Starting phenix.real_space_refine on Sat Sep 12 02:50:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_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 { model { file = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2026/5kgf_8246.map" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 3.07, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 420.8 milliseconds 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: 2.26 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: 2.37 Time building geometry restraints manager: 1.57 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 1.418 1.649 -0.231 2.50e-02 1.60e+03 8.57e+01 ... (remaining 14590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 20648 4.97 - 9.95: 256 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 1.90e+00 2.77e-01 1.43e+02 angle pdb=" O4' DT J 14 " pdb=" C1' DT J 14 " pdb=" N1 DT J 14 " ideal model delta sigma weight residual 108.00 114.15 -6.15 7.00e-01 2.04e+00 7.72e+01 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=" O4' DG J 21 " pdb=" C1' DG J 21 " pdb=" N9 DG J 21 " ideal model delta sigma weight residual 108.00 114.02 -6.02 7.00e-01 2.04e+00 7.40e+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 ... (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 - 0.325: 2377 0.325 - 0.651: 2 0.651 - 0.976: 0 0.976 - 1.302: 0 1.302 - 1.627: 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 2.34 0.71 1.63 2.00e-01 2.50e+01 6.62e+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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.010 0.298 14595 Z= 0.724 Angle : 1.450 24.863 20918 Z= 1.140 Chirality : 0.075 1.627 2380 Planarity : 0.006 0.098 1650 Dihedral : 27.921 158.653 6277 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 27.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.001 ARG D 96 TYR 0.031 0.004 TYR H 37 PHE 0.014 0.002 PHE C 25 HIS 0.015 0.003 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.72 (14595) covalent geometry : angle 1.44980 / 1.14 (20918) hydrogen bonds : bond 0.28533 / 19.20 ( 697) hydrogen bonds : angle 11.50447 / 8.31 ( 1766) *********************** 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 : 0.488 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: A 54 TYR cc_start: 0.8571 (m-80) cc_final: 0.7257 (m-10) REVERT: A 55 GLN cc_start: 0.8695 (mt0) cc_final: 0.8429 (mt0) REVERT: A 56 LYS cc_start: 0.9222 (tttt) cc_final: 0.9013 (tptm) REVERT: A 60 LEU cc_start: 0.9132 (mt) cc_final: 0.7911 (mp) REVERT: A 112 ILE cc_start: 0.9267 (mt) cc_final: 0.8805 (mm) REVERT: A 119 ILE cc_start: 0.9146 (pt) cc_final: 0.8912 (pt) REVERT: B 64 ASN cc_start: 0.9159 (m-40) cc_final: 0.8900 (p0) REVERT: C 39 TYR cc_start: 0.8169 (m-80) cc_final: 0.7915 (m-80) REVERT: C 56 GLU cc_start: 0.8622 (tt0) cc_final: 0.8370 (tt0) REVERT: C 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.8184 (tp30) REVERT: C 92 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6334 (tt0) REVERT: D 38 VAL cc_start: 0.9409 (t) cc_final: 0.9094 (t) REVERT: D 58 ILE cc_start: 0.8846 (mm) cc_final: 0.8632 (mt) REVERT: D 103 LEU cc_start: 0.9075 (tt) cc_final: 0.8483 (tp) REVERT: D 106 HIS cc_start: 0.8647 (m-70) cc_final: 0.7382 (m-70) REVERT: E 56 LYS cc_start: 0.9254 (tttt) cc_final: 0.8967 (tptm) REVERT: E 60 LEU cc_start: 0.9203 (mt) cc_final: 0.8499 (mp) REVERT: E 90 MET cc_start: 0.8530 (mmm) cc_final: 0.8222 (mmp) REVERT: E 94 GLU cc_start: 0.7782 (tp30) cc_final: 0.7565 (tp30) REVERT: E 112 ILE cc_start: 0.9265 (mt) cc_final: 0.8841 (mm) REVERT: E 119 ILE cc_start: 0.9248 (pt) cc_final: 0.9043 (pt) REVERT: E 125 GLN cc_start: 0.9201 (mt0) cc_final: 0.8954 (mm-40) REVERT: E 130 ILE cc_start: 0.9205 (mt) cc_final: 0.8897 (mt) REVERT: F 29 ILE cc_start: 0.9472 (mm) cc_final: 0.9231 (mm) REVERT: F 43 VAL cc_start: 0.9713 (t) cc_final: 0.9296 (p) REVERT: F 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.9198 (ttpt) REVERT: F 84 MET cc_start: 0.8307 (mmm) cc_final: 0.8063 (tpp) REVERT: F 88 TYR cc_start: 0.9315 (m-10) cc_final: 0.8693 (m-80) REVERT: G 41 GLU cc_start: 0.8158 (tt0) cc_final: 0.7944 (mt-10) REVERT: G 64 GLU cc_start: 0.8440 (tp30) cc_final: 0.8111 (tp30) REVERT: G 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8364 (m-30) REVERT: G 74 LYS cc_start: 0.8981 (mttp) cc_final: 0.8446 (tppt) REVERT: G 92 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7867 (tt0) REVERT: G 107 VAL cc_start: 0.9032 (m) cc_final: 0.8818 (t) REVERT: O 3 ILE cc_start: 0.7138 (pt) cc_final: 0.6890 (pt) REVERT: O 17 VAL cc_start: 0.6988 (m) cc_final: 0.5779 (m) REVERT: M 17 VAL cc_start: 0.8074 (m) cc_final: 0.7747 (p) REVERT: M 23 ILE cc_start: 0.7350 (mm) cc_final: 0.6846 (mm) REVERT: M 67 LEU cc_start: 0.8359 (mt) cc_final: 0.8053 (mp) REVERT: M 70 VAL cc_start: 0.4845 (t) cc_final: 0.4504 (t) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.1522 time to fit residues: 87.7990 Evaluate side-chains 277 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 39 HIS E 68 GLN E 76 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052747 restraints weight = 63314.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.054287 restraints weight = 35913.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055305 restraints weight = 24881.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055901 restraints weight = 19811.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056267 restraints weight = 17293.305| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3502 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= 0.240 Angle : 1.090 26.770 20918 Z= 0.569 Chirality : 0.079 2.173 2380 Planarity : 0.009 0.158 1650 Dihedral : 32.650 160.097 4276 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.07 % Favored : 95.51 % 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 : 1.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.23), residues: 958 helix: -0.80 (0.19), residues: 571 sheet: -2.34 (0.49), residues: 50 loop : -1.60 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 54 TYR 0.030 0.003 TYR G 39 PHE 0.017 0.002 PHE O 4 HIS 0.017 0.003 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.24 (14595) covalent geometry : angle 1.09023 / 0.57 (20918) hydrogen bonds : bond 0.08582 / 5.98 ( 697) hydrogen bonds : angle 5.47668 / 3.94 ( 1766) *********************** 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 391 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 0.389 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: A 50 GLU cc_start: 0.8578 (tp30) cc_final: 0.7545 (tp30) REVERT: A 54 TYR cc_start: 0.8477 (m-80) cc_final: 0.7174 (m-10) REVERT: A 56 LYS cc_start: 0.9419 (tttt) cc_final: 0.8977 (tptm) REVERT: A 59 GLU cc_start: 0.7944 (tp30) cc_final: 0.7425 (tp30) REVERT: A 60 LEU cc_start: 0.8644 (mt) cc_final: 0.8443 (mm) REVERT: A 110 CYS cc_start: 0.9470 (m) cc_final: 0.8903 (t) REVERT: B 52 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 63 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8475 (tm-30) REVERT: B 64 ASN cc_start: 0.9208 (m-40) cc_final: 0.8806 (m-40) REVERT: C 41 GLU cc_start: 0.8467 (tt0) cc_final: 0.8198 (tt0) REVERT: C 56 GLU cc_start: 0.8855 (tt0) cc_final: 0.7803 (tt0) REVERT: C 95 LYS cc_start: 0.9074 (tppp) cc_final: 0.8655 (tppp) REVERT: D 58 ILE cc_start: 0.9467 (mm) cc_final: 0.9246 (mt) REVERT: D 65 ASP cc_start: 0.9226 (t0) cc_final: 0.9021 (t0) REVERT: D 66 ILE cc_start: 0.9337 (mt) cc_final: 0.9050 (mt) REVERT: D 86 ILE cc_start: 0.9431 (tp) cc_final: 0.9187 (mt) REVERT: D 103 LEU cc_start: 0.9543 (tt) cc_final: 0.9141 (mt) REVERT: D 112 THR cc_start: 0.9667 (m) cc_final: 0.9283 (p) REVERT: E 54 TYR cc_start: 0.8444 (m-10) cc_final: 0.7651 (m-80) REVERT: E 56 LYS cc_start: 0.9405 (tttt) cc_final: 0.8997 (tptp) REVERT: E 59 GLU cc_start: 0.7967 (tp30) cc_final: 0.7469 (tp30) REVERT: E 60 LEU cc_start: 0.9098 (mt) cc_final: 0.8267 (mp) REVERT: E 61 LEU cc_start: 0.9542 (mm) cc_final: 0.9033 (mm) REVERT: E 70 LEU cc_start: 0.9637 (tp) cc_final: 0.9192 (tp) REVERT: E 80 THR cc_start: 0.8518 (p) cc_final: 0.8253 (p) REVERT: E 90 MET cc_start: 0.9126 (mmm) cc_final: 0.8890 (mmp) REVERT: E 97 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8880 (mt-10) REVERT: E 107 THR cc_start: 0.9030 (m) cc_final: 0.8553 (p) REVERT: E 110 CYS cc_start: 0.9391 (m) cc_final: 0.8755 (m) REVERT: E 115 LYS cc_start: 0.8933 (mptt) cc_final: 0.8697 (mmtt) REVERT: E 119 ILE cc_start: 0.9640 (pt) cc_final: 0.9434 (pt) REVERT: F 25 ASN cc_start: 0.8823 (m-40) cc_final: 0.8563 (t0) REVERT: F 29 ILE cc_start: 0.9493 (mm) cc_final: 0.9240 (tp) REVERT: F 43 VAL cc_start: 0.9504 (t) cc_final: 0.9125 (p) REVERT: F 44 LYS cc_start: 0.9497 (tttt) cc_final: 0.8917 (mtmt) REVERT: F 46 ILE cc_start: 0.9126 (mp) cc_final: 0.8599 (tp) REVERT: F 59 LYS cc_start: 0.9376 (tttp) cc_final: 0.8984 (ttmm) REVERT: F 84 MET cc_start: 0.8887 (mmm) cc_final: 0.8437 (mmt) REVERT: F 88 TYR cc_start: 0.9355 (m-10) cc_final: 0.8818 (m-10) REVERT: F 96 THR cc_start: 0.9068 (m) cc_final: 0.8699 (m) REVERT: G 39 TYR cc_start: 0.9389 (m-10) cc_final: 0.9026 (m-80) REVERT: G 56 GLU cc_start: 0.9165 (tt0) cc_final: 0.8186 (tt0) REVERT: G 64 GLU cc_start: 0.8942 (tp30) cc_final: 0.8271 (tp30) REVERT: G 72 ASP cc_start: 0.9251 (m-30) cc_final: 0.8838 (m-30) REVERT: G 83 LEU cc_start: 0.9791 (mt) cc_final: 0.9585 (mm) REVERT: G 92 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 92 GLN cc_start: 0.9337 (tt0) cc_final: 0.8788 (tt0) REVERT: H 99 LEU cc_start: 0.9475 (tp) cc_final: 0.9239 (tt) REVERT: H 108 VAL cc_start: 0.9413 (t) cc_final: 0.9075 (t) REVERT: H 110 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9130 (mm-30) REVERT: H 112 THR cc_start: 0.9597 (m) cc_final: 0.9372 (p) REVERT: O 17 VAL cc_start: 0.7532 (m) cc_final: 0.7146 (m) REVERT: O 23 ILE cc_start: 0.9164 (mp) cc_final: 0.8927 (mp) REVERT: O 41 GLN cc_start: 0.7592 (mt0) cc_final: 0.7248 (mt0) REVERT: O 42 ARG cc_start: 0.7755 (ttt-90) cc_final: 0.7547 (tpt-90) REVERT: O 43 LEU cc_start: 0.8831 (mm) cc_final: 0.8337 (mm) REVERT: O 44 ILE cc_start: 0.7821 (mt) cc_final: 0.6976 (mm) REVERT: O 68 HIS cc_start: 0.8278 (m170) cc_final: 0.7301 (m170) REVERT: O 72 ARG cc_start: 0.7562 (ptp90) cc_final: 0.7120 (ttp-110) REVERT: M 6 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8261 (ptmm) REVERT: M 13 ILE cc_start: 0.9093 (tt) cc_final: 0.8853 (tt) REVERT: M 18 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6802 (mm-30) REVERT: M 23 ILE cc_start: 0.9053 (mm) cc_final: 0.8517 (mm) REVERT: M 68 HIS cc_start: 0.8594 (m90) cc_final: 0.7881 (m170) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.1245 time to fit residues: 69.9579 Evaluate side-chains 301 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.0670 chunk 119 optimal weight: 0.0030 overall best weight: 1.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052314 restraints weight = 64454.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053901 restraints weight = 36628.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054935 restraints weight = 25467.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055600 restraints weight = 20352.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056033 restraints weight = 17684.150| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14595 Z= 0.176 Angle : 0.892 25.482 20918 Z= 0.478 Chirality : 0.070 2.089 2380 Planarity : 0.007 0.111 1650 Dihedral : 31.946 161.767 4276 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.18 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 958 helix: 0.60 (0.21), residues: 577 sheet: -2.43 (0.56), residues: 48 loop : -1.19 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.024 0.003 TYR G 57 PHE 0.021 0.003 PHE O 4 HIS 0.009 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.18 (14595) covalent geometry : angle 0.89175 / 0.48 (20918) hydrogen bonds : bond 0.06273 / 4.31 ( 697) hydrogen bonds : angle 4.61876 / 3.29 ( 1766) *********************** 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 374 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.401 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: A 50 GLU cc_start: 0.7876 (tp30) cc_final: 0.7514 (mm-30) REVERT: A 54 TYR cc_start: 0.7808 (m-80) cc_final: 0.7043 (m-10) REVERT: A 56 LYS cc_start: 0.9398 (tttt) cc_final: 0.9126 (tptm) REVERT: A 59 GLU cc_start: 0.7611 (tp30) cc_final: 0.7286 (tp30) REVERT: A 60 LEU cc_start: 0.8309 (mt) cc_final: 0.7702 (mm) REVERT: A 90 MET cc_start: 0.9166 (mmt) cc_final: 0.8884 (mmt) REVERT: A 105 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8686 (tp30) REVERT: A 125 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8852 (mm-40) REVERT: A 130 ILE cc_start: 0.9316 (mp) cc_final: 0.8967 (tp) REVERT: B 44 LYS cc_start: 0.9595 (mtpp) cc_final: 0.9366 (mttt) REVERT: B 52 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 53 GLU cc_start: 0.8297 (tp30) cc_final: 0.7506 (tp30) REVERT: B 59 LYS cc_start: 0.9407 (ttpp) cc_final: 0.8937 (tptp) REVERT: B 63 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8322 (tp30) REVERT: C 41 GLU cc_start: 0.8590 (tt0) cc_final: 0.8355 (tt0) REVERT: C 56 GLU cc_start: 0.8766 (tt0) cc_final: 0.7797 (tt0) REVERT: C 57 TYR cc_start: 0.8868 (t80) cc_final: 0.7359 (t80) REVERT: C 79 ILE cc_start: 0.9547 (tt) cc_final: 0.9189 (mm) REVERT: C 82 HIS cc_start: 0.9189 (m90) cc_final: 0.8601 (m-70) REVERT: C 94 ASN cc_start: 0.8982 (t0) cc_final: 0.8149 (t0) REVERT: D 92 GLN cc_start: 0.9549 (tt0) cc_final: 0.8980 (tm-30) REVERT: D 106 HIS cc_start: 0.7521 (m-70) cc_final: 0.7197 (m-70) REVERT: E 50 GLU cc_start: 0.8263 (tp30) cc_final: 0.7527 (tp30) REVERT: E 56 LYS cc_start: 0.9423 (tttt) cc_final: 0.9081 (tptm) REVERT: E 65 LEU cc_start: 0.9218 (mt) cc_final: 0.9018 (mm) REVERT: E 68 GLN cc_start: 0.9375 (tt0) cc_final: 0.9167 (tt0) REVERT: E 70 LEU cc_start: 0.9552 (tp) cc_final: 0.9095 (tp) REVERT: F 29 ILE cc_start: 0.9499 (mm) cc_final: 0.9168 (tp) REVERT: F 44 LYS cc_start: 0.9525 (tttt) cc_final: 0.8972 (mtmt) REVERT: F 52 GLU cc_start: 0.8653 (tp30) cc_final: 0.8434 (tm-30) REVERT: F 53 GLU cc_start: 0.8358 (tp30) cc_final: 0.8093 (tp30) REVERT: F 58 LEU cc_start: 0.9691 (tp) cc_final: 0.9461 (tp) REVERT: F 59 LYS cc_start: 0.9318 (tttp) cc_final: 0.8969 (ttmm) REVERT: F 88 TYR cc_start: 0.9235 (m-10) cc_final: 0.8875 (m-80) REVERT: F 98 TYR cc_start: 0.8878 (m-80) cc_final: 0.8632 (m-80) REVERT: G 39 TYR cc_start: 0.9361 (m-10) cc_final: 0.9100 (m-10) REVERT: G 56 GLU cc_start: 0.9033 (tt0) cc_final: 0.8446 (mt-10) REVERT: G 64 GLU cc_start: 0.8919 (tp30) cc_final: 0.8222 (tp30) REVERT: G 72 ASP cc_start: 0.9338 (m-30) cc_final: 0.8977 (m-30) REVERT: G 83 LEU cc_start: 0.9778 (mt) cc_final: 0.9568 (mm) REVERT: G 111 ILE cc_start: 0.9054 (pt) cc_final: 0.8836 (mm) REVERT: H 32 GLU cc_start: 0.9015 (pm20) cc_final: 0.8806 (pm20) REVERT: H 49 THR cc_start: 0.8479 (m) cc_final: 0.8066 (p) REVERT: H 66 ILE cc_start: 0.9507 (mt) cc_final: 0.9219 (mt) REVERT: H 99 LEU cc_start: 0.9540 (tp) cc_final: 0.9050 (tt) REVERT: H 103 LEU cc_start: 0.9211 (tp) cc_final: 0.8921 (mp) REVERT: H 110 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9073 (mm-30) REVERT: O 17 VAL cc_start: 0.7850 (m) cc_final: 0.7137 (m) REVERT: O 43 LEU cc_start: 0.8800 (mm) cc_final: 0.8171 (mm) REVERT: O 44 ILE cc_start: 0.7811 (mt) cc_final: 0.7531 (mp) REVERT: O 51 GLU cc_start: 0.6177 (pm20) cc_final: 0.5784 (pm20) REVERT: O 68 HIS cc_start: 0.7545 (m170) cc_final: 0.7000 (m170) REVERT: O 72 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7453 (mtm110) REVERT: M 23 ILE cc_start: 0.8489 (mm) cc_final: 0.8116 (mm) REVERT: M 45 PHE cc_start: 0.8158 (t80) cc_final: 0.7782 (t80) REVERT: M 48 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8592 (mmmt) REVERT: M 68 HIS cc_start: 0.8581 (m90) cc_final: 0.8225 (m170) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1266 time to fit residues: 68.0858 Evaluate side-chains 291 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050397 restraints weight = 64695.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051865 restraints weight = 37890.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.052842 restraints weight = 26855.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.053479 restraints weight = 21596.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053855 restraints weight = 18841.545| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 14595 Z= 0.223 Angle : 0.880 25.795 20918 Z= 0.467 Chirality : 0.067 2.064 2380 Planarity : 0.008 0.168 1650 Dihedral : 31.547 163.073 4276 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.07 % Favored : 95.51 % Rotamer: Outliers : 0.24 % Allowed : 3.14 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 958 helix: 0.70 (0.21), residues: 574 sheet: -2.58 (0.85), residues: 24 loop : -1.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 42 TYR 0.026 0.002 TYR C 39 PHE 0.027 0.002 PHE G 25 HIS 0.024 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (14595) covalent geometry : angle 0.88017 / 0.47 (20918) hydrogen bonds : bond 0.05984 / 4.13 ( 697) hydrogen bonds : angle 4.55495 / 3.26 ( 1766) *********************** 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 345 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 0.404 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: 0.8032 (m-80) cc_final: 0.7177 (m-10) REVERT: A 56 LYS cc_start: 0.9435 (tttt) cc_final: 0.9180 (tptm) REVERT: A 97 GLU cc_start: 0.8833 (mt-10) cc_final: 0.7945 (mm-30) REVERT: A 105 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8630 (tp30) REVERT: A 130 ILE cc_start: 0.9278 (mp) cc_final: 0.9056 (tp) REVERT: B 44 LYS cc_start: 0.9613 (mtpp) cc_final: 0.9382 (mttt) REVERT: B 59 LYS cc_start: 0.9256 (tmtt) cc_final: 0.8964 (tptp) REVERT: B 97 LEU cc_start: 0.9311 (tp) cc_final: 0.9103 (tt) REVERT: C 56 GLU cc_start: 0.8618 (tt0) cc_final: 0.7385 (tt0) REVERT: C 64 GLU cc_start: 0.8981 (tp30) cc_final: 0.8561 (tp30) REVERT: C 79 ILE cc_start: 0.9603 (tt) cc_final: 0.9390 (mm) REVERT: C 92 GLU cc_start: 0.8722 (pm20) cc_final: 0.8090 (pm20) REVERT: C 94 ASN cc_start: 0.9105 (t0) cc_final: 0.8388 (t0) REVERT: E 50 GLU cc_start: 0.8395 (tp30) cc_final: 0.7602 (tp30) REVERT: E 56 LYS cc_start: 0.9454 (tttt) cc_final: 0.9159 (tptm) REVERT: E 97 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8877 (mt-10) REVERT: E 123 ASP cc_start: 0.8461 (m-30) cc_final: 0.8189 (m-30) REVERT: F 26 ILE cc_start: 0.9510 (tt) cc_final: 0.9242 (tt) REVERT: F 29 ILE cc_start: 0.9476 (mm) cc_final: 0.9136 (tp) REVERT: F 44 LYS cc_start: 0.9517 (tttt) cc_final: 0.8941 (mtmt) REVERT: F 46 ILE cc_start: 0.9010 (pt) cc_final: 0.8566 (tp) REVERT: F 59 LYS cc_start: 0.9368 (tttp) cc_final: 0.8720 (ttmm) REVERT: F 85 ASP cc_start: 0.8842 (m-30) cc_final: 0.8561 (m-30) REVERT: F 88 TYR cc_start: 0.9311 (m-10) cc_final: 0.8744 (m-80) REVERT: G 56 GLU cc_start: 0.9279 (tt0) cc_final: 0.8889 (tt0) REVERT: G 64 GLU cc_start: 0.8984 (tp30) cc_final: 0.8262 (tp30) REVERT: G 72 ASP cc_start: 0.9377 (m-30) cc_final: 0.9023 (m-30) REVERT: G 92 GLU cc_start: 0.9094 (pt0) cc_final: 0.8765 (pm20) REVERT: G 118 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8036 (mmmt) REVERT: H 49 THR cc_start: 0.8555 (m) cc_final: 0.8264 (p) REVERT: H 56 MET cc_start: 0.8117 (tpt) cc_final: 0.7565 (tpt) REVERT: H 91 ILE cc_start: 0.9656 (mm) cc_final: 0.9447 (mm) REVERT: H 92 GLN cc_start: 0.9305 (tt0) cc_final: 0.8726 (tt0) REVERT: H 98 LEU cc_start: 0.9525 (tp) cc_final: 0.9309 (tt) REVERT: H 110 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9085 (mm-30) REVERT: L 1621 ASN cc_start: 0.6290 (p0) cc_final: 0.5955 (p0) REVERT: O 17 VAL cc_start: 0.7945 (m) cc_final: 0.7455 (m) REVERT: O 41 GLN cc_start: 0.7551 (mt0) cc_final: 0.7010 (mt0) REVERT: O 43 LEU cc_start: 0.8865 (mm) cc_final: 0.8371 (mm) REVERT: O 44 ILE cc_start: 0.8089 (mt) cc_final: 0.7809 (mp) REVERT: O 51 GLU cc_start: 0.6152 (pm20) cc_final: 0.5811 (pm20) REVERT: O 68 HIS cc_start: 0.7845 (m170) cc_final: 0.7148 (m170) REVERT: M 23 ILE cc_start: 0.8352 (mm) cc_final: 0.7946 (mm) REVERT: M 45 PHE cc_start: 0.8193 (t80) cc_final: 0.7914 (t80) REVERT: M 68 HIS cc_start: 0.8538 (m90) cc_final: 0.8170 (m170) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.1235 time to fit residues: 61.4549 Evaluate side-chains 264 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 40.0000 chunk 16 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 97 optimal weight: 40.0000 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 83 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** 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 H 106 HIS ** 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 = 0.3267 r_free = 0.3267 target = 0.065666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048817 restraints weight = 65456.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050320 restraints weight = 37619.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051321 restraints weight = 26390.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051953 restraints weight = 21106.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.052401 restraints weight = 18443.774| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14595 Z= 0.213 Angle : 0.830 25.493 20918 Z= 0.448 Chirality : 0.065 2.044 2380 Planarity : 0.007 0.137 1650 Dihedral : 31.211 162.982 4276 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.49 % Favored : 95.09 % Rotamer: Outliers : 0.12 % Allowed : 2.29 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.27), residues: 958 helix: 0.73 (0.21), residues: 572 sheet: -2.34 (0.63), residues: 48 loop : -1.14 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 54 TYR 0.019 0.002 TYR D 37 PHE 0.020 0.002 PHE F 61 HIS 0.023 0.003 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.21 (14595) covalent geometry : angle 0.83048 / 0.45 (20918) hydrogen bonds : bond 0.05723 / 3.98 ( 697) hydrogen bonds : angle 4.41978 / 3.14 ( 1766) *********************** 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 335 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 0.373 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 54 TYR cc_start: 0.8225 (m-80) cc_final: 0.7948 (m-80) REVERT: A 105 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8569 (tp30) REVERT: A 110 CYS cc_start: 0.9376 (m) cc_final: 0.9174 (m) REVERT: A 130 ILE cc_start: 0.9306 (mp) cc_final: 0.9059 (tp) REVERT: B 53 GLU cc_start: 0.8478 (tp30) cc_final: 0.8065 (tp30) REVERT: B 59 LYS cc_start: 0.9267 (tmtt) cc_final: 0.8987 (tptp) REVERT: B 97 LEU cc_start: 0.9320 (tp) cc_final: 0.9098 (tt) REVERT: C 56 GLU cc_start: 0.8662 (tt0) cc_final: 0.7550 (tt0) REVERT: C 64 GLU cc_start: 0.8927 (tp30) cc_final: 0.8565 (tp30) REVERT: C 79 ILE cc_start: 0.9651 (tt) cc_final: 0.9432 (mm) REVERT: C 92 GLU cc_start: 0.8485 (pm20) cc_final: 0.8076 (pm20) REVERT: D 92 GLN cc_start: 0.9624 (tt0) cc_final: 0.8903 (tp40) REVERT: D 106 HIS cc_start: 0.7076 (m90) cc_final: 0.6753 (m-70) REVERT: E 54 TYR cc_start: 0.8148 (m-10) cc_final: 0.7946 (m-10) REVERT: E 59 GLU cc_start: 0.8014 (tp30) cc_final: 0.7490 (tp30) REVERT: E 60 LEU cc_start: 0.8809 (mm) cc_final: 0.8216 (mm) REVERT: E 96 SER cc_start: 0.9558 (t) cc_final: 0.9322 (p) REVERT: E 123 ASP cc_start: 0.8703 (m-30) cc_final: 0.8487 (m-30) REVERT: E 125 GLN cc_start: 0.9620 (mt0) cc_final: 0.8727 (mm-40) REVERT: F 26 ILE cc_start: 0.9590 (tt) cc_final: 0.9310 (tt) REVERT: F 44 LYS cc_start: 0.9515 (tttt) cc_final: 0.8933 (mtmt) REVERT: F 88 TYR cc_start: 0.9378 (m-10) cc_final: 0.8777 (m-80) REVERT: G 39 TYR cc_start: 0.9495 (m-80) cc_final: 0.9042 (m-80) REVERT: G 56 GLU cc_start: 0.9175 (tt0) cc_final: 0.8809 (tt0) REVERT: G 64 GLU cc_start: 0.8968 (tp30) cc_final: 0.8435 (tp30) REVERT: G 72 ASP cc_start: 0.9447 (m-30) cc_final: 0.9111 (m-30) REVERT: H 49 THR cc_start: 0.8768 (m) cc_final: 0.8535 (p) REVERT: H 56 MET cc_start: 0.8367 (tpt) cc_final: 0.7800 (tpt) REVERT: H 92 GLN cc_start: 0.9198 (tt0) cc_final: 0.8703 (tt0) REVERT: H 98 LEU cc_start: 0.9533 (tp) cc_final: 0.9300 (tt) REVERT: H 99 LEU cc_start: 0.9478 (tp) cc_final: 0.9187 (tt) REVERT: H 110 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9064 (mm-30) REVERT: H 113 LYS cc_start: 0.9351 (mtpt) cc_final: 0.9128 (mtmt) REVERT: L 1621 ASN cc_start: 0.6570 (p0) cc_final: 0.6176 (p0) REVERT: O 41 GLN cc_start: 0.7628 (mt0) cc_final: 0.7186 (mt0) REVERT: O 43 LEU cc_start: 0.8828 (mm) cc_final: 0.8426 (mm) REVERT: O 44 ILE cc_start: 0.8122 (mt) cc_final: 0.7715 (mp) REVERT: O 51 GLU cc_start: 0.5926 (pm20) cc_final: 0.5352 (pm20) REVERT: O 68 HIS cc_start: 0.7554 (m170) cc_final: 0.6872 (m170) REVERT: M 23 ILE cc_start: 0.8555 (mm) cc_final: 0.8055 (mm) REVERT: M 44 ILE cc_start: 0.8042 (mt) cc_final: 0.7752 (mt) REVERT: M 45 PHE cc_start: 0.8157 (t80) cc_final: 0.7892 (t80) REVERT: M 68 HIS cc_start: 0.8513 (m90) cc_final: 0.8071 (m170) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.1239 time to fit residues: 59.8357 Evaluate side-chains 262 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 94 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 H 106 HIS ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.049310 restraints weight = 62791.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050842 restraints weight = 35872.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051848 restraints weight = 25114.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052496 restraints weight = 20095.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052892 restraints weight = 17507.339| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14595 Z= 0.161 Angle : 0.784 25.255 20918 Z= 0.425 Chirality : 0.064 2.035 2380 Planarity : 0.007 0.124 1650 Dihedral : 31.008 164.542 4276 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.70 % Favored : 94.89 % 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 : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 958 helix: 0.80 (0.22), residues: 576 sheet: -2.14 (0.68), residues: 48 loop : -1.09 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 54 TYR 0.016 0.002 TYR D 37 PHE 0.018 0.002 PHE F 61 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (14595) covalent geometry : angle 0.78429 / 0.42 (20918) hydrogen bonds : bond 0.05091 / 3.63 ( 697) hydrogen bonds : angle 4.10399 / 2.91 ( 1766) *********************** 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 337 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.396 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 50 GLU cc_start: 0.8266 (tp30) cc_final: 0.7619 (mm-30) REVERT: A 54 TYR cc_start: 0.8144 (m-80) cc_final: 0.7583 (m-10) REVERT: A 80 THR cc_start: 0.8472 (p) cc_final: 0.7974 (p) REVERT: A 97 GLU cc_start: 0.8802 (mt-10) cc_final: 0.7964 (mm-30) REVERT: A 101 VAL cc_start: 0.9727 (t) cc_final: 0.9502 (p) REVERT: A 110 CYS cc_start: 0.9460 (m) cc_final: 0.9243 (m) REVERT: B 44 LYS cc_start: 0.9590 (mtpp) cc_final: 0.9217 (mttt) REVERT: B 53 GLU cc_start: 0.8432 (tp30) cc_final: 0.8086 (tp30) REVERT: C 56 GLU cc_start: 0.8536 (tt0) cc_final: 0.7507 (tt0) REVERT: C 64 GLU cc_start: 0.9019 (tp30) cc_final: 0.8539 (tp30) REVERT: C 72 ASP cc_start: 0.9417 (m-30) cc_final: 0.9087 (m-30) REVERT: C 79 ILE cc_start: 0.9650 (tt) cc_final: 0.9405 (mm) REVERT: C 94 ASN cc_start: 0.9070 (t0) cc_final: 0.8259 (t0) REVERT: D 92 GLN cc_start: 0.9387 (tt0) cc_final: 0.8821 (tp40) REVERT: D 99 LEU cc_start: 0.9382 (mt) cc_final: 0.8906 (tt) REVERT: D 106 HIS cc_start: 0.7168 (m90) cc_final: 0.6421 (m-70) REVERT: D 110 GLU cc_start: 0.9104 (tp30) cc_final: 0.8895 (tm-30) REVERT: E 59 GLU cc_start: 0.8027 (tp30) cc_final: 0.7468 (tp30) REVERT: E 60 LEU cc_start: 0.8769 (mm) cc_final: 0.7834 (mm) REVERT: E 96 SER cc_start: 0.9566 (t) cc_final: 0.9362 (p) REVERT: E 125 GLN cc_start: 0.9604 (mt0) cc_final: 0.8747 (mm-40) REVERT: F 44 LYS cc_start: 0.9482 (tttt) cc_final: 0.8935 (mtmt) REVERT: F 84 MET cc_start: 0.8762 (tpp) cc_final: 0.8390 (tpt) REVERT: F 85 ASP cc_start: 0.8938 (m-30) cc_final: 0.8705 (m-30) REVERT: F 88 TYR cc_start: 0.9326 (m-10) cc_final: 0.8689 (m-80) REVERT: G 56 GLU cc_start: 0.9182 (tt0) cc_final: 0.8821 (tt0) REVERT: G 64 GLU cc_start: 0.8911 (tp30) cc_final: 0.8350 (tp30) REVERT: G 72 ASP cc_start: 0.9411 (m-30) cc_final: 0.9084 (m-30) REVERT: H 49 THR cc_start: 0.8658 (m) cc_final: 0.8398 (p) REVERT: H 54 LYS cc_start: 0.8148 (mttt) cc_final: 0.7884 (mmtp) REVERT: H 56 MET cc_start: 0.8434 (tpt) cc_final: 0.8032 (tpt) REVERT: H 66 ILE cc_start: 0.9504 (mt) cc_final: 0.9281 (mt) REVERT: H 99 LEU cc_start: 0.9463 (tp) cc_final: 0.9255 (tt) REVERT: H 110 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9024 (mm-30) REVERT: O 43 LEU cc_start: 0.8771 (mm) cc_final: 0.8327 (mm) REVERT: O 44 ILE cc_start: 0.7959 (mt) cc_final: 0.7650 (mt) REVERT: O 51 GLU cc_start: 0.6198 (pm20) cc_final: 0.5847 (pm20) REVERT: O 68 HIS cc_start: 0.7521 (m170) cc_final: 0.6811 (m170) REVERT: M 45 PHE cc_start: 0.8076 (t80) cc_final: 0.7613 (t80) REVERT: M 52 ASP cc_start: 0.7676 (m-30) cc_final: 0.7375 (m-30) REVERT: M 68 HIS cc_start: 0.8539 (m90) cc_final: 0.8142 (m170) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1172 time to fit residues: 58.0131 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 80 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** 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 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 = 0.3267 r_free = 0.3267 target = 0.065497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.048725 restraints weight = 64588.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.050238 restraints weight = 36951.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.051219 restraints weight = 25761.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051823 restraints weight = 20541.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.052011 restraints weight = 17954.749| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 14595 Z= 0.181 Angle : 0.775 24.838 20918 Z= 0.420 Chirality : 0.062 2.007 2380 Planarity : 0.007 0.165 1650 Dihedral : 30.756 167.536 4276 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 958 helix: 0.80 (0.21), residues: 576 sheet: -2.42 (0.63), residues: 52 loop : -1.04 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 54 TYR 0.023 0.002 TYR F 98 PHE 0.011 0.002 PHE A 104 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (14595) covalent geometry : angle 0.77517 / 0.42 (20918) hydrogen bonds : bond 0.05190 / 3.67 ( 697) hydrogen bonds : angle 4.08698 / 2.89 ( 1766) *********************** 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 323 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.395 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: A 50 GLU cc_start: 0.8408 (tp30) cc_final: 0.7464 (mm-30) REVERT: A 54 TYR cc_start: 0.8035 (m-80) cc_final: 0.7331 (m-10) REVERT: A 80 THR cc_start: 0.8552 (p) cc_final: 0.8053 (p) REVERT: A 97 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8094 (mm-30) REVERT: A 105 GLU cc_start: 0.8769 (tp30) cc_final: 0.8298 (tm-30) REVERT: A 106 ASP cc_start: 0.9029 (m-30) cc_final: 0.8799 (t0) REVERT: A 109 LEU cc_start: 0.9794 (mm) cc_final: 0.9176 (mm) REVERT: A 110 CYS cc_start: 0.9446 (m) cc_final: 0.9212 (t) REVERT: B 44 LYS cc_start: 0.9620 (mtpp) cc_final: 0.9221 (mttt) REVERT: B 53 GLU cc_start: 0.8361 (tp30) cc_final: 0.8097 (tp30) REVERT: B 97 LEU cc_start: 0.9323 (tp) cc_final: 0.9107 (tt) REVERT: C 56 GLU cc_start: 0.8669 (tt0) cc_final: 0.7528 (tt0) REVERT: C 64 GLU cc_start: 0.8962 (tp30) cc_final: 0.8571 (tp30) REVERT: C 72 ASP cc_start: 0.9438 (m-30) cc_final: 0.9095 (m-30) REVERT: C 79 ILE cc_start: 0.9606 (tt) cc_final: 0.9394 (mm) REVERT: D 92 GLN cc_start: 0.9410 (tt0) cc_final: 0.8860 (tp40) REVERT: D 99 LEU cc_start: 0.9376 (mt) cc_final: 0.8906 (tt) REVERT: D 106 HIS cc_start: 0.7189 (m90) cc_final: 0.6721 (m-70) REVERT: D 110 GLU cc_start: 0.9118 (tp30) cc_final: 0.8910 (tm-30) REVERT: E 50 GLU cc_start: 0.8321 (tp30) cc_final: 0.7462 (tp30) REVERT: E 54 TYR cc_start: 0.8134 (m-10) cc_final: 0.7883 (m-10) REVERT: E 59 GLU cc_start: 0.7909 (tp30) cc_final: 0.7413 (tp30) REVERT: E 76 GLN cc_start: 0.9300 (tt0) cc_final: 0.8579 (pt0) REVERT: E 125 GLN cc_start: 0.9600 (mt0) cc_final: 0.8678 (mm-40) REVERT: E 130 ILE cc_start: 0.9144 (tp) cc_final: 0.8170 (tp) REVERT: F 44 LYS cc_start: 0.9522 (tttt) cc_final: 0.8937 (mtmt) REVERT: F 52 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7433 (tm-30) REVERT: F 72 TYR cc_start: 0.9479 (m-80) cc_final: 0.9183 (m-10) REVERT: F 84 MET cc_start: 0.8856 (tpp) cc_final: 0.8444 (tpt) REVERT: F 88 TYR cc_start: 0.9282 (m-10) cc_final: 0.8793 (m-80) REVERT: G 39 TYR cc_start: 0.9166 (m-10) cc_final: 0.8312 (m-80) REVERT: G 56 GLU cc_start: 0.9243 (tt0) cc_final: 0.8846 (tt0) REVERT: G 64 GLU cc_start: 0.8940 (tp30) cc_final: 0.8343 (tp30) REVERT: G 72 ASP cc_start: 0.9511 (m-30) cc_final: 0.9155 (m-30) REVERT: H 49 THR cc_start: 0.8766 (m) cc_final: 0.8484 (p) REVERT: H 56 MET cc_start: 0.8529 (tpt) cc_final: 0.8140 (tpt) REVERT: H 68 GLU cc_start: 0.8392 (tt0) cc_final: 0.8102 (mm-30) REVERT: H 99 LEU cc_start: 0.9544 (tp) cc_final: 0.9150 (tt) REVERT: H 110 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9078 (mm-30) REVERT: L 1621 ASN cc_start: 0.6334 (p0) cc_final: 0.5728 (p0) REVERT: O 41 GLN cc_start: 0.7503 (mt0) cc_final: 0.7088 (mt0) REVERT: O 43 LEU cc_start: 0.8775 (mm) cc_final: 0.8291 (mm) REVERT: O 51 GLU cc_start: 0.6254 (pm20) cc_final: 0.5889 (pm20) REVERT: O 68 HIS cc_start: 0.7495 (m170) cc_final: 0.7096 (m170) REVERT: M 45 PHE cc_start: 0.7986 (t80) cc_final: 0.7012 (t80) REVERT: M 48 LYS cc_start: 0.8950 (mmpt) cc_final: 0.8740 (mppt) REVERT: M 52 ASP cc_start: 0.7498 (m-30) cc_final: 0.7214 (m-30) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1141 time to fit residues: 54.5074 Evaluate side-chains 265 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 50.0000 chunk 59 optimal weight: 0.9980 chunk 100 optimal weight: 50.0000 chunk 55 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** 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 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 106 HIS O 2 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.047815 restraints weight = 65599.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.049326 restraints weight = 38195.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.050325 restraints weight = 26622.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050960 restraints weight = 21133.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051371 restraints weight = 18332.555| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 14595 Z= 0.198 Angle : 0.773 24.167 20918 Z= 0.424 Chirality : 0.062 1.949 2380 Planarity : 0.007 0.152 1650 Dihedral : 30.562 169.408 4276 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 958 helix: 0.77 (0.21), residues: 575 sheet: -2.13 (0.69), residues: 52 loop : -0.92 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 131 TYR 0.021 0.002 TYR G 50 PHE 0.011 0.002 PHE M 4 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (14595) covalent geometry : angle 0.77266 / 0.42 (20918) hydrogen bonds : bond 0.05174 / 3.65 ( 697) hydrogen bonds : angle 4.09288 / 2.88 ( 1766) *********************** 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 326 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.388 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 50 GLU cc_start: 0.8422 (tp30) cc_final: 0.7433 (mm-30) REVERT: A 54 TYR cc_start: 0.8016 (m-80) cc_final: 0.7364 (m-10) REVERT: A 80 THR cc_start: 0.8593 (p) cc_final: 0.8068 (p) REVERT: A 93 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8632 (tm-30) REVERT: A 97 GLU cc_start: 0.8955 (mt-10) cc_final: 0.7938 (mm-30) REVERT: A 105 GLU cc_start: 0.8724 (tp30) cc_final: 0.8263 (tm-30) REVERT: A 109 LEU cc_start: 0.9772 (mm) cc_final: 0.9136 (mm) REVERT: B 53 GLU cc_start: 0.8408 (tp30) cc_final: 0.8059 (tp30) REVERT: B 60 VAL cc_start: 0.9502 (p) cc_final: 0.8792 (p) REVERT: B 85 ASP cc_start: 0.8896 (m-30) cc_final: 0.8636 (m-30) REVERT: C 39 TYR cc_start: 0.8762 (m-10) cc_final: 0.8382 (m-80) REVERT: C 41 GLU cc_start: 0.8735 (pt0) cc_final: 0.8475 (pt0) REVERT: C 56 GLU cc_start: 0.8832 (tt0) cc_final: 0.7653 (tt0) REVERT: C 72 ASP cc_start: 0.9419 (m-30) cc_final: 0.9072 (m-30) REVERT: C 79 ILE cc_start: 0.9577 (tt) cc_final: 0.9365 (mm) REVERT: D 59 MET cc_start: 0.9110 (mmm) cc_final: 0.8874 (mmp) REVERT: D 83 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8355 (mmm-85) REVERT: D 92 GLN cc_start: 0.9441 (tt0) cc_final: 0.8760 (tp40) REVERT: D 99 LEU cc_start: 0.9360 (mt) cc_final: 0.8858 (tt) REVERT: D 110 GLU cc_start: 0.9148 (tp30) cc_final: 0.8923 (tm-30) REVERT: E 50 GLU cc_start: 0.8244 (tp30) cc_final: 0.7460 (tp30) REVERT: E 59 GLU cc_start: 0.7952 (tp30) cc_final: 0.7435 (tp30) REVERT: E 76 GLN cc_start: 0.9318 (tt0) cc_final: 0.8639 (pt0) REVERT: E 93 GLN cc_start: 0.9036 (tp40) cc_final: 0.8744 (tp40) REVERT: E 97 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8078 (mt-10) REVERT: E 125 GLN cc_start: 0.9571 (mt0) cc_final: 0.8742 (mm-40) REVERT: F 43 VAL cc_start: 0.9410 (t) cc_final: 0.8817 (p) REVERT: F 44 LYS cc_start: 0.9525 (tttt) cc_final: 0.8896 (mtmt) REVERT: F 53 GLU cc_start: 0.8653 (tp30) cc_final: 0.8338 (tp30) REVERT: F 84 MET cc_start: 0.8811 (tpp) cc_final: 0.8449 (tpt) REVERT: F 88 TYR cc_start: 0.9303 (m-10) cc_final: 0.8813 (m-80) REVERT: G 39 TYR cc_start: 0.9459 (m-10) cc_final: 0.8503 (m-80) REVERT: G 50 TYR cc_start: 0.9349 (t80) cc_final: 0.8389 (t80) REVERT: G 56 GLU cc_start: 0.9220 (tt0) cc_final: 0.8803 (tt0) REVERT: G 64 GLU cc_start: 0.8984 (tp30) cc_final: 0.8417 (tp30) REVERT: G 72 ASP cc_start: 0.9510 (m-30) cc_final: 0.9169 (m-30) REVERT: H 56 MET cc_start: 0.8622 (tpt) cc_final: 0.8228 (tpt) REVERT: H 92 GLN cc_start: 0.9537 (tt0) cc_final: 0.8573 (tp40) REVERT: H 99 LEU cc_start: 0.9461 (tp) cc_final: 0.9060 (tt) REVERT: H 110 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8978 (mm-30) REVERT: O 42 ARG cc_start: 0.7454 (ttt-90) cc_final: 0.6926 (ttt-90) REVERT: O 43 LEU cc_start: 0.8700 (mm) cc_final: 0.8036 (mm) REVERT: O 48 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8431 (mmtm) REVERT: O 51 GLU cc_start: 0.6239 (pm20) cc_final: 0.5897 (pm20) REVERT: O 68 HIS cc_start: 0.7446 (m170) cc_final: 0.6967 (m170) REVERT: M 45 PHE cc_start: 0.8052 (t80) cc_final: 0.7034 (t80) REVERT: M 48 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8684 (mppt) REVERT: M 52 ASP cc_start: 0.7666 (m-30) cc_final: 0.7413 (m-30) REVERT: M 68 HIS cc_start: 0.8125 (m170) cc_final: 0.7744 (m170) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1202 time to fit residues: 57.2868 Evaluate side-chains 265 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 62 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 40.0000 chunk 38 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN D 106 HIS ** E 93 GLN ** 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.047712 restraints weight = 63339.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.049117 restraints weight = 37961.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.050054 restraints weight = 27304.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.050658 restraints weight = 22184.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050934 restraints weight = 19488.553| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 14595 Z= 0.189 Angle : 0.787 23.849 20918 Z= 0.426 Chirality : 0.060 1.896 2380 Planarity : 0.007 0.159 1650 Dihedral : 30.495 170.529 4276 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.32 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.27), residues: 958 helix: 0.79 (0.21), residues: 577 sheet: -2.32 (0.67), residues: 52 loop : -0.96 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 42 TYR 0.036 0.002 TYR G 39 PHE 0.035 0.002 PHE G 25 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (14595) covalent geometry : angle 0.78651 / 0.43 (20918) hydrogen bonds : bond 0.05106 / 3.65 ( 697) hydrogen bonds : angle 4.02013 / 2.83 ( 1766) *********************** 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 314 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.395 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: A 50 GLU cc_start: 0.8383 (tp30) cc_final: 0.7434 (mm-30) REVERT: A 54 TYR cc_start: 0.7959 (m-80) cc_final: 0.7329 (m-10) REVERT: A 60 LEU cc_start: 0.8226 (mm) cc_final: 0.7884 (mm) REVERT: A 80 THR cc_start: 0.8617 (p) cc_final: 0.8063 (p) REVERT: A 97 GLU cc_start: 0.8980 (mt-10) cc_final: 0.7850 (mm-30) REVERT: A 105 GLU cc_start: 0.8547 (tp30) cc_final: 0.8190 (tm-30) REVERT: A 109 LEU cc_start: 0.9776 (mm) cc_final: 0.9131 (mm) REVERT: A 110 CYS cc_start: 0.9373 (m) cc_final: 0.9117 (m) REVERT: B 53 GLU cc_start: 0.8313 (tp30) cc_final: 0.8004 (tp30) REVERT: B 63 GLU cc_start: 0.8549 (pm20) cc_final: 0.8279 (pm20) REVERT: B 85 ASP cc_start: 0.8853 (m-30) cc_final: 0.8644 (m-30) REVERT: C 41 GLU cc_start: 0.8471 (pt0) cc_final: 0.8259 (pt0) REVERT: C 56 GLU cc_start: 0.8806 (tt0) cc_final: 0.7806 (tt0) REVERT: C 72 ASP cc_start: 0.9378 (m-30) cc_final: 0.9033 (m-30) REVERT: C 79 ILE cc_start: 0.9596 (tt) cc_final: 0.9359 (mm) REVERT: D 83 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8390 (mmm-85) REVERT: D 92 GLN cc_start: 0.9456 (tt0) cc_final: 0.8719 (tp40) REVERT: D 99 LEU cc_start: 0.9431 (mt) cc_final: 0.8949 (tt) REVERT: E 50 GLU cc_start: 0.8328 (tp30) cc_final: 0.8063 (tp30) REVERT: E 54 TYR cc_start: 0.8035 (m-10) cc_final: 0.7827 (m-10) REVERT: E 59 GLU cc_start: 0.7823 (tp30) cc_final: 0.7352 (tp30) REVERT: E 76 GLN cc_start: 0.9307 (tt0) cc_final: 0.8678 (pt0) REVERT: E 97 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 125 GLN cc_start: 0.9528 (mt0) cc_final: 0.8567 (mm-40) REVERT: F 43 VAL cc_start: 0.9455 (t) cc_final: 0.8928 (p) REVERT: F 44 LYS cc_start: 0.9520 (tttt) cc_final: 0.8945 (mtmt) REVERT: F 52 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 84 MET cc_start: 0.8723 (tpp) cc_final: 0.8420 (tpt) REVERT: F 88 TYR cc_start: 0.9249 (m-10) cc_final: 0.8784 (m-80) REVERT: G 56 GLU cc_start: 0.9290 (tt0) cc_final: 0.8770 (mt-10) REVERT: G 64 GLU cc_start: 0.8982 (tp30) cc_final: 0.8425 (tp30) REVERT: G 72 ASP cc_start: 0.9503 (m-30) cc_final: 0.9116 (m-30) REVERT: H 56 MET cc_start: 0.8577 (tpt) cc_final: 0.8226 (tpt) REVERT: H 92 GLN cc_start: 0.9506 (tt0) cc_final: 0.8684 (tp40) REVERT: H 99 LEU cc_start: 0.9497 (tp) cc_final: 0.9127 (tt) REVERT: H 108 VAL cc_start: 0.9462 (t) cc_final: 0.9070 (t) REVERT: H 110 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8931 (mm-30) REVERT: O 42 ARG cc_start: 0.6844 (ttt-90) cc_final: 0.6143 (ttt90) REVERT: O 43 LEU cc_start: 0.8859 (mm) cc_final: 0.8265 (mm) REVERT: O 48 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8450 (mmtm) REVERT: O 49 GLN cc_start: 0.6931 (tp40) cc_final: 0.6632 (tp40) REVERT: O 68 HIS cc_start: 0.7509 (m170) cc_final: 0.6969 (m170) REVERT: M 43 LEU cc_start: 0.8675 (mm) cc_final: 0.8137 (mm) REVERT: M 44 ILE cc_start: 0.8366 (mt) cc_final: 0.7840 (mp) REVERT: M 45 PHE cc_start: 0.8071 (t80) cc_final: 0.6812 (t80) REVERT: M 52 ASP cc_start: 0.7660 (m-30) cc_final: 0.7408 (m-30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1186 time to fit residues: 54.5280 Evaluate side-chains 267 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 94 ASN D 106 HIS ** F 25 ASN ** 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 H 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047995 restraints weight = 62599.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049466 restraints weight = 36928.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050438 restraints weight = 26174.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051081 restraints weight = 21059.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051449 restraints weight = 18384.513| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14595 Z= 0.171 Angle : 0.785 23.414 20918 Z= 0.423 Chirality : 0.060 1.863 2380 Planarity : 0.007 0.161 1650 Dihedral : 30.390 171.342 4276 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.70 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.27), residues: 958 helix: 0.81 (0.21), residues: 577 sheet: -2.15 (0.69), residues: 52 loop : -0.87 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 42 TYR 0.048 0.003 TYR G 39 PHE 0.026 0.003 PHE G 25 HIS 0.013 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (14595) covalent geometry : angle 0.78475 / 0.42 (20918) hydrogen bonds : bond 0.04971 / 3.58 ( 697) hydrogen bonds : angle 3.99831 / 2.82 ( 1766) ********************** 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 323 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.408 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: A 50 GLU cc_start: 0.8448 (tp30) cc_final: 0.7543 (mm-30) REVERT: A 54 TYR cc_start: 0.7971 (m-80) cc_final: 0.7326 (m-10) REVERT: A 59 GLU cc_start: 0.7982 (tp30) cc_final: 0.7273 (tp30) REVERT: A 60 LEU cc_start: 0.7931 (mm) cc_final: 0.6874 (mm) REVERT: A 67 PHE cc_start: 0.8463 (t80) cc_final: 0.7873 (t80) REVERT: A 80 THR cc_start: 0.8650 (p) cc_final: 0.8140 (p) REVERT: A 96 SER cc_start: 0.9572 (t) cc_final: 0.9230 (p) REVERT: A 97 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8002 (mm-30) REVERT: A 105 GLU cc_start: 0.8631 (tp30) cc_final: 0.8240 (tm-30) REVERT: A 109 LEU cc_start: 0.9786 (mm) cc_final: 0.9139 (mm) REVERT: A 110 CYS cc_start: 0.9479 (m) cc_final: 0.9255 (m) REVERT: B 53 GLU cc_start: 0.8408 (tp30) cc_final: 0.8085 (tp30) REVERT: B 85 ASP cc_start: 0.8869 (m-30) cc_final: 0.8615 (m-30) REVERT: C 39 TYR cc_start: 0.8903 (m-80) cc_final: 0.8514 (m-80) REVERT: C 41 GLU cc_start: 0.8768 (pt0) cc_final: 0.8554 (pt0) REVERT: C 50 TYR cc_start: 0.9352 (t80) cc_final: 0.8287 (t80) REVERT: C 56 GLU cc_start: 0.8733 (tt0) cc_final: 0.7861 (tt0) REVERT: C 72 ASP cc_start: 0.9409 (m-30) cc_final: 0.9177 (m-30) REVERT: C 79 ILE cc_start: 0.9551 (tt) cc_final: 0.9346 (mm) REVERT: D 92 GLN cc_start: 0.9459 (tt0) cc_final: 0.8687 (tp40) REVERT: D 99 LEU cc_start: 0.9403 (mt) cc_final: 0.8892 (tt) REVERT: E 59 GLU cc_start: 0.7821 (tp30) cc_final: 0.7445 (tp30) REVERT: E 76 GLN cc_start: 0.9310 (tt0) cc_final: 0.8693 (pt0) REVERT: E 84 PHE cc_start: 0.7825 (m-10) cc_final: 0.7607 (m-10) REVERT: E 97 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 125 GLN cc_start: 0.9501 (mt0) cc_final: 0.8539 (mm-40) REVERT: F 43 VAL cc_start: 0.9441 (t) cc_final: 0.8915 (p) REVERT: F 44 LYS cc_start: 0.9487 (tttt) cc_final: 0.8910 (mtmt) REVERT: F 52 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7528 (tm-30) REVERT: F 60 VAL cc_start: 0.9559 (t) cc_final: 0.9351 (t) REVERT: F 84 MET cc_start: 0.8767 (tpp) cc_final: 0.8505 (tpt) REVERT: F 88 TYR cc_start: 0.9252 (m-10) cc_final: 0.8807 (m-80) REVERT: G 56 GLU cc_start: 0.9261 (tt0) cc_final: 0.8729 (mt-10) REVERT: G 64 GLU cc_start: 0.8997 (tp30) cc_final: 0.8442 (tp30) REVERT: G 72 ASP cc_start: 0.9517 (m-30) cc_final: 0.9103 (m-30) REVERT: G 74 LYS cc_start: 0.9519 (mtmm) cc_final: 0.8398 (tppt) REVERT: H 51 ILE cc_start: 0.8652 (mm) cc_final: 0.8221 (tp) REVERT: H 56 MET cc_start: 0.8473 (tpp) cc_final: 0.8239 (tpt) REVERT: H 86 ILE cc_start: 0.8941 (tp) cc_final: 0.8641 (tp) REVERT: H 92 GLN cc_start: 0.9548 (tt0) cc_final: 0.8684 (tp40) REVERT: H 99 LEU cc_start: 0.9498 (tp) cc_final: 0.9113 (tt) REVERT: H 106 HIS cc_start: 0.8832 (m-70) cc_final: 0.8285 (m-70) REVERT: H 110 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8873 (mm-30) REVERT: O 23 ILE cc_start: 0.9069 (mp) cc_final: 0.8808 (mp) REVERT: O 43 LEU cc_start: 0.8818 (mm) cc_final: 0.8584 (mm) REVERT: O 45 PHE cc_start: 0.8009 (t80) cc_final: 0.7573 (t80) REVERT: O 48 LYS cc_start: 0.8817 (mmpt) cc_final: 0.8536 (mppt) REVERT: O 68 HIS cc_start: 0.7436 (m170) cc_final: 0.6799 (m170) REVERT: M 45 PHE cc_start: 0.8085 (t80) cc_final: 0.7596 (t80) REVERT: M 52 ASP cc_start: 0.7576 (m-30) cc_final: 0.7356 (m-30) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1137 time to fit residues: 54.4215 Evaluate side-chains 270 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 40.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 40.0000 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN D 106 HIS ** 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 H 106 HIS O 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.066687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.049269 restraints weight = 62788.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050818 restraints weight = 36722.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051836 restraints weight = 25698.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052465 restraints weight = 20513.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052906 restraints weight = 17968.292| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14595 Z= 0.160 Angle : 0.781 24.389 20918 Z= 0.420 Chirality : 0.060 1.883 2380 Planarity : 0.006 0.156 1650 Dihedral : 30.254 171.765 4276 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.70 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.27), residues: 958 helix: 0.80 (0.21), residues: 575 sheet: -2.25 (0.65), residues: 52 loop : -0.93 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K1627 TYR 0.027 0.002 TYR G 39 PHE 0.033 0.003 PHE A 67 HIS 0.009 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14595) covalent geometry : angle 0.78089 / 0.42 (20918) hydrogen bonds : bond 0.04852 / 3.52 ( 697) hydrogen bonds : angle 3.86696 / 2.73 ( 1766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.63 seconds wall clock time: 38 minutes 49.38 seconds (2329.38 seconds total)