Starting phenix.real_space_refine on Mon Jul 6 21:25:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.map" model { file = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c95_16502/07_2026/8c95_16502.cif" } resolution = 4.92 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= 0.003 sd= 0.069 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 1339 5.49 5 S 27 5.16 5 C 20007 2.51 5 N 7484 2.21 5 O 11315 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40172 Number of models: 1 Model: "" Number of chains: 16 Chain: "2" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 26210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 26210 Classifications: {'RNA': 1220} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 59, 'rna3p_pur': 599, 'rna3p_pyr': 443} Link IDs: {'rna2p': 177, 'rna3p': 1042} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1519 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 1 Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1379 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 725 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 513 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 8.70, per 1000 atoms: 0.22 Number of scatterers: 40172 At special positions: 0 Unit cell: (182.5, 218.75, 172.5, 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 27 16.00 P 1339 15.00 O 11315 8.00 N 7484 7.00 C 20007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 800.0 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 38.4% alpha, 15.5% beta 436 base pairs and 648 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.727A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 21 " --> pdb=" O THR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.582A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.619A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.892A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 4.255A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 20 removed outlier: 4.095A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.100A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.625A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.906A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 107 removed outlier: 3.932A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'O' and resid 3 through 19 removed outlier: 3.660A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'Q' and resid 5 through 19 removed outlier: 4.261A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.128A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.796A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.209A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.996A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 53 through 58 removed outlier: 3.756A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.673A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 43 removed outlier: 3.901A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Y 43 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 39 through 43' Processing helix chain 'Y' and resid 45 through 56 removed outlier: 3.691A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'E' and resid 119 through 121 removed outlier: 6.115A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.140A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 65 through 66 removed outlier: 7.216A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.339A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AA7, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.811A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER O 52 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 35 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 11 through 14 Processing sheet with id=AA9, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.953A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.955A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 10 removed outlier: 4.924A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER S 101 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 63 through 65 removed outlier: 7.298A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS U 23 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP U 80 " --> pdb=" O ILE U 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.845A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AB6, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.854A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 32 through 35 removed outlier: 6.314A pdb=" N ILE W 32 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA W 57 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL W 34 " --> pdb=" O LEU W 55 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE W 56 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 41 through 43 removed outlier: 6.233A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Z' and resid 35 through 38 454 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1107 hydrogen bonds 1772 hydrogen bond angles 0 basepair planarities 436 basepair parallelities 648 stacking parallelities Total time for adding SS restraints: 16.38 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6248 1.33 - 1.45: 17950 1.45 - 1.57: 16840 1.57 - 1.69: 2669 1.69 - 1.81: 52 Bond restraints: 43759 Sorted by residual: bond pdb=" P A A 973 " pdb=" O5' A A 973 " ideal model delta sigma weight residual 1.593 1.642 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O5' G A 974 " pdb=" C5' G A 974 " ideal model delta sigma weight residual 1.424 1.470 -0.046 1.50e-02 4.44e+03 9.55e+00 bond pdb=" O5' A A 973 " pdb=" C5' A A 973 " ideal model delta sigma weight residual 1.420 1.462 -0.042 1.50e-02 4.44e+03 7.82e+00 bond pdb=" P G A 974 " pdb=" O5' G A 974 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.50e-02 4.44e+03 4.45e+00 bond pdb=" O5' U A2390 " pdb=" C5' U A2390 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 ... (remaining 43754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 65596 3.04 - 6.07: 93 6.07 - 9.11: 10 9.11 - 12.14: 1 12.14 - 15.18: 1 Bond angle restraints: 65701 Sorted by residual: angle pdb=" C3' A A 972 " pdb=" O3' A A 972 " pdb=" P A A 973 " ideal model delta sigma weight residual 120.20 105.02 15.18 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C3' U A2390 " pdb=" O3' U A2390 " pdb=" P G A2391 " ideal model delta sigma weight residual 120.20 109.84 10.36 1.50e+00 4.44e-01 4.77e+01 angle pdb=" C3' A A 973 " pdb=" O3' A A 973 " pdb=" P G A 974 " ideal model delta sigma weight residual 120.20 128.19 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" N ILE L 23 " pdb=" CA ILE L 23 " pdb=" C ILE L 23 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sigma weight residual 101.30 106.03 -4.73 1.00e+00 1.00e+00 2.24e+01 ... (remaining 65696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 22304 35.95 - 71.90: 770 71.90 - 107.85: 89 107.85 - 143.80: 11 143.80 - 179.75: 1 Dihedral angle restraints: 23175 sinusoidal: 19015 harmonic: 4160 Sorted by residual: dihedral pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sinusoidal sigma weight residual 36.00 -6.91 42.91 1 8.00e+00 1.56e-02 4.01e+01 dihedral pdb=" O4' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " ideal model delta sinusoidal sigma weight residual -35.00 7.54 -42.54 1 8.00e+00 1.56e-02 3.95e+01 dihedral pdb=" C5' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" O3' A A 973 " ideal model delta sinusoidal sigma weight residual 82.00 122.84 -40.84 1 8.00e+00 1.56e-02 3.65e+01 ... (remaining 23172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 8431 0.128 - 0.257: 11 0.257 - 0.385: 1 0.385 - 0.513: 2 0.513 - 0.642: 1 Chirality restraints: 8446 Sorted by residual: chirality pdb=" P G A 974 " pdb=" OP1 G A 974 " pdb=" OP2 G A 974 " pdb=" O5' G A 974 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P A A 973 " pdb=" OP1 A A 973 " pdb=" OP2 A A 973 " pdb=" O5' A A 973 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" P U A2390 " pdb=" OP1 U A2390 " pdb=" OP2 U A2390 " pdb=" O5' U A2390 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 8443 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.015 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 G A 259 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.032 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.023 2.00e-02 2.50e+03 1.81e-02 7.37e+00 pdb=" N1 C A 418 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 418 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 418 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 418 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 418 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 398 " -0.007 2.00e-02 2.50e+03 1.56e-02 5.51e+00 pdb=" N1 C A 398 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 398 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C A 398 " -0.023 2.00e-02 2.50e+03 pdb=" N3 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 398 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A 398 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 398 " -0.001 2.00e-02 2.50e+03 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 382 2.49 - 3.09: 27863 3.09 - 3.69: 76709 3.69 - 4.30: 106695 4.30 - 4.90: 147329 Nonbonded interactions: 358978 Sorted by model distance: nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 1.886 3.040 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.900 3.040 nonbonded pdb=" O2' A A 191 " pdb=" O2 C A 678 " model vdw 1.911 3.040 nonbonded pdb=" O2' U A2312 " pdb=" OD1 ASN F 36 " model vdw 1.929 3.040 nonbonded pdb=" O6 G A1206 " pdb=" O2 U A1240 " model vdw 1.959 2.432 ... (remaining 358973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.390 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: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 46.360 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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: 0.010 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: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.002 0.049 43759 Z= 0.089 Angle : 0.418 15.179 65701 Z= 0.221 Chirality : 0.029 0.642 8446 Planarity : 0.003 0.033 3325 Dihedral : 14.452 179.750 20485 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1423 helix: 1.66 (0.24), residues: 502 sheet: -0.49 (0.33), residues: 254 loop : -0.76 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 21 TYR 0.006 0.001 TYR O 64 PHE 0.009 0.001 PHE S 75 TRP 0.005 0.001 TRP F 96 HIS 0.003 0.000 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.09 (43759) covalent geometry : angle 0.41785 / 0.22 (65701) hydrogen bonds : bond 0.10071 / 5.91 ( 1561) hydrogen bonds : angle 3.89335 / 2.46 ( 3050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.810 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: 2 12 ARG cc_start: 0.9136 (ttt-90) cc_final: 0.8591 (tpt170) REVERT: 2 41 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7612 (mmm160) REVERT: E 88 ARG cc_start: 0.8757 (mpp80) cc_final: 0.8550 (mmm160) REVERT: E 100 MET cc_start: 0.9411 (mmp) cc_final: 0.9114 (mmm) REVERT: E 136 GLN cc_start: 0.9685 (tp40) cc_final: 0.9417 (tm-30) REVERT: F 95 MET cc_start: 0.4809 (mmm) cc_final: 0.4510 (mmm) REVERT: J 19 ASP cc_start: 0.9081 (p0) cc_final: 0.8769 (p0) REVERT: J 118 MET cc_start: 0.9398 (ptp) cc_final: 0.8986 (ttm) REVERT: L 104 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8177 (tp-100) REVERT: Q 23 TYR cc_start: 0.9156 (m-80) cc_final: 0.8860 (m-80) REVERT: Q 80 ASN cc_start: 0.9588 (t0) cc_final: 0.9340 (t0) REVERT: R 27 ILE cc_start: 0.7701 (tp) cc_final: 0.7455 (tp) REVERT: R 86 GLN cc_start: 0.7976 (pp30) cc_final: 0.7403 (mp10) REVERT: S 1 MET cc_start: 0.7607 (mpp) cc_final: 0.7288 (tmm) REVERT: S 3 THR cc_start: 0.8127 (m) cc_final: 0.7164 (m) REVERT: S 31 GLN cc_start: 0.9758 (tt0) cc_final: 0.9553 (tm-30) REVERT: S 53 SER cc_start: 0.9576 (t) cc_final: 0.9300 (p) REVERT: S 62 ASP cc_start: 0.8950 (m-30) cc_final: 0.8580 (m-30) REVERT: S 77 ASP cc_start: 0.5160 (p0) cc_final: 0.4833 (p0) REVERT: S 78 GLU cc_start: 0.8842 (pp20) cc_final: 0.8624 (pp20) REVERT: U 52 ASN cc_start: 0.8378 (p0) cc_final: 0.8104 (p0) REVERT: W 52 ASP cc_start: 0.8556 (m-30) cc_final: 0.8291 (t70) outliers start: 1 outliers final: 1 residues processed: 195 average time/residue: 0.2399 time to fit residues: 74.8562 Evaluate side-chains 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN J 58 ASN Q 13 HIS R 89 HIS R 91 GLN Y 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.036843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028146 restraints weight = 734323.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028990 restraints weight = 382202.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.029435 restraints weight = 264234.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.029781 restraints weight = 221421.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029990 restraints weight = 193684.655| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43759 Z= 0.174 Angle : 0.552 8.696 65701 Z= 0.278 Chirality : 0.030 0.270 8446 Planarity : 0.004 0.047 3325 Dihedral : 15.251 166.097 17644 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1423 helix: 1.00 (0.23), residues: 503 sheet: -0.78 (0.33), residues: 251 loop : -0.95 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 78 TYR 0.011 0.001 TYR F 21 PHE 0.033 0.002 PHE L 107 TRP 0.008 0.001 TRP R 92 HIS 0.005 0.001 HIS S 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (43759) covalent geometry : angle 0.55246 / 0.28 (65701) hydrogen bonds : bond 0.07878 / 4.83 ( 1561) hydrogen bonds : angle 3.65925 / 2.27 ( 3050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.833 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: 2 41 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7842 (mmm160) REVERT: E 100 MET cc_start: 0.9233 (mmp) cc_final: 0.8817 (mmm) REVERT: F 95 MET cc_start: 0.5591 (mmm) cc_final: 0.5383 (mmm) REVERT: J 19 ASP cc_start: 0.9266 (p0) cc_final: 0.8982 (p0) REVERT: J 103 ILE cc_start: 0.9246 (tp) cc_final: 0.9030 (pt) REVERT: J 118 MET cc_start: 0.9426 (ptp) cc_final: 0.8830 (tpt) REVERT: L 129 LYS cc_start: 0.9270 (mppt) cc_final: 0.9065 (mptt) REVERT: O 80 GLU cc_start: 0.9613 (OUTLIER) cc_final: 0.9298 (pp20) REVERT: Q 48 ASP cc_start: 0.8240 (m-30) cc_final: 0.7889 (m-30) REVERT: R 73 LYS cc_start: 0.8015 (tptp) cc_final: 0.7572 (tptt) REVERT: R 86 GLN cc_start: 0.7552 (pp30) cc_final: 0.7219 (pp30) REVERT: S 53 SER cc_start: 0.9613 (t) cc_final: 0.9356 (p) REVERT: S 78 GLU cc_start: 0.9025 (pp20) cc_final: 0.8720 (pp20) REVERT: S 110 ARG cc_start: 0.9392 (tpm170) cc_final: 0.9182 (tpm170) REVERT: V 24 ASN cc_start: 0.7228 (t0) cc_final: 0.7008 (t0) REVERT: W 49 CYS cc_start: 0.7708 (p) cc_final: 0.7037 (t) REVERT: Z 39 ASP cc_start: 0.9137 (t0) cc_final: 0.8933 (t0) outliers start: 2 outliers final: 1 residues processed: 149 average time/residue: 0.2425 time to fit residues: 58.8731 Evaluate side-chains 103 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 179 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 266 optimal weight: 0.2980 chunk 112 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 258 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 87 GLN R 91 GLN V 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.034901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.026317 restraints weight = 746848.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027102 restraints weight = 387878.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.027611 restraints weight = 268262.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027798 restraints weight = 216995.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.028032 restraints weight = 199166.026| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 43759 Z= 0.176 Angle : 0.562 11.405 65701 Z= 0.283 Chirality : 0.030 0.188 8446 Planarity : 0.004 0.040 3325 Dihedral : 15.648 167.420 17644 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.63 (0.22), residues: 1423 helix: 0.63 (0.23), residues: 509 sheet: -1.18 (0.34), residues: 238 loop : -0.87 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 80 TYR 0.013 0.002 TYR S 38 PHE 0.028 0.002 PHE L 107 TRP 0.012 0.002 TRP R 92 HIS 0.008 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (43759) covalent geometry : angle 0.56220 / 0.28 (65701) hydrogen bonds : bond 0.07803 / 4.73 ( 1561) hydrogen bonds : angle 3.68427 / 2.30 ( 3050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.638 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: 2 41 ARG cc_start: 0.8348 (tpt170) cc_final: 0.7966 (mmm160) REVERT: E 100 MET cc_start: 0.9077 (mmp) cc_final: 0.8662 (mmm) REVERT: J 19 ASP cc_start: 0.9325 (p0) cc_final: 0.9052 (p0) REVERT: J 102 GLU cc_start: 0.9138 (pp20) cc_final: 0.8887 (pp20) REVERT: J 103 ILE cc_start: 0.9260 (tp) cc_final: 0.8989 (pt) REVERT: Q 48 ASP cc_start: 0.7953 (m-30) cc_final: 0.7593 (m-30) REVERT: R 31 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8011 (tm-30) REVERT: R 73 LYS cc_start: 0.8070 (tptp) cc_final: 0.7844 (tptt) REVERT: S 53 SER cc_start: 0.9611 (t) cc_final: 0.9380 (p) REVERT: S 78 GLU cc_start: 0.8979 (pp20) cc_final: 0.8696 (pp20) REVERT: V 50 MET cc_start: 0.6182 (pmm) cc_final: 0.5620 (pmm) REVERT: V 63 ILE cc_start: 0.9171 (mt) cc_final: 0.8844 (tp) REVERT: W 27 VAL cc_start: 0.9490 (m) cc_final: 0.9167 (p) REVERT: W 76 ILE cc_start: 0.9290 (mm) cc_final: 0.9057 (mm) REVERT: Z 39 ASP cc_start: 0.9145 (t0) cc_final: 0.8934 (t0) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.2246 time to fit residues: 51.6348 Evaluate side-chains 98 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 39 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 263 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 141 optimal weight: 0.0030 chunk 56 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 129 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 12.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN 2 16 HIS ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS J 76 HIS L 99 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.030295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.022306 restraints weight = 800749.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022987 restraints weight = 423824.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.023331 restraints weight = 295593.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023655 restraints weight = 245615.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023783 restraints weight = 216152.733| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 43759 Z= 0.390 Angle : 0.928 13.214 65701 Z= 0.453 Chirality : 0.044 0.377 8446 Planarity : 0.007 0.084 3325 Dihedral : 17.296 168.590 17644 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 43.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.21), residues: 1423 helix: -0.59 (0.21), residues: 500 sheet: -1.41 (0.32), residues: 241 loop : -1.54 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 49 TYR 0.017 0.003 TYR R 83 PHE 0.026 0.004 PHE U 72 TRP 0.024 0.003 TRP E 60 HIS 0.010 0.002 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.39 (43759) covalent geometry : angle 0.92797 / 0.45 (65701) hydrogen bonds : bond 0.16488 / 10.03 ( 1561) hydrogen bonds : angle 4.59291 / 2.85 ( 3050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.618 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: E 100 MET cc_start: 0.8952 (mmp) cc_final: 0.8631 (mmm) REVERT: J 19 ASP cc_start: 0.9349 (p0) cc_final: 0.9148 (p0) REVERT: J 67 ASN cc_start: 0.8901 (t0) cc_final: 0.8677 (t0) REVERT: J 92 MET cc_start: 0.8783 (tpt) cc_final: 0.8315 (tpt) REVERT: J 102 GLU cc_start: 0.9211 (pp20) cc_final: 0.8940 (pp20) REVERT: L 117 THR cc_start: 0.7724 (p) cc_final: 0.7476 (p) REVERT: Q 35 PHE cc_start: 0.9322 (m-80) cc_final: 0.8928 (m-80) REVERT: S 53 SER cc_start: 0.9526 (t) cc_final: 0.9288 (p) REVERT: S 78 GLU cc_start: 0.8981 (pp20) cc_final: 0.8742 (pp20) REVERT: V 1 MET cc_start: 0.8690 (ppp) cc_final: 0.8350 (ptt) REVERT: V 63 ILE cc_start: 0.9062 (mt) cc_final: 0.8684 (tp) REVERT: W 76 ILE cc_start: 0.9273 (mm) cc_final: 0.9040 (mm) REVERT: Z 46 MET cc_start: 0.9039 (mmp) cc_final: 0.8695 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2221 time to fit residues: 41.5870 Evaluate side-chains 81 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 135 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 165 HIS Q 55 GLN R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.023143 restraints weight = 775458.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.023841 restraints weight = 405696.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024305 restraints weight = 281195.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.024527 restraints weight = 228275.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.024711 restraints weight = 206184.412| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43759 Z= 0.224 Angle : 0.674 16.443 65701 Z= 0.337 Chirality : 0.035 0.231 8446 Planarity : 0.005 0.042 3325 Dihedral : 17.149 166.738 17644 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.22), residues: 1423 helix: -0.23 (0.22), residues: 497 sheet: -1.53 (0.33), residues: 226 loop : -1.32 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 21 TYR 0.009 0.002 TYR Q 75 PHE 0.032 0.002 PHE V 2 TRP 0.015 0.002 TRP F 96 HIS 0.006 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (43759) covalent geometry : angle 0.67392 / 0.34 (65701) hydrogen bonds : bond 0.10501 / 6.41 ( 1561) hydrogen bonds : angle 4.13429 / 2.58 ( 3050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.529 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: E 1 MET cc_start: 0.8261 (tmm) cc_final: 0.7532 (tmm) REVERT: E 100 MET cc_start: 0.9004 (mmp) cc_final: 0.8661 (mmm) REVERT: J 36 LEU cc_start: 0.9723 (mm) cc_final: 0.9440 (mm) REVERT: J 67 ASN cc_start: 0.8964 (t0) cc_final: 0.8742 (t0) REVERT: J 92 MET cc_start: 0.8797 (tpt) cc_final: 0.8352 (tpt) REVERT: J 102 GLU cc_start: 0.9085 (pp20) cc_final: 0.8698 (pp20) REVERT: J 103 ILE cc_start: 0.9252 (tp) cc_final: 0.8993 (pt) REVERT: Q 35 PHE cc_start: 0.9198 (m-80) cc_final: 0.8791 (m-80) REVERT: R 53 PHE cc_start: 0.9398 (m-80) cc_final: 0.9141 (m-80) REVERT: S 53 SER cc_start: 0.9537 (t) cc_final: 0.9304 (p) REVERT: S 78 GLU cc_start: 0.8777 (pp20) cc_final: 0.8357 (pp20) REVERT: Z 46 MET cc_start: 0.8961 (mmp) cc_final: 0.8680 (mmm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2269 time to fit residues: 43.6734 Evaluate side-chains 84 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.030190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.022152 restraints weight = 786338.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.022725 restraints weight = 415299.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023237 restraints weight = 297680.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023486 restraints weight = 238653.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.023486 restraints weight = 211948.906| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 43759 Z= 0.293 Angle : 0.765 12.892 65701 Z= 0.380 Chirality : 0.038 0.238 8446 Planarity : 0.006 0.053 3325 Dihedral : 17.549 167.421 17644 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 36.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.21), residues: 1423 helix: -0.45 (0.22), residues: 501 sheet: -1.70 (0.32), residues: 236 loop : -1.49 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 32 TYR 0.012 0.002 TYR Q 46 PHE 0.024 0.003 PHE U 72 TRP 0.026 0.002 TRP E 60 HIS 0.012 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.29 (43759) covalent geometry : angle 0.76481 / 0.38 (65701) hydrogen bonds : bond 0.12751 / 7.80 ( 1561) hydrogen bonds : angle 4.33693 / 2.69 ( 3050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8345 (tmm) cc_final: 0.7659 (tmm) REVERT: E 100 MET cc_start: 0.8994 (mmp) cc_final: 0.8658 (mmm) REVERT: J 67 ASN cc_start: 0.8838 (t0) cc_final: 0.8570 (t0) REVERT: J 92 MET cc_start: 0.8834 (tpt) cc_final: 0.8448 (tpt) REVERT: J 102 GLU cc_start: 0.9107 (pp20) cc_final: 0.8802 (pp20) REVERT: Q 35 PHE cc_start: 0.9216 (m-80) cc_final: 0.8787 (m-80) REVERT: R 80 ARG cc_start: 0.9598 (tmm160) cc_final: 0.9334 (tmt170) REVERT: S 53 SER cc_start: 0.9512 (t) cc_final: 0.9261 (p) REVERT: S 78 GLU cc_start: 0.8792 (pp20) cc_final: 0.8525 (pp20) REVERT: V 50 MET cc_start: 0.7273 (pmm) cc_final: 0.6703 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2490 time to fit residues: 47.8031 Evaluate side-chains 86 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 4 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 137 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 HIS Z 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.022781 restraints weight = 772812.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.023502 restraints weight = 409235.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023949 restraints weight = 284088.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.024215 restraints weight = 231028.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.024317 restraints weight = 205487.280| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43759 Z= 0.206 Angle : 0.651 13.120 65701 Z= 0.328 Chirality : 0.035 0.236 8446 Planarity : 0.005 0.038 3325 Dihedral : 17.386 165.665 17644 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1423 helix: -0.26 (0.22), residues: 500 sheet: -1.60 (0.33), residues: 231 loop : -1.44 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Y 23 TYR 0.011 0.002 TYR Q 46 PHE 0.017 0.002 PHE R 77 TRP 0.017 0.002 TRP E 60 HIS 0.015 0.002 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (43759) covalent geometry : angle 0.65102 / 0.33 (65701) hydrogen bonds : bond 0.09573 / 5.89 ( 1561) hydrogen bonds : angle 4.10402 / 2.57 ( 3050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8298 (tmm) cc_final: 0.7714 (tmm) REVERT: E 100 MET cc_start: 0.9008 (mmp) cc_final: 0.8659 (mmm) REVERT: F 25 MET cc_start: 0.8953 (pmm) cc_final: 0.8701 (pmm) REVERT: J 67 ASN cc_start: 0.8909 (t0) cc_final: 0.8668 (t0) REVERT: J 92 MET cc_start: 0.8895 (tpt) cc_final: 0.8464 (tpp) REVERT: J 102 GLU cc_start: 0.9069 (pp20) cc_final: 0.8693 (pp20) REVERT: J 103 ILE cc_start: 0.9269 (tp) cc_final: 0.8914 (pt) REVERT: Q 35 PHE cc_start: 0.9194 (m-80) cc_final: 0.8753 (m-80) REVERT: R 86 GLN cc_start: 0.8693 (mm110) cc_final: 0.8259 (pp30) REVERT: S 53 SER cc_start: 0.9548 (t) cc_final: 0.9285 (p) REVERT: V 1 MET cc_start: 0.8596 (ptt) cc_final: 0.8326 (ppp) REVERT: V 50 MET cc_start: 0.7066 (pmm) cc_final: 0.6483 (pmm) REVERT: W 46 ASN cc_start: 0.9569 (m-40) cc_final: 0.9285 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2471 time to fit residues: 49.4222 Evaluate side-chains 92 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 192 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 121 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 100 optimal weight: 20.0000 chunk 265 optimal weight: 0.9990 chunk 256 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.022603 restraints weight = 775792.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.023310 restraints weight = 412228.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.023751 restraints weight = 287340.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.024009 restraints weight = 233605.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.024106 restraints weight = 207991.562| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 43759 Z= 0.220 Angle : 0.663 13.334 65701 Z= 0.334 Chirality : 0.035 0.248 8446 Planarity : 0.005 0.042 3325 Dihedral : 17.377 165.893 17644 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.21), residues: 1423 helix: -0.25 (0.22), residues: 507 sheet: -1.85 (0.34), residues: 212 loop : -1.36 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 79 TYR 0.011 0.002 TYR Q 46 PHE 0.023 0.002 PHE R 77 TRP 0.017 0.002 TRP E 60 HIS 0.010 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.22 (43759) covalent geometry : angle 0.66269 / 0.33 (65701) hydrogen bonds : bond 0.10118 / 6.25 ( 1561) hydrogen bonds : angle 4.11637 / 2.59 ( 3050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.761 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: E 1 MET cc_start: 0.8268 (tmm) cc_final: 0.7694 (tmm) REVERT: E 100 MET cc_start: 0.9009 (mmp) cc_final: 0.8664 (mmm) REVERT: F 25 MET cc_start: 0.8917 (pmm) cc_final: 0.8705 (pmm) REVERT: J 92 MET cc_start: 0.8803 (tpt) cc_final: 0.8343 (tpp) REVERT: J 102 GLU cc_start: 0.9011 (pp20) cc_final: 0.8636 (pp20) REVERT: J 103 ILE cc_start: 0.9269 (tp) cc_final: 0.8915 (pt) REVERT: Q 35 PHE cc_start: 0.9198 (m-80) cc_final: 0.8782 (m-80) REVERT: R 53 PHE cc_start: 0.9368 (m-80) cc_final: 0.9011 (m-10) REVERT: R 73 LYS cc_start: 0.8268 (tptt) cc_final: 0.7908 (tptt) REVERT: R 80 ARG cc_start: 0.9148 (tmm160) cc_final: 0.8916 (tmt170) REVERT: R 86 GLN cc_start: 0.8483 (mm110) cc_final: 0.8120 (pp30) REVERT: S 53 SER cc_start: 0.9487 (t) cc_final: 0.9206 (p) REVERT: V 50 MET cc_start: 0.6757 (pmm) cc_final: 0.6363 (pmm) REVERT: W 46 ASN cc_start: 0.9561 (m-40) cc_final: 0.9263 (t0) REVERT: Z 46 MET cc_start: 0.8930 (mmp) cc_final: 0.8625 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2613 time to fit residues: 53.2832 Evaluate side-chains 94 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 251 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 41 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.022861 restraints weight = 771005.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.023588 restraints weight = 406978.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.024041 restraints weight = 282187.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.024211 restraints weight = 229720.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024405 restraints weight = 210887.722| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43759 Z= 0.194 Angle : 0.629 13.282 65701 Z= 0.319 Chirality : 0.034 0.251 8446 Planarity : 0.005 0.045 3325 Dihedral : 17.305 164.791 17644 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1423 helix: -0.22 (0.22), residues: 505 sheet: -1.81 (0.33), residues: 212 loop : -1.30 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 23 TYR 0.010 0.002 TYR Q 46 PHE 0.017 0.002 PHE Q 105 TRP 0.015 0.002 TRP E 60 HIS 0.010 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (43759) covalent geometry : angle 0.62869 / 0.32 (65701) hydrogen bonds : bond 0.09047 / 5.64 ( 1561) hydrogen bonds : angle 4.05853 / 2.55 ( 3050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8257 (tmm) cc_final: 0.7666 (tmm) REVERT: E 100 MET cc_start: 0.9037 (mmp) cc_final: 0.8694 (mmm) REVERT: J 74 TYR cc_start: 0.7919 (m-80) cc_final: 0.7664 (m-10) REVERT: J 92 MET cc_start: 0.8801 (tpt) cc_final: 0.8570 (tpp) REVERT: J 102 GLU cc_start: 0.9011 (pp20) cc_final: 0.8646 (pp20) REVERT: J 103 ILE cc_start: 0.9285 (tp) cc_final: 0.8870 (pt) REVERT: Q 35 PHE cc_start: 0.9241 (m-80) cc_final: 0.8778 (m-80) REVERT: R 53 PHE cc_start: 0.9326 (m-80) cc_final: 0.8992 (m-80) REVERT: R 73 LYS cc_start: 0.8221 (tptt) cc_final: 0.7849 (tptt) REVERT: R 80 ARG cc_start: 0.9233 (tmm160) cc_final: 0.9002 (tmt170) REVERT: R 86 GLN cc_start: 0.8449 (mm110) cc_final: 0.8094 (pp30) REVERT: S 53 SER cc_start: 0.9497 (t) cc_final: 0.9221 (p) REVERT: S 66 ILE cc_start: 0.9171 (tt) cc_final: 0.8935 (mm) REVERT: V 50 MET cc_start: 0.6685 (pmm) cc_final: 0.6194 (pmm) REVERT: W 46 ASN cc_start: 0.9542 (m-40) cc_final: 0.9263 (t0) REVERT: Z 46 MET cc_start: 0.9025 (mmp) cc_final: 0.8710 (mmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2644 time to fit residues: 52.2663 Evaluate side-chains 94 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 157 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 256 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.030447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.022366 restraints weight = 774804.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.023086 restraints weight = 407555.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.023529 restraints weight = 281652.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.023784 restraints weight = 228396.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.023929 restraints weight = 203200.150| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43759 Z= 0.228 Angle : 0.672 13.622 65701 Z= 0.338 Chirality : 0.035 0.259 8446 Planarity : 0.005 0.044 3325 Dihedral : 17.471 165.278 17644 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 30.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.21), residues: 1423 helix: -0.26 (0.22), residues: 502 sheet: -1.86 (0.33), residues: 210 loop : -1.34 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 32 TYR 0.010 0.002 TYR Q 46 PHE 0.018 0.002 PHE Q 105 TRP 0.022 0.002 TRP E 60 HIS 0.009 0.002 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.23 (43759) covalent geometry : angle 0.67166 / 0.34 (65701) hydrogen bonds : bond 0.10339 / 6.42 ( 1561) hydrogen bonds : angle 4.15034 / 2.60 ( 3050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.788 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: E 1 MET cc_start: 0.8308 (tmm) cc_final: 0.7757 (tmm) REVERT: E 100 MET cc_start: 0.9064 (mmp) cc_final: 0.8738 (mmm) REVERT: J 74 TYR cc_start: 0.7906 (m-80) cc_final: 0.7609 (m-10) REVERT: J 92 MET cc_start: 0.8822 (tpt) cc_final: 0.8616 (tpp) REVERT: J 102 GLU cc_start: 0.9006 (pp20) cc_final: 0.8612 (pp20) REVERT: J 103 ILE cc_start: 0.9295 (tp) cc_final: 0.8873 (pt) REVERT: J 142 ILE cc_start: 0.7602 (tt) cc_final: 0.7357 (tt) REVERT: L 129 LYS cc_start: 0.9382 (mppt) cc_final: 0.8776 (tptp) REVERT: Q 35 PHE cc_start: 0.9245 (m-80) cc_final: 0.8764 (m-80) REVERT: R 53 PHE cc_start: 0.9380 (m-80) cc_final: 0.9082 (m-80) REVERT: R 73 LYS cc_start: 0.8181 (tptt) cc_final: 0.7852 (tptt) REVERT: R 80 ARG cc_start: 0.9166 (tmm160) cc_final: 0.8847 (tmt170) REVERT: R 86 GLN cc_start: 0.8491 (mm110) cc_final: 0.8075 (pp30) REVERT: S 53 SER cc_start: 0.9518 (t) cc_final: 0.9255 (p) REVERT: S 66 ILE cc_start: 0.9000 (tt) cc_final: 0.8787 (tp) REVERT: V 50 MET cc_start: 0.6459 (pmm) cc_final: 0.5989 (pmm) REVERT: W 46 ASN cc_start: 0.9553 (m-40) cc_final: 0.9243 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2535 time to fit residues: 49.7658 Evaluate side-chains 91 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 145 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 192 optimal weight: 0.0470 chunk 86 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.023028 restraints weight = 780046.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.023780 restraints weight = 410050.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.024233 restraints weight = 284844.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024399 restraints weight = 230245.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.024600 restraints weight = 211444.225| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 43759 Z= 0.176 Angle : 0.611 14.433 65701 Z= 0.310 Chirality : 0.033 0.256 8446 Planarity : 0.004 0.037 3325 Dihedral : 17.293 163.498 17644 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.22), residues: 1423 helix: -0.16 (0.22), residues: 502 sheet: -1.82 (0.33), residues: 211 loop : -1.28 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 79 TYR 0.010 0.001 TYR Q 46 PHE 0.016 0.002 PHE Q 105 TRP 0.015 0.002 TRP F 96 HIS 0.010 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (43759) covalent geometry : angle 0.61088 / 0.31 (65701) hydrogen bonds : bond 0.08508 / 5.37 ( 1561) hydrogen bonds : angle 3.99765 / 2.51 ( 3050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5054.11 seconds wall clock time: 89 minutes 58.39 seconds (5398.39 seconds total)