_start: 0.9305 (mttp) cc_final: 0.8600 (tppt) REVERT: G 116 LEU cc_start: 0.9053 (mt) cc_final: 0.8762 (mm) REVERT: H 49 THR cc_start: 0.8837 (m) cc_final: 0.8623 (p) REVERT: H 56 MET cc_start: 0.8243 (tpp) cc_final: 0.7793 (tpt) REVERT: H 86 ILE cc_start: 0.8722 (tp) cc_final: 0.8521 (tt) REVERT: H 92 GLN cc_start: 0.9625 (tt0) cc_final: 0.8844 (tp40) REVERT: H 106 HIS cc_start: 0.8399 (m90) cc_final: 0.7116 (m90) REVERT: H 110 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9011 (mm-30) REVERT: O 23 ILE cc_start: 0.9038 (mp) cc_final: 0.8784 (mp) REVERT: M 18 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7088 (tm-30) REVERT: M 23 ILE cc_start: 0.8428 (mm) cc_final: 0.8216 (mm) REVERT: M 48 LYS cc_start: 0.8631 (mmpt) cc_final: 0.8399 (mmmt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.2802 time to fit residues: 139.0075 Evaluate side-chains 276 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047533 restraints weight = 64291.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049076 restraints weight = 37458.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050089 restraints weight = 26212.854| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14595 Z= 0.218 Angle : 0.695 11.892 20918 Z= 0.393 Chirality : 0.039 0.231 2380 Planarity : 0.006 0.133 1650 Dihedral : 30.341 162.096 4276 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 958 helix: 0.97 (0.21), residues: 570 sheet: -2.77 (0.55), residues: 50 loop : -0.88 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 106 PHE 0.017 0.002 PHE G 25 TYR 0.027 0.002 TYR G 57 ARG 0.011 0.001 ARG M 54 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 697) hydrogen bonds : angle 3.92066 ( 1766) covalent geometry : bond 0.00483 (14595) covalent geometry : angle 0.69504 (20918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7316 (t-90) cc_final: 0.6979 (t70) REVERT: A 50 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 54 TYR cc_start: 0.8532 (m-80) cc_final: 0.7306 (m-10) REVERT: A 56 LYS cc_start: 0.9554 (tptm) cc_final: 0.9322 (tttt) REVERT: A 57 SER cc_start: 0.9359 (m) cc_final: 0.8991 (m) REVERT: A 93 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 94 GLU cc_start: 0.9324 (tt0) cc_final: 0.8921 (tt0) REVERT: A 97 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8242 (mm-30) REVERT: A 110 CYS cc_start: 0.9561 (m) cc_final: 0.9290 (m) REVERT: B 30 THR cc_start: 0.9151 (p) cc_final: 0.8620 (t) REVERT: B 84 MET cc_start: 0.8675 (mmt) cc_final: 0.8354 (mmp) REVERT: B 85 ASP cc_start: 0.8829 (m-30) cc_final: 0.8594 (m-30) REVERT: C 56 GLU cc_start: 0.8885 (tt0) cc_final: 0.8109 (tt0) REVERT: C 64 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8640 (tp30) REVERT: C 72 ASP cc_start: 0.9476 (m-30) cc_final: 0.9250 (m-30) REVERT: C 94 ASN cc_start: 0.9214 (t0) cc_final: 0.8543 (t0) REVERT: C 95 LYS cc_start: 0.9312 (tppt) cc_final: 0.9044 (tppt) REVERT: D 59 MET cc_start: 0.9083 (mmm) cc_final: 0.8883 (mmp) REVERT: D 83 ARG cc_start: 0.8815 (mmt-90) cc_final: 0.8417 (mmm-85) REVERT: E 57 SER cc_start: 0.9650 (m) cc_final: 0.9399 (t) REVERT: E 59 GLU cc_start: 0.7694 (tp30) cc_final: 0.7476 (tp30) REVERT: E 60 LEU cc_start: 0.8746 (mm) cc_final: 0.8210 (mm) REVERT: E 61 LEU cc_start: 0.9446 (mp) cc_final: 0.9227 (mm) REVERT: E 76 GLN cc_start: 0.9349 (tt0) cc_final: 0.8643 (pt0) REVERT: E 80 THR cc_start: 0.8610 (p) cc_final: 0.8053 (p) REVERT: E 105 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8536 (tp30) REVERT: F 26 ILE cc_start: 0.9443 (tt) cc_final: 0.9171 (tt) REVERT: F 44 LYS cc_start: 0.9572 (tttt) cc_final: 0.8840 (mtmt) REVERT: F 59 LYS cc_start: 0.9430 (tttm) cc_final: 0.8516 (tppt) REVERT: F 60 VAL cc_start: 0.9533 (t) cc_final: 0.9111 (p) REVERT: F 63 GLU cc_start: 0.8920 (pt0) cc_final: 0.8484 (mp0) REVERT: F 98 TYR cc_start: 0.8706 (m-80) cc_final: 0.8230 (m-80) REVERT: G 39 TYR cc_start: 0.9154 (m-80) cc_final: 0.8724 (m-80) REVERT: G 42 ARG cc_start: 0.9560 (ttm110) cc_final: 0.9257 (ttp80) REVERT: G 50 TYR cc_start: 0.9454 (t80) cc_final: 0.9207 (t80) REVERT: G 56 GLU cc_start: 0.9044 (tt0) cc_final: 0.8430 (tt0) REVERT: G 64 GLU cc_start: 0.8971 (tp30) cc_final: 0.8368 (tp30) REVERT: G 72 ASP cc_start: 0.9546 (m-30) cc_final: 0.9141 (m-30) REVERT: G 74 LYS cc_start: 0.9330 (mttp) cc_final: 0.8594 (tppt) REVERT: G 92 GLU cc_start: 0.9073 (pm20) cc_final: 0.8819 (pm20) REVERT: G 116 LEU cc_start: 0.9051 (mt) cc_final: 0.8727 (mm) REVERT: H 49 THR cc_start: 0.8880 (m) cc_final: 0.8658 (p) REVERT: H 54 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8519 (mmtp) REVERT: H 56 MET cc_start: 0.8202 (tpp) cc_final: 0.7809 (tpt) REVERT: H 91 ILE cc_start: 0.9813 (mp) cc_final: 0.9388 (tt) REVERT: H 92 GLN cc_start: 0.9655 (tt0) cc_final: 0.9226 (tm-30) REVERT: H 106 HIS cc_start: 0.8617 (m90) cc_final: 0.8104 (m170) REVERT: H 110 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8854 (mm-30) REVERT: O 52 ASP cc_start: 0.7464 (m-30) cc_final: 0.7109 (m-30) REVERT: M 23 ILE cc_start: 0.8579 (mm) cc_final: 0.8338 (mm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2563 time to fit residues: 121.6188 Evaluate side-chains 255 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.048337 restraints weight = 64105.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049892 restraints weight = 36936.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050938 restraints weight = 25703.481| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14595 Z= 0.176 Angle : 0.664 10.213 20918 Z= 0.376 Chirality : 0.037 0.192 2380 Planarity : 0.005 0.085 1650 Dihedral : 30.135 165.290 4276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.18 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 958 helix: 0.98 (0.21), residues: 571 sheet: -2.65 (0.57), residues: 50 loop : -0.87 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.002 PHE A 78 TYR 0.023 0.002 TYR G 57 ARG 0.015 0.001 ARG O 54 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 697) hydrogen bonds : angle 3.77685 ( 1766) covalent geometry : bond 0.00388 (14595) covalent geometry : angle 0.66391 (20918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7194 (t-90) cc_final: 0.6898 (t70) REVERT: A 50 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7939 (mm-30) REVERT: A 54 TYR cc_start: 0.8468 (m-80) cc_final: 0.7424 (m-10) REVERT: A 56 LYS cc_start: 0.9540 (tptm) cc_final: 0.9244 (ttpt) REVERT: A 57 SER cc_start: 0.9344 (m) cc_final: 0.9106 (m) REVERT: A 60 LEU cc_start: 0.8778 (mm) cc_final: 0.8411 (mm) REVERT: A 80 THR cc_start: 0.8609 (p) cc_final: 0.8311 (p) REVERT: A 94 GLU cc_start: 0.9289 (tt0) cc_final: 0.8998 (tt0) REVERT: A 97 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8330 (mm-30) REVERT: A 110 CYS cc_start: 0.9566 (m) cc_final: 0.9296 (m) REVERT: B 30 THR cc_start: 0.8950 (p) cc_final: 0.8490 (t) REVERT: B 44 LYS cc_start: 0.9519 (mtpp) cc_final: 0.9317 (mttt) REVERT: B 59 LYS cc_start: 0.9437 (ttpt) cc_final: 0.9197 (tppt) REVERT: B 84 MET cc_start: 0.8685 (mmt) cc_final: 0.8385 (mmp) REVERT: B 85 ASP cc_start: 0.8936 (m-30) cc_final: 0.8709 (m-30) REVERT: C 56 GLU cc_start: 0.8815 (tt0) cc_final: 0.8014 (tt0) REVERT: C 64 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8587 (tp30) REVERT: C 72 ASP cc_start: 0.9476 (m-30) cc_final: 0.9258 (m-30) REVERT: D 83 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8262 (mmm-85) REVERT: D 92 GLN cc_start: 0.9444 (tt0) cc_final: 0.8858 (tt0) REVERT: D 99 LEU cc_start: 0.9395 (mt) cc_final: 0.8770 (tt) REVERT: E 57 SER cc_start: 0.9611 (m) cc_final: 0.9364 (t) REVERT: E 59 GLU cc_start: 0.7691 (tp30) cc_final: 0.7464 (tp30) REVERT: E 62 ILE cc_start: 0.9607 (mm) cc_final: 0.9377 (mm) REVERT: E 76 GLN cc_start: 0.9317 (tt0) cc_final: 0.8677 (pt0) REVERT: E 80 THR cc_start: 0.8633 (p) cc_final: 0.8200 (p) REVERT: E 93 GLN cc_start: 0.8945 (tp40) cc_final: 0.8722 (tp40) REVERT: E 97 GLU cc_start: 0.9110 (mt-10) cc_final: 0.7955 (mm-30) REVERT: E 105 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8435 (tp30) REVERT: E 125 GLN cc_start: 0.9400 (mt0) cc_final: 0.8958 (mm-40) REVERT: F 44 LYS cc_start: 0.9539 (tttt) cc_final: 0.8816 (mtmt) REVERT: F 52 GLU cc_start: 0.8482 (tp30) cc_final: 0.7889 (tm-30) REVERT: F 59 LYS cc_start: 0.9378 (tttm) cc_final: 0.8455 (tppt) REVERT: F 60 VAL cc_start: 0.9558 (t) cc_final: 0.9048 (p) REVERT: F 63 GLU cc_start: 0.8943 (pt0) cc_final: 0.8436 (mp0) REVERT: F 98 TYR cc_start: 0.8733 (m-80) cc_final: 0.8374 (m-80) REVERT: G 38 ASN cc_start: 0.9009 (m110) cc_final: 0.8742 (t0) REVERT: G 39 TYR cc_start: 0.9082 (m-80) cc_final: 0.8616 (m-80) REVERT: G 42 ARG cc_start: 0.9568 (ttm110) cc_final: 0.9326 (ttp80) REVERT: G 50 TYR cc_start: 0.9428 (t80) cc_final: 0.9225 (t80) REVERT: G 56 GLU cc_start: 0.9207 (tt0) cc_final: 0.8570 (mt-10) REVERT: G 64 GLU cc_start: 0.8988 (tp30) cc_final: 0.8587 (tp30) REVERT: G 72 ASP cc_start: 0.9535 (m-30) cc_final: 0.9118 (m-30) REVERT: G 74 LYS cc_start: 0.9356 (mttp) cc_final: 0.8627 (tppt) REVERT: G 78 ILE cc_start: 0.8801 (pt) cc_final: 0.8588 (pt) REVERT: G 92 GLU cc_start: 0.8868 (pm20) cc_final: 0.8521 (pm20) REVERT: H 51 ILE cc_start: 0.8440 (mm) cc_final: 0.8122 (tp) REVERT: H 56 MET cc_start: 0.8201 (tpp) cc_final: 0.7867 (tpt) REVERT: H 91 ILE cc_start: 0.9777 (mp) cc_final: 0.9312 (tt) REVERT: H 106 HIS cc_start: 0.7993 (m90) cc_final: 0.7503 (m90) REVERT: H 110 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8851 (mm-30) REVERT: O 58 ASP cc_start: 0.8189 (m-30) cc_final: 0.7826 (m-30) REVERT: M 52 ASP cc_start: 0.7504 (m-30) cc_final: 0.7273 (m-30) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2581 time to fit residues: 121.0546 Evaluate side-chains 271 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 94 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047997 restraints weight = 63786.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049494 restraints weight = 37050.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050444 restraints weight = 25983.896| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14595 Z= 0.187 Angle : 0.666 11.264 20918 Z= 0.377 Chirality : 0.037 0.183 2380 Planarity : 0.004 0.048 1650 Dihedral : 29.989 167.445 4276 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 958 helix: 1.03 (0.21), residues: 571 sheet: -2.25 (0.63), residues: 50 loop : -0.90 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.014 0.002 PHE A 104 TYR 0.019 0.002 TYR D 37 ARG 0.009 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 697) hydrogen bonds : angle 3.75696 ( 1766) covalent geometry : bond 0.00418 (14595) covalent geometry : angle 0.66634 (20918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7223 (t-90) cc_final: 0.6836 (t70) REVERT: A 50 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7954 (mm-30) REVERT: A 54 TYR cc_start: 0.8403 (m-80) cc_final: 0.7332 (m-10) REVERT: A 56 LYS cc_start: 0.9485 (tptm) cc_final: 0.9237 (ttpt) REVERT: A 68 GLN cc_start: 0.9080 (tt0) cc_final: 0.8267 (tm-30) REVERT: A 80 THR cc_start: 0.8556 (p) cc_final: 0.7898 (p) REVERT: A 93 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 94 GLU cc_start: 0.9162 (tt0) cc_final: 0.8779 (tt0) REVERT: A 97 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8031 (mm-30) REVERT: A 110 CYS cc_start: 0.9512 (m) cc_final: 0.9228 (m) REVERT: B 26 ILE cc_start: 0.9281 (tt) cc_final: 0.8783 (tt) REVERT: B 30 THR cc_start: 0.8950 (p) cc_final: 0.8514 (t) REVERT: B 44 LYS cc_start: 0.9491 (mtpp) cc_final: 0.9086 (mttt) REVERT: B 85 ASP cc_start: 0.8836 (m-30) cc_final: 0.8631 (m-30) REVERT: C 38 ASN cc_start: 0.9111 (m110) cc_final: 0.8243 (m110) REVERT: C 41 GLU cc_start: 0.8574 (pt0) cc_final: 0.8371 (pt0) REVERT: C 56 GLU cc_start: 0.8933 (tt0) cc_final: 0.8173 (tt0) REVERT: C 64 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8694 (tp30) REVERT: C 72 ASP cc_start: 0.9454 (m-30) cc_final: 0.9243 (m-30) REVERT: D 45 VAL cc_start: 0.8686 (m) cc_final: 0.8466 (p) REVERT: D 56 MET cc_start: 0.8460 (tpp) cc_final: 0.8154 (tpp) REVERT: D 83 ARG cc_start: 0.8697 (mmt-90) cc_final: 0.8258 (mmm-85) REVERT: D 92 GLN cc_start: 0.9429 (tt0) cc_final: 0.8791 (tt0) REVERT: D 99 LEU cc_start: 0.9401 (mt) cc_final: 0.8791 (tt) REVERT: E 37 LYS cc_start: 0.6610 (mtpp) cc_final: 0.6385 (mppt) REVERT: E 50 GLU cc_start: 0.8351 (tp30) cc_final: 0.7961 (tp30) REVERT: E 56 LYS cc_start: 0.9528 (tttt) cc_final: 0.9318 (ttpt) REVERT: E 57 SER cc_start: 0.9651 (m) cc_final: 0.9401 (t) REVERT: E 59 GLU cc_start: 0.7705 (tp30) cc_final: 0.7415 (tp30) REVERT: E 61 LEU cc_start: 0.9395 (mp) cc_final: 0.9056 (mm) REVERT: E 62 ILE cc_start: 0.9588 (mm) cc_final: 0.9371 (mm) REVERT: E 70 LEU cc_start: 0.9603 (tp) cc_final: 0.9137 (tp) REVERT: E 76 GLN cc_start: 0.9300 (tt0) cc_final: 0.8685 (pt0) REVERT: E 80 THR cc_start: 0.8539 (p) cc_final: 0.7951 (p) REVERT: E 97 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8087 (mm-30) REVERT: E 125 GLN cc_start: 0.9416 (mt0) cc_final: 0.8875 (mm-40) REVERT: F 25 ASN cc_start: 0.9045 (m-40) cc_final: 0.8766 (t0) REVERT: F 44 LYS cc_start: 0.9559 (tttt) cc_final: 0.8833 (mtmt) REVERT: F 52 GLU cc_start: 0.8484 (tp30) cc_final: 0.7916 (tm-30) REVERT: F 59 LYS cc_start: 0.9258 (tttm) cc_final: 0.8796 (tppt) REVERT: F 60 VAL cc_start: 0.9575 (t) cc_final: 0.9211 (p) REVERT: F 63 GLU cc_start: 0.8890 (pt0) cc_final: 0.8477 (pt0) REVERT: F 98 TYR cc_start: 0.8542 (m-80) cc_final: 0.8183 (m-80) REVERT: G 38 ASN cc_start: 0.9092 (m110) cc_final: 0.8772 (t0) REVERT: G 39 TYR cc_start: 0.9024 (m-80) cc_final: 0.8667 (m-80) REVERT: G 42 ARG cc_start: 0.9560 (ttm110) cc_final: 0.9344 (ttp80) REVERT: G 50 TYR cc_start: 0.9474 (t80) cc_final: 0.8418 (t80) REVERT: G 56 GLU cc_start: 0.9151 (tt0) cc_final: 0.8549 (mt-10) REVERT: G 64 GLU cc_start: 0.9017 (tp30) cc_final: 0.8452 (tp30) REVERT: G 72 ASP cc_start: 0.9511 (m-30) cc_final: 0.9110 (m-30) REVERT: G 74 LYS cc_start: 0.9263 (mttp) cc_final: 0.8532 (tppt) REVERT: G 116 LEU cc_start: 0.9184 (mm) cc_final: 0.8862 (mm) REVERT: G 118 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8295 (mmmt) REVERT: H 51 ILE cc_start: 0.8471 (mm) cc_final: 0.8152 (tp) REVERT: H 56 MET cc_start: 0.8337 (tpp) cc_final: 0.8003 (tpt) REVERT: H 91 ILE cc_start: 0.9764 (mp) cc_final: 0.9311 (tt) REVERT: H 92 GLN cc_start: 0.9600 (tt0) cc_final: 0.8396 (tp40) REVERT: H 110 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8919 (mm-30) REVERT: O 1 MET cc_start: 0.8113 (tpt) cc_final: 0.7808 (tpp) REVERT: O 23 ILE cc_start: 0.9117 (mp) cc_final: 0.8591 (mp) REVERT: O 24 GLU cc_start: 0.9021 (tp30) cc_final: 0.8794 (pt0) REVERT: O 58 ASP cc_start: 0.8176 (m-30) cc_final: 0.7841 (m-30) REVERT: M 23 ILE cc_start: 0.8569 (mm) cc_final: 0.8313 (mm) REVERT: M 43 LEU cc_start: 0.8004 (mm) cc_final: 0.6462 (mm) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2547 time to fit residues: 118.6786 Evaluate side-chains 272 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 81 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.047422 restraints weight = 63241.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048922 restraints weight = 36458.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.049931 restraints weight = 25573.565| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14595 Z= 0.188 Angle : 0.669 9.776 20918 Z= 0.377 Chirality : 0.037 0.176 2380 Planarity : 0.004 0.048 1650 Dihedral : 29.925 169.007 4276 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.11 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 958 helix: 0.93 (0.21), residues: 579 sheet: -2.25 (0.65), residues: 52 loop : -0.92 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS D 106 PHE 0.016 0.002 PHE G 25 TYR 0.028 0.002 TYR B 98 ARG 0.009 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 697) hydrogen bonds : angle 3.78950 ( 1766) covalent geometry : bond 0.00418 (14595) covalent geometry : angle 0.66851 (20918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7131 (t-90) cc_final: 0.6757 (t70) REVERT: A 50 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 54 TYR cc_start: 0.8453 (m-80) cc_final: 0.7405 (m-10) REVERT: A 56 LYS cc_start: 0.9501 (tptm) cc_final: 0.9226 (ttpt) REVERT: A 80 THR cc_start: 0.8683 (p) cc_final: 0.8124 (p) REVERT: A 93 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 94 GLU cc_start: 0.9240 (tt0) cc_final: 0.8877 (tt0) REVERT: A 97 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8326 (mm-30) REVERT: A 110 CYS cc_start: 0.9479 (m) cc_final: 0.9230 (m) REVERT: B 26 ILE cc_start: 0.9215 (tt) cc_final: 0.8825 (tt) REVERT: B 30 THR cc_start: 0.9002 (p) cc_final: 0.8625 (t) REVERT: B 85 ASP cc_start: 0.8807 (m-30) cc_final: 0.8587 (m-30) REVERT: C 38 ASN cc_start: 0.9152 (m110) cc_final: 0.8268 (m110) REVERT: C 39 TYR cc_start: 0.8786 (m-80) cc_final: 0.8523 (m-80) REVERT: C 56 GLU cc_start: 0.8988 (tt0) cc_final: 0.8224 (tt0) REVERT: C 64 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8647 (tp30) REVERT: C 72 ASP cc_start: 0.9451 (m-30) cc_final: 0.9246 (m-30) REVERT: D 45 VAL cc_start: 0.8741 (m) cc_final: 0.8536 (p) REVERT: D 56 MET cc_start: 0.8521 (tpp) cc_final: 0.8169 (tpp) REVERT: D 58 ILE cc_start: 0.9684 (mm) cc_final: 0.9439 (mt) REVERT: D 83 ARG cc_start: 0.8722 (mmt-90) cc_final: 0.8267 (mmm-85) REVERT: D 92 GLN cc_start: 0.9432 (tt0) cc_final: 0.8791 (tt0) REVERT: D 99 LEU cc_start: 0.9410 (mt) cc_final: 0.8765 (tt) REVERT: D 106 HIS cc_start: 0.7918 (m-70) cc_final: 0.7122 (m-70) REVERT: E 37 LYS cc_start: 0.6619 (mtpp) cc_final: 0.6400 (mppt) REVERT: E 50 GLU cc_start: 0.8280 (tp30) cc_final: 0.7640 (tp30) REVERT: E 54 TYR cc_start: 0.7943 (m-10) cc_final: 0.7636 (m-10) REVERT: E 57 SER cc_start: 0.9651 (m) cc_final: 0.9386 (t) REVERT: E 59 GLU cc_start: 0.7714 (tp30) cc_final: 0.7412 (tp30) REVERT: E 60 LEU cc_start: 0.8852 (mm) cc_final: 0.7592 (mm) REVERT: E 61 LEU cc_start: 0.9432 (mp) cc_final: 0.9027 (mm) REVERT: E 62 ILE cc_start: 0.9547 (mm) cc_final: 0.9315 (mm) REVERT: E 70 LEU cc_start: 0.9587 (tp) cc_final: 0.9070 (tp) REVERT: E 80 THR cc_start: 0.8564 (p) cc_final: 0.8011 (p) REVERT: E 93 GLN cc_start: 0.8996 (tp40) cc_final: 0.8612 (tp40) REVERT: E 97 GLU cc_start: 0.9119 (mt-10) cc_final: 0.7905 (mm-30) REVERT: E 123 ASP cc_start: 0.8543 (m-30) cc_final: 0.8125 (m-30) REVERT: E 125 GLN cc_start: 0.9380 (mt0) cc_final: 0.8770 (mm-40) REVERT: F 25 ASN cc_start: 0.8956 (m110) cc_final: 0.8718 (t0) REVERT: F 44 LYS cc_start: 0.9525 (tttt) cc_final: 0.8889 (mtmt) REVERT: F 52 GLU cc_start: 0.8473 (tp30) cc_final: 0.8163 (tm-30) REVERT: F 59 LYS cc_start: 0.9236 (tttm) cc_final: 0.8306 (tppt) REVERT: F 60 VAL cc_start: 0.9577 (t) cc_final: 0.9075 (p) REVERT: F 63 GLU cc_start: 0.8906 (pt0) cc_final: 0.8430 (mp0) REVERT: F 98 TYR cc_start: 0.8438 (m-80) cc_final: 0.8153 (m-80) REVERT: G 38 ASN cc_start: 0.9130 (m110) cc_final: 0.8763 (t0) REVERT: G 39 TYR cc_start: 0.9034 (m-80) cc_final: 0.8699 (m-80) REVERT: G 50 TYR cc_start: 0.9450 (t80) cc_final: 0.9228 (t80) REVERT: G 56 GLU cc_start: 0.9177 (tt0) cc_final: 0.8566 (mt-10) REVERT: G 64 GLU cc_start: 0.9048 (tp30) cc_final: 0.8639 (tp30) REVERT: G 72 ASP cc_start: 0.9548 (m-30) cc_final: 0.9147 (m-30) REVERT: G 74 LYS cc_start: 0.9272 (mttp) cc_final: 0.8526 (tppt) REVERT: G 92 GLU cc_start: 0.8898 (pm20) cc_final: 0.8419 (pm20) REVERT: G 116 LEU cc_start: 0.9181 (mm) cc_final: 0.8896 (mm) REVERT: H 51 ILE cc_start: 0.8483 (mm) cc_final: 0.8141 (tp) REVERT: H 91 ILE cc_start: 0.9752 (mp) cc_final: 0.9270 (tt) REVERT: H 92 GLN cc_start: 0.9597 (tt0) cc_final: 0.8517 (tm-30) REVERT: H 110 GLU cc_start: 0.9375 (mm-30) cc_final: 0.8953 (mm-30) REVERT: L 1621 ASN cc_start: 0.6699 (p0) cc_final: 0.5553 (t0) REVERT: O 23 ILE cc_start: 0.9072 (mp) cc_final: 0.8686 (mp) REVERT: O 24 GLU cc_start: 0.9024 (tp30) cc_final: 0.8788 (pt0) REVERT: O 48 LYS cc_start: 0.8917 (mppt) cc_final: 0.8690 (mmtm) REVERT: M 23 ILE cc_start: 0.8515 (mm) cc_final: 0.8258 (mm) REVERT: M 51 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2414 time to fit residues: 118.2860 Evaluate side-chains 276 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.0670 overall best weight: 5.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046548 restraints weight = 65724.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.048026 restraints weight = 38044.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.049002 restraints weight = 26721.640| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14595 Z= 0.231 Angle : 0.715 12.488 20918 Z= 0.399 Chirality : 0.038 0.187 2380 Planarity : 0.005 0.075 1650 Dihedral : 29.892 171.852 4276 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.43 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 958 helix: 0.93 (0.21), residues: 579 sheet: -2.05 (0.70), residues: 52 loop : -0.96 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS D 106 PHE 0.035 0.003 PHE A 67 TYR 0.023 0.002 TYR D 37 ARG 0.009 0.001 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 697) hydrogen bonds : angle 3.96898 ( 1766) covalent geometry : bond 0.00513 (14595) covalent geometry : angle 0.71487 (20918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7242 (t-90) cc_final: 0.6846 (t70) REVERT: A 50 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 54 TYR cc_start: 0.8528 (m-80) cc_final: 0.7297 (m-10) REVERT: A 56 LYS cc_start: 0.9502 (tptm) cc_final: 0.9209 (ttpt) REVERT: A 68 GLN cc_start: 0.9108 (tt0) cc_final: 0.8480 (tm-30) REVERT: A 76 GLN cc_start: 0.9177 (tt0) cc_final: 0.8536 (pt0) REVERT: A 80 THR cc_start: 0.8716 (p) cc_final: 0.8155 (p) REVERT: A 93 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 94 GLU cc_start: 0.9008 (tt0) cc_final: 0.8705 (tt0) REVERT: A 97 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8320 (mm-30) REVERT: A 110 CYS cc_start: 0.9444 (m) cc_final: 0.9223 (m) REVERT: B 25 ASN cc_start: 0.7813 (t0) cc_final: 0.7479 (t0) REVERT: B 26 ILE cc_start: 0.9057 (tt) cc_final: 0.8669 (tt) REVERT: B 44 LYS cc_start: 0.9398 (mttt) cc_final: 0.8923 (mmtp) REVERT: B 85 ASP cc_start: 0.8751 (m-30) cc_final: 0.8539 (m-30) REVERT: C 39 TYR cc_start: 0.8981 (m-80) cc_final: 0.8677 (m-80) REVERT: C 56 GLU cc_start: 0.9050 (tt0) cc_final: 0.8245 (tt0) REVERT: C 64 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8613 (tp30) REVERT: C 72 ASP cc_start: 0.9447 (m-30) cc_final: 0.9222 (m-30) REVERT: D 56 MET cc_start: 0.8570 (tpp) cc_final: 0.8206 (tpp) REVERT: D 92 GLN cc_start: 0.9366 (tt0) cc_final: 0.8691 (tt0) REVERT: D 99 LEU cc_start: 0.9377 (mt) cc_final: 0.8855 (tp) REVERT: E 37 LYS cc_start: 0.6505 (mtpp) cc_final: 0.6249 (mppt) REVERT: E 57 SER cc_start: 0.9666 (m) cc_final: 0.9430 (t) REVERT: E 70 LEU cc_start: 0.9563 (tp) cc_final: 0.8912 (tp) REVERT: E 93 GLN cc_start: 0.8995 (tp40) cc_final: 0.8769 (tp40) REVERT: E 125 GLN cc_start: 0.9389 (mt0) cc_final: 0.8780 (mm-40) REVERT: F 25 ASN cc_start: 0.8954 (m110) cc_final: 0.8752 (t0) REVERT: F 52 GLU cc_start: 0.8559 (tp30) cc_final: 0.8337 (tm-30) REVERT: F 59 LYS cc_start: 0.9241 (tttm) cc_final: 0.8349 (tppp) REVERT: F 60 VAL cc_start: 0.9551 (t) cc_final: 0.9133 (p) REVERT: F 63 GLU cc_start: 0.8924 (pt0) cc_final: 0.8373 (mp0) REVERT: F 98 TYR cc_start: 0.8527 (m-80) cc_final: 0.8236 (m-80) REVERT: G 39 TYR cc_start: 0.9006 (m-80) cc_final: 0.8718 (m-80) REVERT: G 50 TYR cc_start: 0.9471 (t80) cc_final: 0.9243 (t80) REVERT: G 56 GLU cc_start: 0.9250 (tt0) cc_final: 0.8880 (tt0) REVERT: G 64 GLU cc_start: 0.9043 (tp30) cc_final: 0.8628 (tp30) REVERT: G 72 ASP cc_start: 0.9544 (m-30) cc_final: 0.9215 (m-30) REVERT: H 51 ILE cc_start: 0.8179 (mm) cc_final: 0.7910 (tp) REVERT: H 91 ILE cc_start: 0.9748 (mp) cc_final: 0.9274 (tt) REVERT: H 92 GLN cc_start: 0.9619 (tt0) cc_final: 0.8624 (tm-30) REVERT: H 110 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9096 (mm-30) REVERT: L 1621 ASN cc_start: 0.7261 (p0) cc_final: 0.6766 (p0) REVERT: O 1 MET cc_start: 0.8244 (tpt) cc_final: 0.7941 (tpp) REVERT: O 24 GLU cc_start: 0.9004 (tp30) cc_final: 0.8744 (pt0) REVERT: O 48 LYS cc_start: 0.8907 (mppt) cc_final: 0.8653 (mmtm) REVERT: O 61 ILE cc_start: 0.5921 (mm) cc_final: 0.5637 (mm) REVERT: M 23 ILE cc_start: 0.8512 (mm) cc_final: 0.8261 (mm) REVERT: M 48 LYS cc_start: 0.8219 (mmpt) cc_final: 0.7927 (mmmt) REVERT: M 51 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7355 (tm-30) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2529 time to fit residues: 117.3893 Evaluate side-chains 256 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.045073 restraints weight = 67424.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046512 restraints weight = 38941.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.047457 restraints weight = 27545.530| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14595 Z= 0.291 Angle : 0.747 11.763 20918 Z= 0.418 Chirality : 0.041 0.218 2380 Planarity : 0.005 0.063 1650 Dihedral : 29.986 177.053 4276 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 958 helix: 0.75 (0.21), residues: 579 sheet: -2.11 (0.72), residues: 52 loop : -1.02 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.046 0.004 PHE A 67 TYR 0.025 0.002 TYR D 37 ARG 0.014 0.001 ARG O 74 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 697) hydrogen bonds : angle 4.20814 ( 1766) covalent geometry : bond 0.00643 (14595) covalent geometry : angle 0.74654 (20918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.29 seconds wall clock time: 70 minutes 34.15 seconds (4234.15 seconds total)