Starting phenix.real_space_refine on Sun Aug 9 23:17:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c95_16502/08_2026/8c95_16502.cif" } resolution = 4.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1339 5.49 5 S 27 5.16 5 C 20007 2.51 5 N 7484 2.21 5 O 11315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40172 Number of models: 1 Model: "" Number of chains: 16 Chain: "2" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 26210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 26210 Classifications: {'RNAv2': 1220} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 59, 'rna3p_pur': 599, 'rna3p_pyr': 443} Link IDs: {'rna2p': 177, 'rna3p': 1042} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNAv2': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1519 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 1 Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1379 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 725 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 513 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 8.21, per 1000 atoms: 0.20 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: 2.90 Conformation dependent library (CDL) restraints added in 818.2 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 38.4% alpha, 15.5% beta 436 base pairs and 648 stacking pairs defined. Time for finding SS restraints: 5.65 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: 14.11 Time building geometry restraints manager: 4.17 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 2.00e-02 2.50e+03 5.90e+00 bond pdb=" O5' G A 974 " pdb=" C5' G A 974 " ideal model delta sigma weight residual 1.427 1.470 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 bond pdb=" O5' A A 973 " pdb=" C5' A A 973 " ideal model delta sigma weight residual 1.427 1.462 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" N ALA Z 1 " pdb=" CA ALA Z 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 43754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 64866 2.94 - 5.87: 822 5.87 - 8.81: 11 8.81 - 11.74: 1 11.74 - 14.68: 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 119.70 105.02 14.68 1.20e+00 6.94e-01 1.50e+02 angle pdb=" C3' U A2390 " pdb=" O3' U A2390 " pdb=" P G A2391 " ideal model delta sigma weight residual 119.70 109.84 9.86 1.20e+00 6.94e-01 6.75e+01 angle pdb=" C3' A A 973 " pdb=" O3' A A 973 " pdb=" P G A 974 " ideal model delta sigma weight residual 119.70 128.19 -8.49 1.20e+00 6.94e-01 5.00e+01 angle pdb=" C3' G A2389 " pdb=" O3' G A2389 " pdb=" P U A2390 " ideal model delta sigma weight residual 119.70 113.49 6.21 1.20e+00 6.94e-01 2.68e+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 ... (remaining 65696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 20723 35.95 - 71.90: 2362 71.90 - 107.85: 88 107.85 - 143.80: 1 143.80 - 179.75: 1 Dihedral angle restraints: 23175 sinusoidal: 19015 harmonic: 4160 Sorted by residual: dihedral pdb=" C4' G A 974 " pdb=" C3' G A 974 " pdb=" C2' G A 974 " pdb=" C1' G A 974 " ideal model delta sinusoidal sigma weight residual 36.34 -42.27 78.61 1 3.10e+00 1.04e-01 8.02e+02 dihedral pdb=" C4' A A 404 " pdb=" C3' A A 404 " pdb=" C2' A A 404 " pdb=" C1' A A 404 " ideal model delta sinusoidal sigma weight residual 36.35 -38.02 74.37 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' U A 434 " pdb=" C3' U A 434 " pdb=" C2' U A 434 " pdb=" C1' U A 434 " ideal model delta sinusoidal sigma weight residual 36.35 -37.42 73.77 1 3.10e+00 1.04e-01 7.20e+02 ... (remaining 23172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 6734 0.176 - 0.351: 1708 0.351 - 0.527: 0 0.527 - 0.703: 2 0.703 - 0.878: 2 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 2.17 -3.05 -0.88 2.00e-01 2.50e+01 1.93e+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 2.17 -2.90 -0.73 2.00e-01 2.50e+01 1.32e+01 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 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 8443 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.015 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 G A 259 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.032 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.023 2.00e-02 2.50e+03 1.81e-02 7.37e+00 pdb=" N1 C A 418 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 418 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 418 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 418 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 418 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 398 " -0.007 2.00e-02 2.50e+03 1.56e-02 5.51e+00 pdb=" N1 C A 398 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 398 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C A 398 " -0.023 2.00e-02 2.50e+03 pdb=" N3 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 398 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A 398 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 398 " -0.001 2.00e-02 2.50e+03 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 382 2.49 - 3.09: 27863 3.09 - 3.69: 76709 3.69 - 4.30: 106695 4.30 - 4.90: 147329 Nonbonded interactions: 358978 Sorted by model distance: nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 1.886 3.040 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.900 3.040 nonbonded pdb=" O2' A A 191 " pdb=" O2 C A 678 " model vdw 1.911 3.040 nonbonded pdb=" O2' U A2312 " pdb=" OD1 ASN F 36 " model vdw 1.929 3.040 nonbonded pdb=" O6 G A1206 " pdb=" O2 U A1240 " model vdw 1.959 2.432 ... (remaining 358973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 42.740 Find NCS groups from input model: 0.200 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43759 Z= 0.131 Angle : 0.859 14.679 65701 Z= 0.356 Chirality : 0.115 0.878 8446 Planarity : 0.003 0.033 3325 Dihedral : 20.681 179.750 20485 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1423 helix: 1.66 (0.24), residues: 502 sheet: -0.49 (0.33), residues: 254 loop : -0.76 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 21 TYR 0.006 0.001 TYR O 64 PHE 0.009 0.001 PHE S 75 TRP 0.005 0.001 TRP F 96 HIS 0.003 0.000 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (43759) covalent geometry : angle 0.85894 / 0.36 (65701) hydrogen bonds : bond 0.10071 / 5.32 ( 1561) hydrogen bonds : angle 3.89335 / 2.07 ( 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 : 0.727 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: 0.2575 time to fit residues: 80.5440 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 : 0.580 ------------------------------------------------------------------------------- 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: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 165 HIS L 99 ASN R 89 HIS Y 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.037430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028681 restraints weight = 734029.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.029534 restraints weight = 391219.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.030092 restraints weight = 270592.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.030413 restraints weight = 217687.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.030615 restraints weight = 192393.310| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 43759 Z= 0.266 Angle : 1.399 21.298 65701 Z= 0.553 Chirality : 0.109 1.299 8446 Planarity : 0.005 0.059 3325 Dihedral : 20.056 161.597 17644 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.17 % Allowed : 2.72 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1423 helix: 1.11 (0.23), residues: 502 sheet: -0.77 (0.33), residues: 253 loop : -0.91 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 9 TYR 0.009 0.001 TYR F 21 PHE 0.025 0.002 PHE L 107 TRP 0.008 0.001 TRP F 96 HIS 0.005 0.001 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 (43759) covalent geometry : angle 1.39899 / 0.55 (65701) hydrogen bonds : bond 0.08312 / 4.81 ( 1561) hydrogen bonds : angle 3.69494 / 1.88 ( 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 152 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.779 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 12 ARG cc_start: 0.9068 (ttt-90) cc_final: 0.8572 (tpt170) REVERT: 2 41 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7778 (mmm160) REVERT: E 100 MET cc_start: 0.9241 (mmp) cc_final: 0.8867 (mmm) REVERT: J 19 ASP cc_start: 0.9212 (p0) cc_final: 0.8909 (p0) REVERT: J 102 GLU cc_start: 0.9081 (pp20) cc_final: 0.8869 (pp20) REVERT: J 103 ILE cc_start: 0.9248 (tp) cc_final: 0.9012 (pt) REVERT: J 118 MET cc_start: 0.9409 (ptp) cc_final: 0.8832 (tpt) REVERT: L 76 GLU cc_start: 0.9392 (pp20) cc_final: 0.9176 (mm-30) REVERT: Q 23 TYR cc_start: 0.9247 (m-80) cc_final: 0.9004 (m-80) REVERT: Q 48 ASP cc_start: 0.8126 (m-30) cc_final: 0.7734 (m-30) REVERT: R 73 LYS cc_start: 0.7970 (tptp) cc_final: 0.7543 (tptt) REVERT: R 86 GLN cc_start: 0.7561 (pp30) cc_final: 0.7198 (pp30) REVERT: S 53 SER cc_start: 0.9630 (t) cc_final: 0.9346 (p) REVERT: S 78 GLU cc_start: 0.9008 (pp20) cc_final: 0.8674 (pp20) REVERT: V 24 ASN cc_start: 0.7103 (t0) cc_final: 0.6867 (t0) REVERT: V 48 MET cc_start: 0.7896 (mpp) cc_final: 0.7612 (mpp) REVERT: W 49 CYS cc_start: 0.7801 (p) cc_final: 0.7096 (t) outliers start: 2 outliers final: 2 residues processed: 152 average time/residue: 0.2531 time to fit residues: 62.9049 Evaluate side-chains 109 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 266 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN J 58 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 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 = 0.2974 r_free = 0.2974 target = 0.033500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.025171 restraints weight = 777303.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.025950 restraints weight = 399847.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.026452 restraints weight = 274928.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.026751 restraints weight = 221647.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.026888 restraints weight = 196111.913| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 43759 Z= 0.321 Angle : 1.257 20.683 65701 Z= 0.501 Chirality : 0.085 1.040 8446 Planarity : 0.006 0.056 3325 Dihedral : 20.440 179.494 17644 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 0.17 % Allowed : 4.68 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1423 helix: 0.28 (0.22), residues: 506 sheet: -1.16 (0.34), residues: 225 loop : -1.04 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 32 TYR 0.014 0.002 TYR Q 44 PHE 0.031 0.003 PHE E 124 TRP 0.014 0.002 TRP F 96 HIS 0.006 0.002 HIS J 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.32 (43759) covalent geometry : angle 1.25720 / 0.50 (65701) hydrogen bonds : bond 0.12100 / 6.91 ( 1561) hydrogen bonds : angle 4.08854 / 2.03 ( 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 136 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.853 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 100 MET cc_start: 0.9147 (mmp) cc_final: 0.8752 (mmm) REVERT: J 19 ASP cc_start: 0.9296 (p0) cc_final: 0.9019 (p0) REVERT: J 74 TYR cc_start: 0.8121 (m-80) cc_final: 0.7904 (m-10) REVERT: J 102 GLU cc_start: 0.9130 (pp20) cc_final: 0.8847 (pp20) REVERT: J 103 ILE cc_start: 0.9267 (tp) cc_final: 0.9022 (pt) REVERT: L 76 GLU cc_start: 0.9354 (pp20) cc_final: 0.8902 (mm-30) REVERT: Q 48 ASP cc_start: 0.8093 (m-30) cc_final: 0.7756 (m-30) REVERT: R 73 LYS cc_start: 0.8086 (tptp) cc_final: 0.7686 (tptt) REVERT: R 86 GLN cc_start: 0.7908 (pp30) cc_final: 0.7678 (pp30) REVERT: S 53 SER cc_start: 0.9594 (t) cc_final: 0.9332 (p) REVERT: V 48 MET cc_start: 0.8601 (mpp) cc_final: 0.8346 (mpp) REVERT: V 50 MET cc_start: 0.6315 (pmm) cc_final: 0.5816 (pmm) REVERT: V 63 ILE cc_start: 0.9160 (mt) cc_final: 0.8786 (tp) REVERT: W 27 VAL cc_start: 0.9421 (m) cc_final: 0.9074 (p) REVERT: W 76 ILE cc_start: 0.9302 (mm) cc_final: 0.9015 (mm) REVERT: Z 46 MET cc_start: 0.8974 (mmp) cc_final: 0.8711 (mmm) outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 0.2473 time to fit residues: 56.0026 Evaluate side-chains 97 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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: 5.9990 chunk 263 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 chunk 129 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.032092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.023964 restraints weight = 787409.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.024707 restraints weight = 410428.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.025055 restraints weight = 278828.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.025387 restraints weight = 231503.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.025504 restraints weight = 204737.453| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 43759 Z= 0.292 Angle : 1.232 18.590 65701 Z= 0.492 Chirality : 0.084 1.136 8446 Planarity : 0.006 0.118 3325 Dihedral : 20.614 176.681 17644 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1423 helix: -0.04 (0.22), residues: 497 sheet: -1.46 (0.33), residues: 237 loop : -1.23 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 41 TYR 0.027 0.002 TYR J 16 PHE 0.021 0.003 PHE V 91 TRP 0.016 0.002 TRP E 60 HIS 0.007 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.29 (43759) covalent geometry : angle 1.23243 / 0.49 (65701) hydrogen bonds : bond 0.11535 / 6.60 ( 1561) hydrogen bonds : angle 4.13612 / 2.07 ( 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 126 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 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: E 100 MET cc_start: 0.9049 (mmp) cc_final: 0.8733 (mmm) REVERT: F 25 MET cc_start: 0.9054 (pmm) cc_final: 0.8828 (pmm) REVERT: J 19 ASP cc_start: 0.9369 (p0) cc_final: 0.9150 (p0) REVERT: J 92 MET cc_start: 0.8716 (tpt) cc_final: 0.8353 (tpt) REVERT: J 102 GLU cc_start: 0.9193 (pp20) cc_final: 0.8898 (pp20) REVERT: J 103 ILE cc_start: 0.9239 (tp) cc_final: 0.8994 (pt) REVERT: Q 48 ASP cc_start: 0.8205 (m-30) cc_final: 0.7959 (m-30) REVERT: S 53 SER cc_start: 0.9524 (t) cc_final: 0.9313 (p) REVERT: S 78 GLU cc_start: 0.8976 (pp20) cc_final: 0.8541 (pp20) REVERT: W 76 ILE cc_start: 0.9304 (mm) cc_final: 0.9057 (mm) REVERT: Z 46 MET cc_start: 0.8987 (mmp) cc_final: 0.8761 (mmm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2470 time to fit residues: 52.0120 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 : 0.807 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 162 optimal weight: 0.0270 chunk 159 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.2941 r_free = 0.2941 target = 0.032605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.024391 restraints weight = 782396.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.025172 restraints weight = 404749.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.025667 restraints weight = 278251.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.025948 restraints weight = 223567.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.026116 restraints weight = 198636.841| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43759 Z= 0.226 Angle : 1.128 18.225 65701 Z= 0.449 Chirality : 0.080 1.010 8446 Planarity : 0.005 0.037 3325 Dihedral : 20.501 178.911 17644 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1423 helix: 0.14 (0.22), residues: 497 sheet: -1.56 (0.33), residues: 233 loop : -1.18 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 47 TYR 0.008 0.001 TYR F 127 PHE 0.023 0.002 PHE F 99 TRP 0.011 0.002 TRP Q 60 HIS 0.007 0.001 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (43759) covalent geometry : angle 1.12756 / 0.45 (65701) hydrogen bonds : bond 0.10411 / 6.04 ( 1561) hydrogen bonds : angle 3.99372 / 1.99 ( 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 127 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8894 (tpm170) cc_final: 0.8487 (tpm170) REVERT: E 1 MET cc_start: 0.8285 (tmm) cc_final: 0.7640 (tmm) REVERT: E 100 MET cc_start: 0.9089 (mmp) cc_final: 0.8758 (mmm) REVERT: J 36 LEU cc_start: 0.9734 (mm) cc_final: 0.9341 (mm) REVERT: J 92 MET cc_start: 0.8766 (tpt) cc_final: 0.8454 (tpt) REVERT: J 102 GLU cc_start: 0.9161 (pp20) cc_final: 0.8857 (pp20) REVERT: J 103 ILE cc_start: 0.9224 (tp) cc_final: 0.8993 (pt) REVERT: Q 48 ASP cc_start: 0.8039 (m-30) cc_final: 0.6156 (m-30) REVERT: R 80 ARG cc_start: 0.9335 (tmm160) cc_final: 0.9111 (tmt170) REVERT: S 53 SER cc_start: 0.9564 (t) cc_final: 0.9324 (p) REVERT: S 78 GLU cc_start: 0.9009 (pp20) cc_final: 0.8510 (pp20) REVERT: V 50 MET cc_start: 0.7070 (pmm) cc_final: 0.6577 (pmm) REVERT: W 76 ILE cc_start: 0.9316 (mm) cc_final: 0.9097 (mm) REVERT: Z 46 MET cc_start: 0.9038 (mmp) cc_final: 0.8813 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2385 time to fit residues: 50.2220 Evaluate side-chains 93 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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: 30.0000 chunk 22 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 141 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.023130 restraints weight = 795658.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.023878 restraints weight = 415412.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024360 restraints weight = 284568.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.024636 restraints weight = 228939.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.024724 restraints weight = 201347.240| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 43759 Z= 0.308 Angle : 1.234 18.573 65701 Z= 0.491 Chirality : 0.082 0.992 8446 Planarity : 0.005 0.047 3325 Dihedral : 20.635 179.829 17644 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 35.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1423 helix: -0.28 (0.22), residues: 503 sheet: -1.60 (0.31), residues: 244 loop : -1.35 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 79 TYR 0.013 0.002 TYR R 83 PHE 0.022 0.003 PHE F 99 TRP 0.021 0.002 TRP E 60 HIS 0.007 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.31 (43759) covalent geometry : angle 1.23424 / 0.49 (65701) hydrogen bonds : bond 0.12820 / 7.40 ( 1561) hydrogen bonds : angle 4.25074 / 2.10 ( 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 123 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 12 ARG cc_start: 0.9201 (ttt-90) cc_final: 0.8934 (tpt170) REVERT: E 100 MET cc_start: 0.9061 (mmp) cc_final: 0.8746 (mmm) REVERT: F 25 MET cc_start: 0.8962 (pmm) cc_final: 0.8742 (pmm) REVERT: J 92 MET cc_start: 0.8794 (tpt) cc_final: 0.8283 (tpp) REVERT: J 102 GLU cc_start: 0.9096 (pp20) cc_final: 0.8809 (pp20) REVERT: Q 48 ASP cc_start: 0.7870 (m-30) cc_final: 0.6929 (m-30) REVERT: R 53 PHE cc_start: 0.9472 (m-80) cc_final: 0.9177 (m-80) REVERT: S 53 SER cc_start: 0.9507 (t) cc_final: 0.9249 (p) REVERT: V 50 MET cc_start: 0.6899 (pmm) cc_final: 0.6265 (pmm) REVERT: Z 46 MET cc_start: 0.9113 (mmp) cc_final: 0.8842 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2226 time to fit residues: 46.1227 Evaluate side-chains 89 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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: 20.0000 chunk 137 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.023531 restraints weight = 792525.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.024318 restraints weight = 409065.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.024794 restraints weight = 281183.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.025076 restraints weight = 226586.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.025182 restraints weight = 201081.952| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6208 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= 0.251 Angle : 1.151 17.605 65701 Z= 0.459 Chirality : 0.080 0.898 8446 Planarity : 0.005 0.037 3325 Dihedral : 20.599 178.998 17644 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.22), residues: 1423 helix: -0.21 (0.22), residues: 493 sheet: -1.54 (0.32), residues: 245 loop : -1.31 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG Y 23 TYR 0.010 0.002 TYR Q 44 PHE 0.020 0.002 PHE F 99 TRP 0.018 0.002 TRP E 60 HIS 0.013 0.001 HIS J 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (43759) covalent geometry : angle 1.15094 / 0.46 (65701) hydrogen bonds : bond 0.10774 / 6.30 ( 1561) hydrogen bonds : angle 4.13130 / 2.05 ( 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 126 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8376 (tmm) cc_final: 0.7723 (tmm) REVERT: E 100 MET cc_start: 0.9113 (mmp) cc_final: 0.8784 (mmm) REVERT: J 92 MET cc_start: 0.8789 (tpt) cc_final: 0.8259 (tpp) REVERT: J 102 GLU cc_start: 0.9080 (pp20) cc_final: 0.8716 (pp20) REVERT: J 103 ILE cc_start: 0.9251 (tp) cc_final: 0.8920 (pt) REVERT: Q 48 ASP cc_start: 0.7789 (m-30) cc_final: 0.6854 (m-30) REVERT: R 80 ARG cc_start: 0.9323 (tmm160) cc_final: 0.9077 (tmt170) REVERT: S 53 SER cc_start: 0.9508 (t) cc_final: 0.9240 (p) REVERT: V 50 MET cc_start: 0.7141 (pmm) cc_final: 0.6647 (pmm) REVERT: W 46 ASN cc_start: 0.9638 (m-40) cc_final: 0.9294 (t0) REVERT: Z 46 MET cc_start: 0.9136 (mmp) cc_final: 0.8834 (mmm) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2147 time to fit residues: 45.1635 Evaluate side-chains 90 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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: 0.9980 chunk 170 optimal weight: 30.0000 chunk 272 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.023134 restraints weight = 789514.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.023893 restraints weight = 410792.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.024223 restraints weight = 280764.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.024599 restraints weight = 233569.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.024766 restraints weight = 204761.591| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 43759 Z= 0.274 Angle : 1.180 17.570 65701 Z= 0.470 Chirality : 0.080 0.836 8446 Planarity : 0.005 0.045 3325 Dihedral : 20.640 179.503 17644 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 33.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.22), residues: 1423 helix: -0.23 (0.22), residues: 494 sheet: -1.68 (0.32), residues: 230 loop : -1.39 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 23 TYR 0.010 0.002 TYR Q 46 PHE 0.019 0.002 PHE F 99 TRP 0.025 0.002 TRP E 60 HIS 0.008 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.27 (43759) covalent geometry : angle 1.17950 / 0.47 (65701) hydrogen bonds : bond 0.11658 / 6.82 ( 1561) hydrogen bonds : angle 4.17226 / 2.06 ( 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 122 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.9021 (tpm170) cc_final: 0.8499 (tpm170) REVERT: E 1 MET cc_start: 0.8285 (tmm) cc_final: 0.7636 (tmm) REVERT: E 100 MET cc_start: 0.9089 (mmp) cc_final: 0.8762 (mmm) REVERT: J 92 MET cc_start: 0.8848 (tpt) cc_final: 0.8349 (tpp) REVERT: J 102 GLU cc_start: 0.9038 (pp20) cc_final: 0.8688 (pp20) REVERT: J 103 ILE cc_start: 0.9227 (tp) cc_final: 0.8908 (pt) REVERT: R 53 PHE cc_start: 0.9451 (m-80) cc_final: 0.9046 (m-80) REVERT: S 53 SER cc_start: 0.9505 (t) cc_final: 0.9241 (p) REVERT: V 50 MET cc_start: 0.6956 (pmm) cc_final: 0.6367 (pmm) REVERT: W 46 ASN cc_start: 0.9606 (m-40) cc_final: 0.9268 (t0) REVERT: Z 46 MET cc_start: 0.9108 (mmp) cc_final: 0.8821 (mmm) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2350 time to fit residues: 47.1926 Evaluate side-chains 89 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.023901 restraints weight = 783062.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.024720 restraints weight = 402893.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.025204 restraints weight = 275313.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.025490 restraints weight = 221399.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.025640 restraints weight = 195863.502| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43759 Z= 0.214 Angle : 1.098 16.701 65701 Z= 0.438 Chirality : 0.077 0.760 8446 Planarity : 0.005 0.038 3325 Dihedral : 20.521 179.448 17644 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.22), residues: 1423 helix: -0.11 (0.22), residues: 499 sheet: -1.61 (0.34), residues: 217 loop : -1.29 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG O 7 TYR 0.014 0.002 TYR Q 46 PHE 0.016 0.002 PHE F 99 TRP 0.022 0.002 TRP E 60 HIS 0.009 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (43759) covalent geometry : angle 1.09841 / 0.44 (65701) hydrogen bonds : bond 0.09694 / 5.76 ( 1561) hydrogen bonds : angle 3.99150 / 1.99 ( 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 123 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.9077 (tpm170) cc_final: 0.8602 (tpm170) REVERT: E 1 MET cc_start: 0.8365 (tmm) cc_final: 0.7691 (tmm) REVERT: E 100 MET cc_start: 0.9130 (mmp) cc_final: 0.8796 (mmm) REVERT: F 25 MET cc_start: 0.8977 (pmm) cc_final: 0.8703 (pmm) REVERT: J 92 MET cc_start: 0.8762 (tpt) cc_final: 0.8380 (tpp) REVERT: J 102 GLU cc_start: 0.9012 (pp20) cc_final: 0.8665 (pp20) REVERT: J 103 ILE cc_start: 0.9256 (tp) cc_final: 0.8908 (pt) REVERT: L 117 THR cc_start: 0.7677 (p) cc_final: 0.7246 (p) REVERT: Q 35 PHE cc_start: 0.9630 (t80) cc_final: 0.9095 (t80) REVERT: R 53 PHE cc_start: 0.9405 (m-80) cc_final: 0.9136 (m-80) REVERT: R 80 ARG cc_start: 0.9363 (tmm160) cc_final: 0.9088 (tmt170) REVERT: S 53 SER cc_start: 0.9491 (t) cc_final: 0.9237 (p) REVERT: V 50 MET cc_start: 0.6836 (pmm) cc_final: 0.6275 (pmm) REVERT: W 46 ASN cc_start: 0.9576 (m-40) cc_final: 0.9261 (t0) REVERT: Z 46 MET cc_start: 0.9152 (mmp) cc_final: 0.8846 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2329 time to fit residues: 47.7972 Evaluate side-chains 89 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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: 8.9990 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 251 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 256 optimal weight: 30.0000 chunk 191 optimal weight: 0.0170 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 136 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** ** 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 = 0.2922 r_free = 0.2922 target = 0.032125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.023898 restraints weight = 775715.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.024692 restraints weight = 402700.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.025042 restraints weight = 277228.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.025424 restraints weight = 230770.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.025547 restraints weight = 201709.888| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43759 Z= 0.208 Angle : 1.092 16.558 65701 Z= 0.436 Chirality : 0.077 0.768 8446 Planarity : 0.005 0.037 3325 Dihedral : 20.466 179.843 17644 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % 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 are not related in a simple way. whole: -1.42 (0.22), residues: 1423 helix: -0.07 (0.22), residues: 499 sheet: -1.70 (0.35), residues: 214 loop : -1.28 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 52 TYR 0.015 0.001 TYR Q 44 PHE 0.018 0.002 PHE Q 105 TRP 0.022 0.002 TRP E 60 HIS 0.006 0.001 HIS V 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (43759) covalent geometry : angle 1.09162 / 0.44 (65701) hydrogen bonds : bond 0.09773 / 5.81 ( 1561) hydrogen bonds : angle 3.99758 / 1.99 ( 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 124 residues out of total 1178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.635 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: 0.9073 (tpm170) cc_final: 0.8557 (mmm160) REVERT: E 1 MET cc_start: 0.8390 (tmm) cc_final: 0.7696 (tmm) REVERT: E 100 MET cc_start: 0.9137 (mmp) cc_final: 0.8801 (mmm) REVERT: F 25 MET cc_start: 0.8921 (pmm) cc_final: 0.8650 (pmm) REVERT: F 82 TYR cc_start: 0.7275 (t80) cc_final: 0.7075 (t80) REVERT: F 95 MET cc_start: 0.3859 (mmm) cc_final: 0.3619 (mmm) REVERT: J 74 TYR cc_start: 0.7861 (m-80) cc_final: 0.7584 (m-10) REVERT: J 102 GLU cc_start: 0.9003 (pp20) cc_final: 0.8639 (pp20) REVERT: J 103 ILE cc_start: 0.9225 (tp) cc_final: 0.8804 (pt) REVERT: J 142 ILE cc_start: 0.7485 (tt) cc_final: 0.7285 (tt) REVERT: Q 55 GLN cc_start: 0.9444 (mt0) cc_final: 0.9117 (pp30) REVERT: R 53 PHE cc_start: 0.9420 (m-80) cc_final: 0.9129 (m-80) REVERT: R 80 ARG cc_start: 0.9300 (tmm160) cc_final: 0.9075 (tmt170) REVERT: S 53 SER cc_start: 0.9495 (t) cc_final: 0.9245 (p) REVERT: V 50 MET cc_start: 0.6825 (pmm) cc_final: 0.6283 (pmm) REVERT: W 46 ASN cc_start: 0.9562 (m-40) cc_final: 0.9259 (t0) REVERT: Z 46 MET cc_start: 0.9130 (mmp) cc_final: 0.8830 (mmm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2211 time to fit residues: 46.0650 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 : 0.641 ------------------------------------------------------------------------------- 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: 7.9990 chunk 176 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 192 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 201 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 200 optimal weight: 50.0000 chunk 124 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.2853 r_free = 0.2853 target = 0.030229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.022387 restraints weight = 803894.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023110 restraints weight = 420061.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.023557 restraints weight = 288407.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.023814 restraints weight = 232665.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.023964 restraints weight = 206693.892| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 43759 Z= 0.338 Angle : 1.284 17.296 65701 Z= 0.510 Chirality : 0.081 0.846 8446 Planarity : 0.006 0.058 3325 Dihedral : 20.777 178.955 17644 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 40.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % 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 are not related in a simple way. whole: -1.90 (0.21), residues: 1423 helix: -0.54 (0.21), residues: 500 sheet: -1.77 (0.32), residues: 230 loop : -1.56 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 7 TYR 0.015 0.002 TYR Q 44 PHE 0.017 0.003 PHE F 99 TRP 0.043 0.003 TRP E 60 HIS 0.010 0.002 HIS E 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.34 (43759) covalent geometry : angle 1.28365 / 0.51 (65701) hydrogen bonds : bond 0.13792 / 8.00 ( 1561) hydrogen bonds : angle 4.38019 / 2.15 ( 3050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5152.46 seconds wall clock time: 91 minutes 38.60 seconds (5498.60 seconds total)