Starting phenix.real_space_refine on Sun Mar 24 04:41:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_16502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_16502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_16502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_16502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c95_16502/03_2024/8c95_16502.pdb" } resolution = 4.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40172 Number of models: 1 Model: "" Number of chains: 16 Chain: "2" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 26210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1220, 26210 Classifications: {'RNA': 1220} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 59, 'rna3p_pur': 599, 'rna3p_pyr': 443} Link IDs: {'rna2p': 177, 'rna3p': 1042} Chain breaks: 7 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "E" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1519 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 1 Chain: "F" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1379 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 725 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain breaks: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 513 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 22.25, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 23.46 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 18.92 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: 32.64 Time building geometry restraints manager: 24.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6248 1.33 - 1.45: 17950 1.45 - 1.57: 16840 1.57 - 1.69: 2669 1.69 - 1.81: 52 Bond restraints: 43759 Sorted by residual: bond pdb=" P A A 973 " pdb=" O5' A A 973 " ideal model delta sigma weight residual 1.593 1.642 -0.049 1.50e-02 4.44e+03 1.05e+01 bond pdb=" O5' G A 974 " pdb=" C5' G A 974 " ideal model delta sigma weight residual 1.424 1.470 -0.046 1.50e-02 4.44e+03 9.55e+00 bond pdb=" O5' A A 973 " pdb=" C5' A A 973 " ideal model delta sigma weight residual 1.420 1.462 -0.042 1.50e-02 4.44e+03 7.82e+00 bond pdb=" P G A 974 " pdb=" O5' G A 974 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.50e-02 4.44e+03 4.45e+00 bond pdb=" O5' U A2390 " pdb=" C5' U A2390 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 ... (remaining 43754 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 7615 106.16 - 113.12: 25514 113.12 - 120.07: 15646 120.07 - 127.03: 13679 127.03 - 133.98: 3247 Bond angle restraints: 65701 Sorted by residual: angle pdb=" C3' A A 972 " pdb=" O3' A A 972 " pdb=" P A A 973 " ideal model delta sigma weight residual 120.20 105.02 15.18 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C3' U A2390 " pdb=" O3' U A2390 " pdb=" P G A2391 " ideal model delta sigma weight residual 120.20 109.84 10.36 1.50e+00 4.44e-01 4.77e+01 angle pdb=" C3' A A 973 " pdb=" O3' A A 973 " pdb=" P G A 974 " ideal model delta sigma weight residual 120.20 128.19 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" N ILE L 23 " pdb=" CA ILE L 23 " pdb=" C ILE L 23 " ideal model delta sigma weight residual 112.96 108.10 4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sigma weight residual 101.30 106.03 -4.73 1.00e+00 1.00e+00 2.24e+01 ... (remaining 65696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 24424 35.95 - 71.90: 3142 71.90 - 107.85: 383 107.85 - 143.80: 11 143.80 - 179.75: 1 Dihedral angle restraints: 27961 sinusoidal: 23801 harmonic: 4160 Sorted by residual: dihedral pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " pdb=" C1' A A 973 " ideal model delta sinusoidal sigma weight residual 36.00 -6.91 42.91 1 8.00e+00 1.56e-02 4.01e+01 dihedral pdb=" O4' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" C2' A A 973 " ideal model delta sinusoidal sigma weight residual -35.00 7.54 -42.54 1 8.00e+00 1.56e-02 3.95e+01 dihedral pdb=" C5' A A 973 " pdb=" C4' A A 973 " pdb=" C3' A A 973 " pdb=" O3' A A 973 " ideal model delta sinusoidal sigma weight residual 82.00 122.84 -40.84 1 8.00e+00 1.56e-02 3.65e+01 ... (remaining 27958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 8431 0.128 - 0.257: 11 0.257 - 0.385: 1 0.385 - 0.513: 2 0.513 - 0.642: 1 Chirality restraints: 8446 Sorted by residual: chirality pdb=" P G A 974 " pdb=" OP1 G A 974 " pdb=" OP2 G A 974 " pdb=" O5' G A 974 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P A A 973 " pdb=" OP1 A A 973 " pdb=" OP2 A A 973 " pdb=" O5' A A 973 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" P U A2390 " pdb=" OP1 U A2390 " pdb=" OP2 U A2390 " pdb=" O5' U A2390 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 8443 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.015 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 G A 259 " -0.009 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 259 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.042 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.032 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.023 2.00e-02 2.50e+03 1.81e-02 7.37e+00 pdb=" N1 C A 418 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O2 C A 418 " -0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 418 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 418 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 418 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 398 " -0.007 2.00e-02 2.50e+03 1.56e-02 5.51e+00 pdb=" N1 C A 398 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 398 " 0.039 2.00e-02 2.50e+03 pdb=" O2 C A 398 " -0.023 2.00e-02 2.50e+03 pdb=" N3 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 398 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C A 398 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A 398 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 398 " -0.001 2.00e-02 2.50e+03 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 382 2.49 - 3.09: 27863 3.09 - 3.69: 76709 3.69 - 4.30: 106695 4.30 - 4.90: 147329 Nonbonded interactions: 358978 Sorted by model distance: nonbonded pdb=" OP1 U B 5 " pdb=" O2' G B 61 " model vdw 1.886 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.900 2.440 nonbonded pdb=" O2' A A 191 " pdb=" O2 C A 678 " model vdw 1.911 2.440 nonbonded pdb=" O2' U A2312 " pdb=" OD1 ASN F 36 " model vdw 1.929 2.440 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.130 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 136.110 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 43759 Z= 0.100 Angle : 0.418 15.179 65701 Z= 0.221 Chirality : 0.029 0.642 8446 Planarity : 0.003 0.033 3325 Dihedral : 23.210 179.750 25271 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.09 % Allowed : 2.64 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (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 TRP 0.005 0.001 TRP F 96 HIS 0.003 0.000 HIS V 44 PHE 0.009 0.001 PHE S 75 TYR 0.006 0.001 TYR O 64 ARG 0.004 0.000 ARG U 21 *********************** 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 fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 2.197 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: 0.4501 (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: 0.7452 (tp) REVERT: R 86 GLN cc_start: 0.7976 (pp30) cc_final: 0.7404 (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: 0.7152 (m) REVERT: S 53 SER cc_start: 0.9576 (t) cc_final: 0.9297 (p) REVERT: S 62 ASP cc_start: 0.8950 (m-30) cc_final: 0.8583 (m-30) REVERT: S 77 ASP cc_start: 0.5160 (p0) cc_final: 0.4835 (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: 0.8105 (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: 0.5860 time to fit residues: 180.8849 Evaluate side-chains 115 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 159 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 16 HIS ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 43759 Z= 0.373 Angle : 0.798 10.226 65701 Z= 0.394 Chirality : 0.039 0.262 8446 Planarity : 0.006 0.076 3325 Dihedral : 24.734 178.229 22430 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 36.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.51 % Allowed : 4.42 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1423 helix: 0.20 (0.22), residues: 506 sheet: -0.97 (0.34), residues: 228 loop : -1.21 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 60 HIS 0.007 0.002 HIS E 165 PHE 0.030 0.003 PHE W 65 TYR 0.016 0.002 TYR Q 23 ARG 0.023 0.001 ARG W 51 *********************** 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 139 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 12 ARG cc_start: 0.9248 (ttt-90) cc_final: 0.8919 (tpt170) REVERT: E 100 MET cc_start: 0.9317 (mmp) cc_final: 0.8940 (mmm) REVERT: F 37 MET cc_start: 0.7194 (mpp) cc_final: 0.6990 (mmp) REVERT: J 19 ASP cc_start: 0.9287 (p0) cc_final: 0.8987 (p0) REVERT: J 92 MET cc_start: 0.8572 (tpt) cc_final: 0.8367 (tpt) REVERT: L 117 THR cc_start: 0.7499 (p) cc_final: 0.7290 (p) REVERT: O 80 GLU cc_start: 0.9650 (OUTLIER) cc_final: 0.9376 (pp20) REVERT: V 50 MET cc_start: 0.6213 (pmm) cc_final: 0.5767 (pmm) REVERT: W 20 LYS cc_start: 0.9169 (mppt) cc_final: 0.8962 (mptt) REVERT: W 27 VAL cc_start: 0.9217 (m) cc_final: 0.8880 (p) REVERT: W 49 CYS cc_start: 0.8159 (p) cc_final: 0.7387 (t) REVERT: W 76 ILE cc_start: 0.9231 (mm) cc_final: 0.8972 (mm) REVERT: Z 39 ASP cc_start: 0.9270 (t0) cc_final: 0.9042 (t0) REVERT: Z 46 MET cc_start: 0.9074 (mmp) cc_final: 0.8847 (mmp) outliers start: 6 outliers final: 2 residues processed: 139 average time/residue: 0.5316 time to fit residues: 121.1064 Evaluate side-chains 91 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 246 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 overall best weight: 8.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS F 20 ASN J 76 HIS L 99 ASN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 43759 Z= 0.290 Angle : 0.668 11.962 65701 Z= 0.336 Chirality : 0.035 0.218 8446 Planarity : 0.005 0.111 3325 Dihedral : 25.067 179.933 22430 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.52 % Favored : 92.41 % Rotamer: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1423 helix: -0.01 (0.22), residues: 506 sheet: -1.25 (0.32), residues: 252 loop : -1.27 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 60 HIS 0.007 0.002 HIS E 165 PHE 0.020 0.003 PHE E 124 TYR 0.012 0.002 TYR Q 46 ARG 0.013 0.001 ARG 2 41 *********************** 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 127 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8692 (tpm170) cc_final: 0.8004 (mmm160) REVERT: E 100 MET cc_start: 0.9164 (mmp) cc_final: 0.8869 (mmm) REVERT: J 19 ASP cc_start: 0.9322 (p0) cc_final: 0.9073 (p0) REVERT: J 92 MET cc_start: 0.8559 (tpt) cc_final: 0.8157 (tpt) REVERT: R 80 ARG cc_start: 0.9435 (tmm160) cc_final: 0.9188 (tmt170) REVERT: S 65 ASP cc_start: 0.7221 (t0) cc_final: 0.7010 (t0) REVERT: V 50 MET cc_start: 0.6775 (pmm) cc_final: 0.6295 (pmm) REVERT: V 63 ILE cc_start: 0.9195 (mt) cc_final: 0.8891 (tp) REVERT: W 76 ILE cc_start: 0.9248 (mm) cc_final: 0.8992 (mm) REVERT: Z 46 MET cc_start: 0.9097 (mmp) cc_final: 0.8822 (mmm) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.5304 time to fit residues: 110.2023 Evaluate side-chains 85 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 43759 Z= 0.275 Angle : 0.670 11.921 65701 Z= 0.336 Chirality : 0.035 0.220 8446 Planarity : 0.005 0.079 3325 Dihedral : 25.102 175.962 22430 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 36.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1423 helix: -0.19 (0.22), residues: 504 sheet: -1.36 (0.33), residues: 224 loop : -1.28 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 60 HIS 0.006 0.001 HIS J 132 PHE 0.018 0.002 PHE W 56 TYR 0.011 0.002 TYR Q 44 ARG 0.015 0.001 ARG Q 47 *********************** 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 127 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 2.304 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: 0.9251 (ttt-90) cc_final: 0.8510 (tpt170) REVERT: E 100 MET cc_start: 0.9117 (mmp) cc_final: 0.8809 (mmm) REVERT: J 19 ASP cc_start: 0.9341 (p0) cc_final: 0.9094 (p0) REVERT: S 69 LEU cc_start: 0.8700 (mt) cc_final: 0.8398 (mt) REVERT: V 50 MET cc_start: 0.6873 (pmm) cc_final: 0.6458 (pmm) REVERT: W 76 ILE cc_start: 0.9257 (mm) cc_final: 0.9000 (mm) REVERT: Z 46 MET cc_start: 0.9234 (mmp) cc_final: 0.8867 (mmt) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.5487 time to fit residues: 113.6919 Evaluate side-chains 87 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 3 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 225 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 236 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43759 Z= 0.228 Angle : 0.619 12.858 65701 Z= 0.313 Chirality : 0.033 0.256 8446 Planarity : 0.005 0.056 3325 Dihedral : 25.097 176.551 22430 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 34.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.22), residues: 1423 helix: -0.04 (0.22), residues: 498 sheet: -1.46 (0.32), residues: 230 loop : -1.27 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 60 HIS 0.007 0.001 HIS V 44 PHE 0.019 0.002 PHE R 77 TYR 0.024 0.002 TYR Q 44 ARG 0.009 0.001 ARG Y 23 *********************** 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 122 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 12 ARG cc_start: 0.9272 (ttt-90) cc_final: 0.8553 (tpt170) REVERT: 2 41 ARG cc_start: 0.9006 (tpm170) cc_final: 0.8431 (mmm160) REVERT: E 100 MET cc_start: 0.9105 (mmp) cc_final: 0.8817 (mmm) REVERT: J 19 ASP cc_start: 0.9335 (p0) cc_final: 0.9104 (p0) REVERT: L 129 LYS cc_start: 0.9636 (mtmm) cc_final: 0.9429 (mttp) REVERT: Q 48 ASP cc_start: 0.7598 (m-30) cc_final: 0.6532 (m-30) REVERT: S 110 ARG cc_start: 0.9506 (tpm170) cc_final: 0.9196 (tpm170) REVERT: V 50 MET cc_start: 0.6841 (pmm) cc_final: 0.6316 (pmm) REVERT: V 63 ILE cc_start: 0.9249 (mt) cc_final: 0.8930 (tp) REVERT: Z 46 MET cc_start: 0.9137 (mmp) cc_final: 0.8851 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.5398 time to fit residues: 107.6676 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 219 optimal weight: 40.0000 chunk 122 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 overall best weight: 11.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 43759 Z= 0.367 Angle : 0.801 13.226 65701 Z= 0.398 Chirality : 0.040 0.293 8446 Planarity : 0.006 0.089 3325 Dihedral : 25.464 177.059 22430 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 50.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1423 helix: -0.48 (0.22), residues: 497 sheet: -1.74 (0.31), residues: 224 loop : -1.60 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP F 96 HIS 0.012 0.002 HIS E 165 PHE 0.024 0.003 PHE W 65 TYR 0.017 0.002 TYR Q 44 ARG 0.012 0.001 ARG Q 47 *********************** 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 111 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.9044 (tpm170) cc_final: 0.8746 (tpm170) REVERT: E 100 MET cc_start: 0.9053 (mmp) cc_final: 0.8796 (mmm) REVERT: J 101 ILE cc_start: 0.9385 (mm) cc_final: 0.9148 (mm) REVERT: Q 48 ASP cc_start: 0.6868 (m-30) cc_final: 0.6010 (m-30) REVERT: R 80 ARG cc_start: 0.9567 (tmm160) cc_final: 0.9158 (tmt170) REVERT: S 110 ARG cc_start: 0.9544 (tpm170) cc_final: 0.9128 (tpm170) REVERT: V 50 MET cc_start: 0.7332 (pmm) cc_final: 0.6944 (pmm) REVERT: V 63 ILE cc_start: 0.9256 (mt) cc_final: 0.8954 (tp) REVERT: Z 46 MET cc_start: 0.9074 (mmp) cc_final: 0.8784 (mmm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.5656 time to fit residues: 104.7147 Evaluate side-chains 80 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 121 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN Q 55 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43759 Z= 0.230 Angle : 0.658 13.498 65701 Z= 0.332 Chirality : 0.035 0.264 8446 Planarity : 0.005 0.060 3325 Dihedral : 25.381 174.077 22430 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 38.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.21), residues: 1423 helix: -0.36 (0.22), residues: 499 sheet: -1.84 (0.31), residues: 209 loop : -1.45 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 60 HIS 0.009 0.002 HIS V 44 PHE 0.015 0.002 PHE F 99 TYR 0.017 0.002 TYR Q 44 ARG 0.007 0.001 ARG Q 47 *********************** 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 118 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.9074 (tpm170) cc_final: 0.8572 (tpm170) REVERT: E 100 MET cc_start: 0.9067 (mmp) cc_final: 0.8793 (mmm) REVERT: O 58 ILE cc_start: 0.7650 (mt) cc_final: 0.7288 (tp) REVERT: Q 48 ASP cc_start: 0.7086 (m-30) cc_final: 0.6355 (m-30) REVERT: R 80 ARG cc_start: 0.9442 (tmm160) cc_final: 0.9231 (tmt170) REVERT: S 110 ARG cc_start: 0.9561 (tpm170) cc_final: 0.9147 (tpm170) REVERT: V 63 ILE cc_start: 0.9268 (mt) cc_final: 0.8961 (tp) REVERT: W 76 ILE cc_start: 0.9372 (mm) cc_final: 0.9122 (mm) REVERT: Z 46 MET cc_start: 0.8746 (mmm) cc_final: 0.8483 (mmm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.5452 time to fit residues: 104.5766 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 157 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43759 Z= 0.245 Angle : 0.656 12.894 65701 Z= 0.331 Chirality : 0.035 0.265 8446 Planarity : 0.005 0.060 3325 Dihedral : 25.353 173.690 22430 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 39.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1423 helix: -0.25 (0.22), residues: 496 sheet: -1.93 (0.30), residues: 227 loop : -1.43 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 60 HIS 0.010 0.002 HIS E 165 PHE 0.016 0.002 PHE W 22 TYR 0.016 0.002 TYR Q 46 ARG 0.012 0.001 ARG R 90 *********************** 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 117 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 12 ARG cc_start: 0.9386 (ttt-90) cc_final: 0.8826 (tpt170) REVERT: 2 41 ARG cc_start: 0.9085 (tpm170) cc_final: 0.8590 (tpm170) REVERT: E 100 MET cc_start: 0.9060 (mmp) cc_final: 0.8791 (mmm) REVERT: J 118 MET cc_start: 0.9519 (ptp) cc_final: 0.9053 (ttm) REVERT: O 58 ILE cc_start: 0.7619 (mt) cc_final: 0.7295 (tp) REVERT: Q 48 ASP cc_start: 0.6916 (m-30) cc_final: 0.6271 (m-30) REVERT: R 80 ARG cc_start: 0.9373 (tmm160) cc_final: 0.9167 (tmt170) REVERT: S 110 ARG cc_start: 0.9557 (tpm170) cc_final: 0.9173 (tpm170) REVERT: V 50 MET cc_start: 0.7183 (pmm) cc_final: 0.6895 (pmm) REVERT: V 63 ILE cc_start: 0.9276 (mt) cc_final: 0.8980 (tp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.5498 time to fit residues: 105.3296 Evaluate side-chains 91 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 147 optimal weight: 0.0770 chunk 106 optimal weight: 50.0000 chunk 192 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 overall best weight: 3.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 43759 Z= 0.169 Angle : 0.585 13.744 65701 Z= 0.297 Chirality : 0.032 0.260 8446 Planarity : 0.004 0.047 3325 Dihedral : 25.187 171.546 22430 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.21), residues: 1423 helix: -0.02 (0.22), residues: 493 sheet: -1.83 (0.30), residues: 230 loop : -1.30 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 96 HIS 0.010 0.001 HIS V 44 PHE 0.013 0.002 PHE F 99 TYR 0.016 0.002 TYR O 64 ARG 0.006 0.001 ARG L 132 *********************** 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 122 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.283 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: 2 12 ARG cc_start: 0.9382 (ttt-90) cc_final: 0.8842 (tpt170) REVERT: 2 41 ARG cc_start: 0.9082 (tpm170) cc_final: 0.8628 (mmm160) REVERT: E 100 MET cc_start: 0.9068 (mmp) cc_final: 0.8792 (mmm) REVERT: J 118 MET cc_start: 0.9580 (ptp) cc_final: 0.8954 (ttm) REVERT: Q 48 ASP cc_start: 0.6970 (m-30) cc_final: 0.6041 (m-30) REVERT: S 65 ASP cc_start: 0.8407 (t0) cc_final: 0.8188 (t0) REVERT: S 110 ARG cc_start: 0.9560 (tpm170) cc_final: 0.9179 (tpm170) REVERT: V 50 MET cc_start: 0.6912 (pmm) cc_final: 0.6516 (pmm) REVERT: V 63 ILE cc_start: 0.9249 (mt) cc_final: 0.8961 (tp) REVERT: Z 46 MET cc_start: 0.9040 (mmp) cc_final: 0.8706 (mmm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.5592 time to fit residues: 110.6457 Evaluate side-chains 90 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 10.0000 chunk 259 optimal weight: 40.0000 chunk 158 optimal weight: 9.9990 chunk 123 optimal weight: 40.0000 chunk 180 optimal weight: 6.9990 chunk 271 optimal weight: 50.0000 chunk 250 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 167 optimal weight: 0.0670 chunk 132 optimal weight: 20.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43759 Z= 0.201 Angle : 0.598 13.480 65701 Z= 0.303 Chirality : 0.033 0.264 8446 Planarity : 0.004 0.047 3325 Dihedral : 25.174 171.950 22430 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1423 helix: -0.07 (0.22), residues: 496 sheet: -1.81 (0.30), residues: 235 loop : -1.30 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 96 HIS 0.007 0.001 HIS E 165 PHE 0.015 0.002 PHE Q 105 TYR 0.015 0.002 TYR O 64 ARG 0.007 0.001 ARG Q 47 ********************** 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 120 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.118 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: 2 12 ARG cc_start: 0.9393 (ttt-90) cc_final: 0.8822 (tpt170) REVERT: 2 41 ARG cc_start: 0.9081 (tpm170) cc_final: 0.8572 (tpm170) REVERT: E 100 MET cc_start: 0.9073 (mmp) cc_final: 0.8799 (mmm) REVERT: J 19 ASP cc_start: 0.9342 (p0) cc_final: 0.9139 (p0) REVERT: J 118 MET cc_start: 0.9486 (ptp) cc_final: 0.9055 (ttm) REVERT: Q 48 ASP cc_start: 0.6955 (m-30) cc_final: 0.6046 (m-30) REVERT: R 80 ARG cc_start: 0.9391 (tmm160) cc_final: 0.9081 (tmt170) REVERT: S 65 ASP cc_start: 0.8282 (t0) cc_final: 0.8075 (t0) REVERT: S 110 ARG cc_start: 0.9559 (tpm170) cc_final: 0.9212 (tpm170) REVERT: V 50 MET cc_start: 0.6955 (pmm) cc_final: 0.6514 (pmm) REVERT: V 63 ILE cc_start: 0.9258 (mt) cc_final: 0.8966 (tp) REVERT: Z 46 MET cc_start: 0.9040 (mmp) cc_final: 0.8743 (mmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.5575 time to fit residues: 108.4343 Evaluate side-chains 96 residues out of total 1178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.0570 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 216 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 overall best weight: 9.7908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 51 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** 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 = 0.2824 r_free = 0.2824 target = 0.029382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.021588 restraints weight = 801171.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.022273 restraints weight = 419068.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.022683 restraints weight = 289629.322| |-----------------------------------------------------------------------------| r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 43759 Z= 0.319 Angle : 0.749 13.466 65701 Z= 0.373 Chirality : 0.038 0.278 8446 Planarity : 0.006 0.069 3325 Dihedral : 25.557 173.443 22430 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 49.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1423 helix: -0.36 (0.22), residues: 493 sheet: -2.13 (0.30), residues: 227 loop : -1.49 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 60 HIS 0.013 0.002 HIS E 165 PHE 0.015 0.003 PHE E 183 TYR 0.021 0.002 TYR O 64 ARG 0.009 0.001 ARG Q 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.78 seconds wall clock time: 93 minutes 53.83 seconds (5633.83 seconds total)