Starting phenix.real_space_refine on Tue Aug 26 17:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_16502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_16502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_16502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_16502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2025/8c95_16502.map" } 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-2.0-5787/lib/python3.9/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: 12 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: 6.89, per 1000 atoms: 0.17 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: 2.38 Conformation dependent library (CDL) restraints added in 687.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 5.94 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: 11.62 Time building geometry restraints manager: 3.28 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: 24424 35.95 - 71.90: 3142 71.90 - 107.85: 383 107.85 - 143.80: 11 143.80 - 179.75: 1 Dihedral angle restraints: 27961 sinusoidal: 23801 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 27958 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 23.210 179.750 25271 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 aren 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 covalent geometry : bond 0.00161 (43759) covalent geometry : angle 0.41785 (65701) hydrogen bonds : bond 0.10071 ( 1561) hydrogen bonds : angle 3.89335 ( 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 : 0.649 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: 0.2449 time to fit residues: 75.9851 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 : 0.744 ------------------------------------------------------------------------------- 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: 9.9990 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: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN J 58 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN R 89 HIS Y 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027999 restraints weight = 736156.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.028807 restraints weight = 382370.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.029342 restraints weight = 264376.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029527 restraints weight = 213948.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029778 restraints weight = 196490.347| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43759 Z= 0.186 Angle : 0.568 8.433 65701 Z= 0.285 Chirality : 0.030 0.190 8446 Planarity : 0.005 0.052 3325 Dihedral : 24.292 166.521 22430 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.17 % Allowed : 2.98 % Favored : 96.85 % 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 aren not related in a simple way. whole: -0.32 (0.23), residues: 1423 helix: 1.06 (0.23), residues: 503 sheet: -0.69 (0.33), residues: 248 loop : -0.96 (0.24), residues: 672 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 0.030 0.002 PHE L 107 TRP 0.009 0.001 TRP R 92 HIS 0.005 0.001 HIS S 60 Details of bonding type rmsd covalent geometry : bond 0.00347 (43759) covalent geometry : angle 0.56821 (65701) hydrogen bonds : bond 0.08028 ( 1561) hydrogen bonds : angle 3.68433 ( 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 150 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.692 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: 2 41 ARG cc_start: 0.8202 (tpt170) cc_final: 0.7855 (mmm160) REVERT: E 100 MET cc_start: 0.9217 (mmp) cc_final: 0.8824 (mmm) REVERT: J 19 ASP cc_start: 0.9266 (p0) cc_final: 0.8987 (p0) REVERT: J 103 ILE cc_start: 0.9264 (tp) cc_final: 0.9047 (pt) REVERT: J 118 MET cc_start: 0.9433 (ptp) cc_final: 0.8830 (tpt) REVERT: O 80 GLU cc_start: 0.9605 (OUTLIER) cc_final: 0.9271 (pp20) REVERT: Q 48 ASP cc_start: 0.8179 (m-30) cc_final: 0.7790 (m-30) REVERT: R 73 LYS cc_start: 0.8023 (tptp) cc_final: 0.7572 (tptt) REVERT: R 86 GLN cc_start: 0.7335 (pp30) cc_final: 0.7036 (pp30) REVERT: S 53 SER cc_start: 0.9601 (t) cc_final: 0.9347 (p) REVERT: S 78 GLU cc_start: 0.9032 (pp20) cc_final: 0.8738 (pp20) REVERT: W 49 CYS cc_start: 0.7790 (p) cc_final: 0.7075 (t) REVERT: Z 39 ASP cc_start: 0.9174 (t0) cc_final: 0.8963 (t0) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.2263 time to fit residues: 55.3594 Evaluate side-chains 101 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 30.0000 chunk 15 optimal weight: 20.0000 chunk 240 optimal weight: 0.0970 chunk 6 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 112 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 overall best weight: 7.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.032779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.024473 restraints weight = 776433.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.025157 restraints weight = 423121.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.025552 restraints weight = 290940.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.025856 restraints weight = 242835.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.025993 restraints weight = 213410.033| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 43759 Z= 0.262 Angle : 0.696 11.699 65701 Z= 0.348 Chirality : 0.036 0.268 8446 Planarity : 0.006 0.061 3325 Dihedral : 24.799 168.943 22430 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.34 % Allowed : 6.55 % Favored : 93.11 % 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 aren not related in a simple way. whole: -0.99 (0.22), residues: 1423 helix: 0.23 (0.22), residues: 504 sheet: -1.24 (0.34), residues: 222 loop : -1.06 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 18 TYR 0.012 0.002 TYR Q 44 PHE 0.031 0.003 PHE L 107 TRP 0.020 0.003 TRP F 96 HIS 0.008 0.002 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00484 (43759) covalent geometry : angle 0.69563 (65701) hydrogen bonds : bond 0.11033 ( 1561) hydrogen bonds : angle 4.02827 ( 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 137 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.704 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: 2 41 ARG cc_start: 0.8398 (tpt170) cc_final: 0.7984 (mmm160) REVERT: E 1 MET cc_start: 0.8153 (tmm) cc_final: 0.7437 (tmm) REVERT: E 100 MET cc_start: 0.8954 (mmp) cc_final: 0.8550 (mmm) REVERT: J 19 ASP cc_start: 0.9329 (p0) cc_final: 0.9103 (p0) REVERT: J 67 ASN cc_start: 0.8942 (t0) cc_final: 0.8729 (t0) REVERT: J 92 MET cc_start: 0.8710 (tpt) cc_final: 0.8508 (tpt) REVERT: Q 48 ASP cc_start: 0.7942 (m-30) cc_final: 0.7647 (m-30) REVERT: R 31 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8136 (tm-30) REVERT: R 68 ARG cc_start: 0.9384 (mpp-170) cc_final: 0.9133 (mpp80) REVERT: R 73 LYS cc_start: 0.7905 (tptp) cc_final: 0.7510 (tptp) REVERT: S 53 SER cc_start: 0.9596 (t) cc_final: 0.9338 (p) REVERT: S 65 ASP cc_start: 0.8217 (t0) cc_final: 0.8004 (t0) REVERT: V 50 MET cc_start: 0.6222 (pmm) cc_final: 0.5919 (pmm) REVERT: V 63 ILE cc_start: 0.9159 (mt) cc_final: 0.8856 (tp) REVERT: W 27 VAL cc_start: 0.9412 (m) cc_final: 0.9070 (p) REVERT: W 76 ILE cc_start: 0.9257 (mm) cc_final: 0.9003 (mm) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.2192 time to fit residues: 48.7804 Evaluate side-chains 95 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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: 4.9990 chunk 263 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 16 HIS J 76 HIS R 87 GLN R 91 GLN S 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023957 restraints weight = 777370.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.024693 restraints weight = 409991.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.025072 restraints weight = 286454.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.025442 restraints weight = 241746.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.025538 restraints weight = 210453.939| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43759 Z= 0.223 Angle : 0.636 12.205 65701 Z= 0.319 Chirality : 0.033 0.219 8446 Planarity : 0.005 0.090 3325 Dihedral : 24.896 166.203 22430 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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 aren not related in a simple way. whole: -1.15 (0.22), residues: 1423 helix: 0.07 (0.22), residues: 505 sheet: -1.33 (0.34), residues: 230 loop : -1.11 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 21 TYR 0.010 0.002 TYR F 21 PHE 0.024 0.002 PHE V 91 TRP 0.013 0.002 TRP E 60 HIS 0.006 0.001 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00417 (43759) covalent geometry : angle 0.63595 (65701) hydrogen bonds : bond 0.09891 ( 1561) hydrogen bonds : angle 3.94864 ( 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 124 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.742 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: 0.8523 (tpt170) cc_final: 0.8212 (mmm160) REVERT: E 100 MET cc_start: 0.8993 (mmp) cc_final: 0.8635 (mmm) REVERT: J 19 ASP cc_start: 0.9348 (p0) cc_final: 0.9137 (p0) REVERT: J 36 LEU cc_start: 0.9665 (mm) cc_final: 0.9405 (mm) REVERT: J 67 ASN cc_start: 0.8962 (t0) cc_final: 0.8706 (t0) REVERT: J 92 MET cc_start: 0.8742 (tpt) cc_final: 0.8339 (tpt) REVERT: J 102 GLU cc_start: 0.9134 (pp20) cc_final: 0.8818 (pp20) REVERT: J 103 ILE cc_start: 0.9223 (tp) cc_final: 0.8966 (pt) REVERT: Q 48 ASP cc_start: 0.7948 (m-30) cc_final: 0.7744 (m-30) REVERT: R 68 ARG cc_start: 0.9382 (mpp-170) cc_final: 0.9135 (mpp80) REVERT: R 73 LYS cc_start: 0.8201 (tptp) cc_final: 0.7624 (tptt) REVERT: S 53 SER cc_start: 0.9552 (t) cc_final: 0.9281 (p) REVERT: V 50 MET cc_start: 0.6533 (pmm) cc_final: 0.5983 (pmm) REVERT: W 27 VAL cc_start: 0.9412 (m) cc_final: 0.9073 (p) REVERT: W 76 ILE cc_start: 0.9314 (mm) cc_final: 0.9085 (mm) REVERT: Z 46 MET cc_start: 0.8825 (mmp) cc_final: 0.8622 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2186 time to fit residues: 44.9172 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 : 0.676 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 30.0000 chunk 156 optimal weight: 8.9990 chunk 162 optimal weight: 0.0030 chunk 159 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 120 optimal weight: 40.0000 chunk 135 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 overall best weight: 7.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 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** Y 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.031262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.022997 restraints weight = 772953.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.023671 restraints weight = 407913.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.024152 restraints weight = 294252.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024439 restraints weight = 235520.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.024552 restraints weight = 207000.220| |-----------------------------------------------------------------------------| r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 43759 Z= 0.243 Angle : 0.680 15.856 65701 Z= 0.340 Chirality : 0.035 0.292 8446 Planarity : 0.005 0.051 3325 Dihedral : 25.072 167.608 22430 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 30.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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 aren not related in a simple way. whole: -1.49 (0.21), residues: 1423 helix: -0.13 (0.22), residues: 496 sheet: -1.72 (0.32), residues: 237 loop : -1.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 52 TYR 0.010 0.002 TYR E 101 PHE 0.019 0.002 PHE F 99 TRP 0.017 0.002 TRP E 60 HIS 0.022 0.002 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00455 (43759) covalent geometry : angle 0.68027 (65701) hydrogen bonds : bond 0.10700 ( 1561) hydrogen bonds : angle 4.06125 ( 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 120 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8292 (tmm) cc_final: 0.7578 (tmm) REVERT: E 100 MET cc_start: 0.8967 (mmp) cc_final: 0.8615 (mmm) REVERT: F 25 MET cc_start: 0.8960 (pmm) cc_final: 0.8748 (pmm) REVERT: J 36 LEU cc_start: 0.9693 (mm) cc_final: 0.9452 (mm) REVERT: J 67 ASN cc_start: 0.8988 (t0) cc_final: 0.8725 (t0) REVERT: J 92 MET cc_start: 0.8815 (tpt) cc_final: 0.8494 (tpp) REVERT: J 102 GLU cc_start: 0.9092 (pp20) cc_final: 0.8785 (pp20) REVERT: L 117 THR cc_start: 0.7816 (p) cc_final: 0.7530 (p) REVERT: L 129 LYS cc_start: 0.9377 (mppt) cc_final: 0.9157 (mptt) REVERT: Q 48 ASP cc_start: 0.7965 (m-30) cc_final: 0.6355 (m-30) REVERT: R 53 PHE cc_start: 0.9391 (m-80) cc_final: 0.9121 (m-10) REVERT: S 53 SER cc_start: 0.9537 (t) cc_final: 0.9311 (p) REVERT: V 50 MET cc_start: 0.6358 (pmm) cc_final: 0.5780 (pmm) REVERT: W 76 ILE cc_start: 0.9296 (mm) cc_final: 0.9090 (mm) REVERT: Y 30 MET cc_start: 0.9502 (tpp) cc_final: 0.9177 (tpp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2017 time to fit residues: 40.5311 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 : 0.698 ------------------------------------------------------------------------------- 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: 9.9990 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 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: 40.0000 overall best weight: 6.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.024011 restraints weight = 799103.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.024782 restraints weight = 409606.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.025135 restraints weight = 279475.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.025499 restraints weight = 232025.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.025606 restraints weight = 201763.405| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43759 Z= 0.221 Angle : 0.646 12.622 65701 Z= 0.326 Chirality : 0.034 0.221 8446 Planarity : 0.005 0.044 3325 Dihedral : 25.098 165.762 22430 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 0.09 % Allowed : 3.15 % 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 aren not related in a simple way. whole: -1.37 (0.22), residues: 1423 helix: -0.10 (0.22), residues: 503 sheet: -1.60 (0.33), residues: 227 loop : -1.19 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 21 TYR 0.013 0.002 TYR Q 46 PHE 0.017 0.002 PHE F 99 TRP 0.017 0.002 TRP E 60 HIS 0.014 0.002 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00410 (43759) covalent geometry : angle 0.64640 (65701) hydrogen bonds : bond 0.09904 ( 1561) hydrogen bonds : angle 4.00303 ( 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 116 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.639 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: 0.8295 (tmm) cc_final: 0.7506 (tmm) REVERT: E 100 MET cc_start: 0.8993 (mmp) cc_final: 0.8629 (mmm) REVERT: F 95 MET cc_start: 0.4699 (mmm) cc_final: 0.4424 (mmm) REVERT: J 67 ASN cc_start: 0.8963 (t0) cc_final: 0.8733 (t0) REVERT: J 92 MET cc_start: 0.8779 (tpt) cc_final: 0.8459 (tpp) REVERT: J 102 GLU cc_start: 0.9106 (pp20) cc_final: 0.8840 (pp20) REVERT: L 3 LEU cc_start: 0.9211 (mp) cc_final: 0.8924 (pp) REVERT: R 73 LYS cc_start: 0.8282 (tptt) cc_final: 0.7706 (tptt) REVERT: R 80 ARG cc_start: 0.9545 (tmm160) cc_final: 0.9170 (tmt170) REVERT: S 53 SER cc_start: 0.9516 (t) cc_final: 0.9280 (p) REVERT: V 50 MET cc_start: 0.6745 (pmm) cc_final: 0.6067 (pmm) REVERT: W 76 ILE cc_start: 0.9272 (mm) cc_final: 0.9064 (mm) REVERT: Z 46 MET cc_start: 0.8952 (mmp) cc_final: 0.8644 (mmm) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.2326 time to fit residues: 44.0154 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 : 0.781 ------------------------------------------------------------------------------- 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: 7.9990 chunk 220 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 HIS Y 15 ASN Z 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.030632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.022521 restraints weight = 774514.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.023232 restraints weight = 408515.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.023553 restraints weight = 282410.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.023873 restraints weight = 235647.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.024049 restraints weight = 208792.675| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43759 Z= 0.238 Angle : 0.678 12.722 65701 Z= 0.340 Chirality : 0.035 0.246 8446 Planarity : 0.005 0.048 3325 Dihedral : 25.217 165.560 22430 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 31.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.57 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 aren not related in a simple way. whole: -1.57 (0.21), residues: 1423 helix: -0.36 (0.22), residues: 498 sheet: -1.39 (0.33), residues: 222 loop : -1.36 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 23 TYR 0.019 0.002 TYR Q 46 PHE 0.018 0.002 PHE F 99 TRP 0.022 0.002 TRP E 60 HIS 0.010 0.002 HIS E 165 Details of bonding type rmsd covalent geometry : bond 0.00443 (43759) covalent geometry : angle 0.67794 (65701) hydrogen bonds : bond 0.10556 ( 1561) hydrogen bonds : angle 4.08476 ( 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 115 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8508 (tpt170) cc_final: 0.8193 (mmm160) REVERT: E 1 MET cc_start: 0.8310 (tmm) cc_final: 0.7570 (tmm) REVERT: E 100 MET cc_start: 0.9011 (mmp) cc_final: 0.8665 (mmm) REVERT: F 95 MET cc_start: 0.4959 (mmm) cc_final: 0.4637 (mmm) REVERT: J 92 MET cc_start: 0.8739 (tpt) cc_final: 0.8416 (tpt) REVERT: J 102 GLU cc_start: 0.9102 (pp20) cc_final: 0.8712 (pp20) REVERT: J 103 ILE cc_start: 0.9258 (tp) cc_final: 0.8913 (pt) REVERT: L 3 LEU cc_start: 0.9225 (mp) cc_final: 0.9008 (pp) REVERT: L 129 LYS cc_start: 0.9355 (mppt) cc_final: 0.8770 (tptp) REVERT: R 53 PHE cc_start: 0.9355 (m-80) cc_final: 0.8944 (m-10) REVERT: R 73 LYS cc_start: 0.8154 (tptt) cc_final: 0.7853 (tptt) REVERT: R 80 ARG cc_start: 0.9322 (tmm160) cc_final: 0.9109 (tmt170) REVERT: S 53 SER cc_start: 0.9521 (t) cc_final: 0.9251 (p) REVERT: V 50 MET cc_start: 0.6818 (pmm) cc_final: 0.6320 (pmm) REVERT: Y 30 MET cc_start: 0.9448 (tpt) cc_final: 0.9121 (tpp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2222 time to fit residues: 42.0307 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 : 0.462 ------------------------------------------------------------------------------- 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: 6.9990 chunk 170 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 121 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 chunk 79 optimal weight: 20.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Z 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.031465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.023201 restraints weight = 765329.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.023940 restraints weight = 402760.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.024409 restraints weight = 279682.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.024686 restraints weight = 226043.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.024790 restraints weight = 200602.284| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43759 Z= 0.166 Angle : 0.599 13.492 65701 Z= 0.303 Chirality : 0.033 0.244 8446 Planarity : 0.004 0.037 3325 Dihedral : 25.105 163.626 22430 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.10 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: -1.29 (0.22), residues: 1423 helix: -0.08 (0.22), residues: 501 sheet: -1.44 (0.34), residues: 220 loop : -1.17 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG S 110 TYR 0.016 0.001 TYR Q 46 PHE 0.021 0.002 PHE F 99 TRP 0.013 0.002 TRP E 60 HIS 0.009 0.001 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00308 (43759) covalent geometry : angle 0.59907 (65701) hydrogen bonds : bond 0.08519 ( 1561) hydrogen bonds : angle 3.87001 ( 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 121 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8590 (tpt170) cc_final: 0.8217 (mmm160) REVERT: E 1 MET cc_start: 0.8341 (tmm) cc_final: 0.7571 (tmm) REVERT: E 100 MET cc_start: 0.9027 (mmp) cc_final: 0.8670 (mmm) REVERT: F 95 MET cc_start: 0.4623 (mmm) cc_final: 0.4338 (mmm) REVERT: J 92 MET cc_start: 0.8745 (tpt) cc_final: 0.8530 (tpp) REVERT: J 102 GLU cc_start: 0.9031 (pp20) cc_final: 0.8676 (pp20) REVERT: J 103 ILE cc_start: 0.9264 (tp) cc_final: 0.8855 (pt) REVERT: J 118 MET cc_start: 0.9414 (ptp) cc_final: 0.8901 (ttm) REVERT: L 3 LEU cc_start: 0.9211 (mp) cc_final: 0.8997 (pp) REVERT: R 53 PHE cc_start: 0.9313 (m-80) cc_final: 0.9017 (m-80) REVERT: R 80 ARG cc_start: 0.9313 (tmm160) cc_final: 0.9098 (tmt170) REVERT: S 53 SER cc_start: 0.9531 (t) cc_final: 0.9275 (p) REVERT: S 110 ARG cc_start: 0.9607 (tpm170) cc_final: 0.9383 (tpm170) REVERT: V 50 MET cc_start: 0.6546 (pmm) cc_final: 0.6075 (pmm) REVERT: W 46 ASN cc_start: 0.9534 (m-40) cc_final: 0.9305 (t0) REVERT: Y 30 MET cc_start: 0.9457 (tpt) cc_final: 0.9106 (tpp) REVERT: Z 46 MET cc_start: 0.8953 (mmp) cc_final: 0.8677 (mmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2336 time to fit residues: 45.9892 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 : 0.744 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 41 optimal weight: 50.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 55 GLN ** 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** Z 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.032072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.023772 restraints weight = 762659.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.024535 restraints weight = 401787.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.025012 restraints weight = 277875.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.025183 restraints weight = 225782.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.025385 restraints weight = 207371.169| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43759 Z= 0.146 Angle : 0.571 13.243 65701 Z= 0.290 Chirality : 0.031 0.240 8446 Planarity : 0.004 0.035 3325 Dihedral : 24.910 163.387 22430 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % 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 aren not related in a simple way. whole: -1.10 (0.22), residues: 1423 helix: 0.16 (0.23), residues: 501 sheet: -1.32 (0.35), residues: 216 loop : -1.14 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 81 TYR 0.014 0.001 TYR Q 46 PHE 0.019 0.002 PHE F 99 TRP 0.011 0.001 TRP E 60 HIS 0.014 0.001 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00273 (43759) covalent geometry : angle 0.57053 (65701) hydrogen bonds : bond 0.07748 ( 1561) hydrogen bonds : angle 3.80470 ( 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 127 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8556 (tpt170) cc_final: 0.8093 (mmm160) REVERT: E 1 MET cc_start: 0.8254 (tmm) cc_final: 0.7462 (tmm) REVERT: E 100 MET cc_start: 0.9053 (mmp) cc_final: 0.8687 (mmm) REVERT: J 74 TYR cc_start: 0.7848 (m-80) cc_final: 0.7608 (m-10) REVERT: J 102 GLU cc_start: 0.9067 (pp20) cc_final: 0.8761 (pp20) REVERT: J 103 ILE cc_start: 0.9305 (tp) cc_final: 0.8871 (pt) REVERT: J 118 MET cc_start: 0.9418 (ptp) cc_final: 0.8909 (ttm) REVERT: L 3 LEU cc_start: 0.9197 (mp) cc_final: 0.8976 (pt) REVERT: L 129 LYS cc_start: 0.9249 (mppt) cc_final: 0.8595 (tptp) REVERT: O 93 ASP cc_start: 0.9045 (t0) cc_final: 0.8471 (m-30) REVERT: R 53 PHE cc_start: 0.9334 (m-80) cc_final: 0.9065 (m-80) REVERT: S 53 SER cc_start: 0.9571 (t) cc_final: 0.9286 (p) REVERT: S 110 ARG cc_start: 0.9642 (tpm170) cc_final: 0.9240 (tpm170) REVERT: V 50 MET cc_start: 0.6222 (pmm) cc_final: 0.5776 (pmm) REVERT: W 46 ASN cc_start: 0.9534 (m-40) cc_final: 0.9310 (t0) REVERT: Y 30 MET cc_start: 0.9468 (tpt) cc_final: 0.9110 (tpp) REVERT: Z 46 MET cc_start: 0.8988 (mmp) cc_final: 0.8765 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2209 time to fit residues: 46.0764 Evaluate side-chains 95 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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: 4.9990 chunk 57 optimal weight: 30.0000 chunk 10 optimal weight: 30.0000 chunk 222 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 251 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 256 optimal weight: 30.0000 chunk 191 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 55 GLN ** 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** Z 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.030370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.022312 restraints weight = 776646.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.023014 restraints weight = 409935.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.023327 restraints weight = 284745.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.023672 restraints weight = 237770.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.023787 restraints weight = 208639.207| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 43759 Z= 0.256 Angle : 0.701 17.140 65701 Z= 0.351 Chirality : 0.036 0.352 8446 Planarity : 0.005 0.063 3325 Dihedral : 25.198 164.428 22430 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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 aren not related in a simple way. whole: -1.45 (0.22), residues: 1423 helix: -0.19 (0.22), residues: 500 sheet: -1.40 (0.33), residues: 234 loop : -1.32 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Y 23 TYR 0.013 0.002 TYR Q 46 PHE 0.018 0.002 PHE Q 105 TRP 0.027 0.003 TRP F 96 HIS 0.024 0.002 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00474 (43759) covalent geometry : angle 0.70125 (65701) hydrogen bonds : bond 0.11206 ( 1561) hydrogen bonds : angle 4.14680 ( 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 : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8573 (tpt170) cc_final: 0.8244 (mmm160) REVERT: E 1 MET cc_start: 0.8264 (tmm) cc_final: 0.7702 (tmm) REVERT: E 100 MET cc_start: 0.9070 (mmp) cc_final: 0.8740 (mmm) REVERT: J 74 TYR cc_start: 0.7906 (m-80) cc_final: 0.7643 (m-80) REVERT: J 92 MET cc_start: 0.9049 (tpp) cc_final: 0.8698 (tpp) REVERT: J 102 GLU cc_start: 0.9057 (pp20) cc_final: 0.8795 (pp20) REVERT: J 118 MET cc_start: 0.9440 (ptp) cc_final: 0.8834 (ttm) REVERT: J 142 ILE cc_start: 0.7759 (tt) cc_final: 0.7526 (tt) REVERT: L 3 LEU cc_start: 0.9248 (mp) cc_final: 0.9025 (pp) REVERT: L 129 LYS cc_start: 0.9324 (mppt) cc_final: 0.8782 (tptp) REVERT: R 53 PHE cc_start: 0.9450 (m-80) cc_final: 0.9223 (m-80) REVERT: R 80 ARG cc_start: 0.9380 (tmm160) cc_final: 0.9148 (tmt170) REVERT: S 53 SER cc_start: 0.9511 (t) cc_final: 0.9253 (p) REVERT: S 110 ARG cc_start: 0.9665 (tpm170) cc_final: 0.9204 (tpm170) REVERT: V 50 MET cc_start: 0.6565 (pmm) cc_final: 0.6161 (pmm) REVERT: W 46 ASN cc_start: 0.9531 (m-40) cc_final: 0.9243 (t0) REVERT: Y 30 MET cc_start: 0.9372 (tpt) cc_final: 0.9035 (tpp) REVERT: Z 46 MET cc_start: 0.9096 (mmp) cc_final: 0.8869 (mmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2336 time to fit residues: 45.1952 Evaluate side-chains 87 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 201 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2866 r_free = 0.2866 target = 0.030619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.022507 restraints weight = 777817.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.023230 restraints weight = 406552.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.023663 restraints weight = 280801.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023934 restraints weight = 227691.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.024037 restraints weight = 201839.535| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 43759 Z= 0.218 Angle : 0.653 13.252 65701 Z= 0.330 Chirality : 0.035 0.266 8446 Planarity : 0.005 0.063 3325 Dihedral : 25.231 162.316 22430 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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 aren not related in a simple way. whole: -1.45 (0.22), residues: 1423 helix: -0.17 (0.22), residues: 500 sheet: -1.66 (0.33), residues: 216 loop : -1.24 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 21 TYR 0.014 0.002 TYR Q 46 PHE 0.018 0.002 PHE R 77 TRP 0.016 0.002 TRP E 60 HIS 0.021 0.002 HIS V 44 Details of bonding type rmsd covalent geometry : bond 0.00405 (43759) covalent geometry : angle 0.65278 (65701) hydrogen bonds : bond 0.09703 ( 1561) hydrogen bonds : angle 4.05180 ( 3050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.21 seconds wall clock time: 82 minutes 30.86 seconds (4950.86 seconds total)