Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 07:38:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c96_16503/10_2023/8c96_16503.pdb" } resolution = 4.43 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= 0.073 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 1475 5.49 5 S 35 5.16 5 C 21970 2.51 5 N 8289 2.21 5 O 12445 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-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 44214 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 31713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1475, 31713 Classifications: {'RNA': 1475} Modifications used: {'rna2p_pur': 143, 'rna2p_pyr': 75, 'rna3p_pur': 728, 'rna3p_pyr': 529} Link IDs: {'rna2p': 218, 'rna3p': 1256} Chain breaks: 7 Chain: "D" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1306 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "E" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1438 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} 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: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} 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: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} 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: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 312 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 21.02, per 1000 atoms: 0.48 Number of scatterers: 44214 At special positions: 0 Unit cell: (148.75, 183.75, 206.25, 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 35 16.00 P 1475 15.00 O 12445 8.00 N 8289 7.00 C 21970 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: 25.80 Conformation dependent library (CDL) restraints added in 2.2 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 33.5% alpha, 16.9% beta 484 base pairs and 703 stacking pairs defined. Time for finding SS restraints: 19.89 Creating SS restraints... Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.512A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.719A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.561A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.510A 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 Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 199 Processing helix chain 'J' and resid 24 through 38 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 109 removed outlier: 3.902A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.574A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.128A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.797A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 33 removed outlier: 4.130A pdb=" N GLY L 31 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 33' Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.539A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.845A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.813A 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: 4.122A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.754A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.252A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.886A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.001A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 62 removed outlier: 3.923A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 8 Processing helix chain 'Y' and resid 9 through 30 removed outlier: 4.482A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.136A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.183A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.946A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.733A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.306A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR D 35 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 96 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.985A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.517A pdb=" N ILE E 119 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET E 188 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.590A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 73 through 74 Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 10 removed outlier: 7.099A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE K 41 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.584A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG K 78 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.554A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.588A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.591A pdb=" N VAL R 4 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.752A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 72 through 77 Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.723A pdb=" N ILE S 103 " --> pdb=" O HIS S 7 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB8, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.551A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.992A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AC2, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC4, first strand: chain 'Z' and resid 35 through 37 removed outlier: 3.848A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1236 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 484 basepair parallelities 703 stacking parallelities Total time for adding SS restraints: 45.12 Time building geometry restraints manager: 27.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7165 1.33 - 1.45: 20009 1.45 - 1.57: 17983 1.57 - 1.69: 2943 1.69 - 1.81: 67 Bond restraints: 48167 Sorted by residual: bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.574 -0.094 1.50e-02 4.44e+03 3.90e+01 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ALA Q 1 " pdb=" CA ALA Q 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 48162 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.04: 8970 107.04 - 113.77: 29645 113.77 - 120.51: 17442 120.51 - 127.24: 12950 127.24 - 133.97: 3343 Bond angle restraints: 72350 Sorted by residual: angle pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sigma weight residual 120.20 123.80 -3.60 1.50e+00 4.44e-01 5.75e+00 angle pdb=" C4' G A 271 " pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 109.40 112.92 -3.52 1.50e+00 4.44e-01 5.52e+00 angle pdb=" C HIS N 31 " pdb=" N GLU N 32 " pdb=" CA GLU N 32 " ideal model delta sigma weight residual 121.54 125.82 -4.28 1.91e+00 2.74e-01 5.01e+00 angle pdb=" C2' A A1287 " pdb=" C1' A A1287 " pdb=" N9 A A1287 " ideal model delta sigma weight residual 112.00 115.09 -3.09 1.50e+00 4.44e-01 4.23e+00 angle pdb=" N LYS D 62 " pdb=" CA LYS D 62 " pdb=" C LYS D 62 " ideal model delta sigma weight residual 109.81 114.30 -4.49 2.21e+00 2.05e-01 4.13e+00 ... (remaining 72345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 24711 34.99 - 69.98: 716 69.98 - 104.96: 65 104.96 - 139.95: 15 139.95 - 174.94: 4 Dihedral angle restraints: 25511 sinusoidal: 20950 harmonic: 4561 Sorted by residual: dihedral pdb=" O4' U A 828 " pdb=" C1' U A 828 " pdb=" N1 U A 828 " pdb=" C2 U A 828 " ideal model delta sinusoidal sigma weight residual -128.00 45.69 -173.69 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 -12.02 -115.98 1 1.70e+01 3.46e-03 4.78e+01 dihedral pdb=" C4' U A 828 " pdb=" C3' U A 828 " pdb=" O3' U A 828 " pdb=" P A A 829 " ideal model delta sinusoidal sigma weight residual -110.00 64.94 -174.94 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 25508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7389 0.031 - 0.062: 1624 0.062 - 0.093: 149 0.093 - 0.124: 144 0.124 - 0.154: 12 Chirality restraints: 9318 Sorted by residual: chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE N 33 " pdb=" N ILE N 33 " pdb=" C ILE N 33 " pdb=" CB ILE N 33 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE R 74 " pdb=" N ILE R 74 " pdb=" C ILE R 74 " pdb=" CB ILE R 74 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 9315 not shown) Planarity restraints: 3647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 259 " 0.010 2.00e-02 2.50e+03 1.32e-02 5.22e+00 pdb=" N9 G A 259 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 259 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G A 259 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A 259 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 259 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 259 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G A 259 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 259 " -0.035 2.00e-02 2.50e+03 pdb=" N2 G A 259 " 0.026 2.00e-02 2.50e+03 pdb=" N3 G A 259 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 259 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 175 " 0.012 2.00e-02 2.50e+03 1.19e-02 4.28e+00 pdb=" N9 G A 175 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 175 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 175 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 175 " 0.030 2.00e-02 2.50e+03 pdb=" O6 G A 175 " -0.017 2.00e-02 2.50e+03 pdb=" N1 G A 175 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 175 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G A 175 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 175 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " 0.006 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C A 269 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.028 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.018 2.00e-02 2.50e+03 pdb=" N3 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.007 2.00e-02 2.50e+03 ... (remaining 3644 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 392 2.52 - 3.12: 32713 3.12 - 3.71: 84293 3.71 - 4.31: 115317 4.31 - 4.90: 159244 Nonbonded interactions: 391959 Sorted by model distance: nonbonded pdb=" O2' A A1009 " pdb=" O4' A A1010 " model vdw 1.928 2.440 nonbonded pdb=" O2' A A2632 " pdb=" O2' G A2811 " model vdw 1.941 2.440 nonbonded pdb=" O2' G A 214 " pdb=" O4' G A 215 " model vdw 1.949 2.440 nonbonded pdb=" OP2 G A 117 " pdb=" O2' A A 119 " model vdw 1.957 2.440 nonbonded pdb=" O2' G A 261 " pdb=" O2' C A 610 " model vdw 1.972 2.440 ... (remaining 391954 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.420 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 150.180 Find NCS groups from input model: 0.900 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.001 0.094 48167 Z= 0.090 Angle : 0.364 5.780 72350 Z= 0.188 Chirality : 0.026 0.154 9318 Planarity : 0.002 0.029 3647 Dihedral : 13.382 174.940 22563 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % 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: 0.57 (0.22), residues: 1569 helix: 2.09 (0.25), residues: 474 sheet: 0.52 (0.33), residues: 241 loop : -0.66 (0.21), residues: 854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 2.299 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 outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.5979 time to fit residues: 297.1188 Evaluate side-chains 183 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 175 optimal weight: 0.0570 chunk 273 optimal weight: 9.9990 overall best weight: 7.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 173 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS J 136 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 48167 Z= 0.294 Angle : 0.681 9.384 72350 Z= 0.344 Chirality : 0.035 0.204 9318 Planarity : 0.005 0.056 3647 Dihedral : 14.860 179.086 19449 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.15 % Allowed : 3.82 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.20), residues: 1569 helix: 0.92 (0.23), residues: 481 sheet: 0.04 (0.32), residues: 242 loop : -1.05 (0.20), residues: 846 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 2.162 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 outliers start: 2 outliers final: 0 residues processed: 238 average time/residue: 0.5656 time to fit residues: 222.6185 Evaluate side-chains 167 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 186 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 273 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN J 58 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48167 Z= 0.199 Angle : 0.523 9.045 72350 Z= 0.267 Chirality : 0.030 0.213 9318 Planarity : 0.004 0.040 3647 Dihedral : 14.868 179.164 19449 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.20), residues: 1569 helix: 0.92 (0.23), residues: 487 sheet: -0.52 (0.30), residues: 272 loop : -1.12 (0.21), residues: 810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.5727 time to fit residues: 206.2739 Evaluate side-chains 166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3828 time to fit residues: 3.1601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 274 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 48167 Z= 0.250 Angle : 0.583 8.646 72350 Z= 0.299 Chirality : 0.033 0.219 9318 Planarity : 0.004 0.063 3647 Dihedral : 15.320 179.119 19449 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.69 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -0.80 (0.20), residues: 1569 helix: 0.69 (0.23), residues: 485 sheet: -0.67 (0.30), residues: 257 loop : -1.23 (0.20), residues: 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.5663 time to fit residues: 206.4117 Evaluate side-chains 162 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 216 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN P 65 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 48167 Z= 0.229 Angle : 0.573 9.526 72350 Z= 0.292 Chirality : 0.032 0.232 9318 Planarity : 0.004 0.059 3647 Dihedral : 15.565 179.484 19449 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -0.92 (0.20), residues: 1569 helix: 0.64 (0.23), residues: 480 sheet: -0.74 (0.29), residues: 280 loop : -1.33 (0.21), residues: 809 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.5694 time to fit residues: 208.8087 Evaluate side-chains 168 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 48167 Z= 0.281 Angle : 0.648 9.989 72350 Z= 0.328 Chirality : 0.035 0.245 9318 Planarity : 0.005 0.101 3647 Dihedral : 16.120 179.413 19449 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.15 (0.20), residues: 1569 helix: 0.54 (0.23), residues: 473 sheet: -1.14 (0.28), residues: 282 loop : -1.40 (0.21), residues: 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.5769 time to fit residues: 194.0764 Evaluate side-chains 157 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 212 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 162 optimal weight: 0.0270 chunk 290 optimal weight: 0.0980 chunk 181 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 overall best weight: 2.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN J 136 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN S 57 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 48167 Z= 0.150 Angle : 0.526 9.805 72350 Z= 0.267 Chirality : 0.030 0.256 9318 Planarity : 0.004 0.051 3647 Dihedral : 15.543 179.251 19449 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -0.96 (0.20), residues: 1569 helix: 0.73 (0.24), residues: 472 sheet: -0.93 (0.29), residues: 273 loop : -1.36 (0.21), residues: 824 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.352 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 outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.5837 time to fit residues: 213.8634 Evaluate side-chains 165 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 197 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 chunk 27 optimal weight: 40.0000 chunk 228 optimal weight: 0.0050 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 48167 Z= 0.235 Angle : 0.592 8.933 72350 Z= 0.300 Chirality : 0.033 0.273 9318 Planarity : 0.005 0.068 3647 Dihedral : 15.855 179.145 19449 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -1.15 (0.20), residues: 1569 helix: 0.69 (0.23), residues: 470 sheet: -1.20 (0.29), residues: 277 loop : -1.48 (0.20), residues: 822 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.5787 time to fit residues: 198.6251 Evaluate side-chains 157 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 48167 Z= 0.223 Angle : 0.583 9.094 72350 Z= 0.296 Chirality : 0.033 0.299 9318 Planarity : 0.004 0.048 3647 Dihedral : 15.974 179.509 19449 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.15 % Allowed : 0.76 % Favored : 99.08 % 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: -1.31 (0.20), residues: 1569 helix: 0.56 (0.23), residues: 468 sheet: -1.37 (0.28), residues: 289 loop : -1.53 (0.20), residues: 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 0.5892 time to fit residues: 201.4673 Evaluate side-chains 154 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 198 optimal weight: 50.0000 chunk 299 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 238 optimal weight: 0.2980 chunk 24 optimal weight: 30.0000 chunk 184 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN P 65 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 48167 Z= 0.256 Angle : 0.628 10.197 72350 Z= 0.319 Chirality : 0.035 0.317 9318 Planarity : 0.005 0.051 3647 Dihedral : 16.295 179.405 19449 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 32.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.43 (0.20), residues: 1569 helix: 0.45 (0.23), residues: 469 sheet: -1.46 (0.28), residues: 282 loop : -1.60 (0.20), residues: 818 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.424 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 outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.5867 time to fit residues: 197.2161 Evaluate side-chains 156 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 220 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 239 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 7.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** R 89 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 = 0.3214 r_free = 0.3214 target = 0.043566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.031121 restraints weight = 508150.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032068 restraints weight = 229374.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.032600 restraints weight = 148606.508| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 48167 Z= 0.279 Angle : 0.655 10.317 72350 Z= 0.332 Chirality : 0.036 0.327 9318 Planarity : 0.005 0.077 3647 Dihedral : 16.563 179.325 19449 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 33.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.68 (0.20), residues: 1569 helix: 0.21 (0.23), residues: 472 sheet: -1.64 (0.27), residues: 304 loop : -1.72 (0.20), residues: 793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.16 seconds wall clock time: 108 minutes 47.47 seconds (6527.47 seconds total)