Starting phenix.real_space_refine (version: dev) on Wed May 18 03:21:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/05_2022/6w77_21569.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 47940 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 32594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32594 Classifications: {'RNA': 1519} Modifications used: {'rna3p_pyr': 569, 'rna2p_pur': 111, 'rna3p_pur': 755, 'rna2p_pyr': 84} Link IDs: {'rna3p': 1324, 'rna2p': 194} Chain breaks: 3 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1016 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 114, 'PCIS': 1} Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 27.83, per 1000 atoms: 0.58 Number of scatterers: 47940 At special positions: 0 Unit cell: (204.943, 221.038, 168.461, 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 54 16.00 P 1519 15.00 O 13285 8.00 N 8951 7.00 C 24131 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 2.6 seconds 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 40.6% alpha, 18.3% beta 487 base pairs and 770 stacking pairs defined. Time for finding SS restraints: 18.18 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.627A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.879A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.857A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 139 removed outlier: 4.068A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.660A pdb=" N GLY C 144 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.018A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.505A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.962A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 4.435A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.731A pdb=" N ILE E 164 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.878A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.986A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.666A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.922A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.517A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 43 through 47' Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.671A pdb=" N GLU I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.682A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 removed outlier: 3.884A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 4.926A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 72 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'L' and resid 3 through 9 Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 4.587A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 78 Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.665A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.759A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 31 removed outlier: 4.421A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 48 removed outlier: 3.537A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 39 Processing helix chain 'O' and resid 41 through 45 removed outlier: 4.100A pdb=" N GLU O 45 " --> pdb=" O HIS O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.659A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.521A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.635A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.077A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'S' and resid 11 through 24 Processing helix chain 'S' and resid 40 through 44 Processing helix chain 'S' and resid 69 through 74 Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.789A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 84 removed outlier: 3.713A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.802A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.554A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 182 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 12 through 17 removed outlier: 4.912A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.768A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 46 removed outlier: 7.803A pdb=" N HIS F 37 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N GLU F 65 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 24 through 28 removed outlier: 6.181A pdb=" N GLU H 58 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL H 51 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU H 60 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE H 49 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR H 62 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.951A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.044A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 18.981A pdb=" N LYS I 26 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 14.205A pdb=" N VAL I 66 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.653A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 41 through 44 removed outlier: 7.024A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE K 23 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K 84 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR K 111 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.800A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 50 through 51 removed outlier: 6.196A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 8 through 14 removed outlier: 8.484A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Q 11 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER Q 72 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR Q 74 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.802A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1224 hydrogen bonds 1964 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 770 stacking parallelities Total time for adding SS restraints: 45.79 Time building geometry restraints manager: 25.00 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: 7077 1.33 - 1.45: 21313 1.45 - 1.57: 20542 1.57 - 1.69: 3031 1.69 - 1.81: 95 Bond restraints: 52058 Sorted by residual: bond pdb=" O3' U A1078 " pdb=" P G A1079 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' U A1075 " pdb=" P U A1076 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.50e-02 4.44e+03 8.11e+00 bond pdb=" O3' G A1079 " pdb=" P A A1080 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 6.17e+00 bond pdb=" C3' U A1083 " pdb=" O3' U A1083 " ideal model delta sigma weight residual 1.417 1.454 -0.037 1.50e-02 4.44e+03 5.95e+00 bond pdb=" O3' A A1082 " pdb=" P U A1083 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.54e+00 ... (remaining 52053 not shown) Histogram of bond angle deviations from ideal: 90.92 - 99.53: 5 99.53 - 108.15: 15425 108.15 - 116.76: 31168 116.76 - 125.38: 25420 125.38 - 133.99: 5794 Bond angle restraints: 77812 Sorted by residual: angle pdb=" O2' C A 924 " pdb=" C2' C A 924 " pdb=" C1' C A 924 " ideal model delta sigma weight residual 108.40 90.92 17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb=" O3' C A 924 " pdb=" C3' C A 924 " pdb=" C2' C A 924 " ideal model delta sigma weight residual 113.70 96.51 17.19 1.50e+00 4.44e-01 1.31e+02 angle pdb=" C3' C A 924 " pdb=" C2' C A 924 " pdb=" O2' C A 924 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.50e+00 4.44e-01 6.29e+01 angle pdb=" O2' A A1082 " pdb=" C2' A A1082 " pdb=" C1' A A1082 " ideal model delta sigma weight residual 108.40 97.95 10.45 1.50e+00 4.44e-01 4.86e+01 angle pdb=" C3' U A1076 " pdb=" C2' U A1076 " pdb=" O2' U A1076 " ideal model delta sigma weight residual 110.70 101.75 8.95 1.50e+00 4.44e-01 3.56e+01 ... (remaining 77807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 26847 35.82 - 71.64: 936 71.64 - 107.45: 83 107.45 - 143.27: 9 143.27 - 179.09: 12 Dihedral angle restraints: 27887 sinusoidal: 22306 harmonic: 5581 Sorted by residual: dihedral pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" C2' A A1431 " pdb=" C1' A A1431 " ideal model delta sinusoidal sigma weight residual -35.00 30.96 -65.96 1 8.00e+00 1.56e-02 8.89e+01 dihedral pdb=" O4' U A 439 " pdb=" C1' U A 439 " pdb=" N1 U A 439 " pdb=" C2 U A 439 " ideal model delta sinusoidal sigma weight residual 200.00 35.96 164.04 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" C5' A A1431 " pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" O3' A A1431 " ideal model delta sinusoidal sigma weight residual 147.00 84.17 62.83 1 8.00e+00 1.56e-02 8.15e+01 ... (remaining 27884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 9824 0.117 - 0.235: 100 0.235 - 0.352: 6 0.352 - 0.469: 2 0.469 - 0.587: 1 Chirality restraints: 9933 Sorted by residual: chirality pdb=" C3' U A1065 " pdb=" C4' U A1065 " pdb=" O3' U A1065 " pdb=" C2' U A1065 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" C3' C A 924 " pdb=" C4' C A 924 " pdb=" O3' C A 924 " pdb=" C2' C A 924 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C2' U A1073 " pdb=" C3' U A1073 " pdb=" O2' U A1073 " pdb=" C1' U A1073 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 9930 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1077 " -0.062 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" N9 G A1077 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G A1077 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A1077 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1077 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G A1077 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A1077 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G A1077 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1083 " 0.031 2.00e-02 2.50e+03 1.49e-02 5.03e+00 pdb=" N1 U A1083 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U A1083 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A1083 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A1083 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U A1083 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A1083 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1082 " -0.027 2.00e-02 2.50e+03 1.32e-02 4.80e+00 pdb=" N9 A A1082 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A A1082 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A1082 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A1082 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A A1082 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A1082 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A A1082 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A1082 " 0.002 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1568 2.65 - 3.21: 39875 3.21 - 3.77: 92755 3.77 - 4.34: 120307 4.34 - 4.90: 162775 Nonbonded interactions: 417280 Sorted by model distance: nonbonded pdb=" OP1 C A 738 " pdb=" OH TYR F 4 " model vdw 2.084 2.440 nonbonded pdb=" O2' G A 925 " pdb=" O4' G A 926 " model vdw 2.147 2.440 nonbonded pdb=" O6 G A1419 " pdb=" O4 U A1481 " model vdw 2.158 2.432 nonbonded pdb=" O6 G A1064 " pdb=" N4 C A1192 " model vdw 2.171 2.520 nonbonded pdb=" OG SER D 192 " pdb=" OD1 ASP D 194 " model vdw 2.181 2.440 ... (remaining 417275 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1519 5.49 5 S 54 5.16 5 C 24131 2.51 5 N 8951 2.21 5 O 13285 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.630 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: 10.490 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.380 Process input model: 157.900 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 0.057 52058 Z= 0.133 Angle : 0.530 17.481 77812 Z= 0.301 Chirality : 0.033 0.587 9933 Planarity : 0.003 0.040 4217 Dihedral : 14.955 179.089 24283 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -3.22 (0.17), residues: 1913 helix: -1.41 (0.17), residues: 666 sheet: -1.79 (0.24), residues: 346 loop : -2.85 (0.18), residues: 901 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 575 time to evaluate : 2.881 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: 575 average time/residue: 0.7030 time to fit residues: 620.9971 Evaluate side-chains 394 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 264 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 30.0000 chunk 196 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 HIS C 101 ASN C 138 GLN C 175 HIS D 74 ASN D 120 HIS D 131 ASN D 136 GLN D 164 GLN E 70 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN H 16 ASN H 21 ASN I 49 GLN J 58 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN K 119 ASN L 5 ASN M 7 ASN O 40 GLN ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS R 31 ASN R 52 GLN T 21 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.101 52058 Z= 0.398 Angle : 0.904 12.260 77812 Z= 0.450 Chirality : 0.046 0.285 9933 Planarity : 0.008 0.100 4217 Dihedral : 15.732 173.564 20401 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.35 % Favored : 89.49 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.07 (0.17), residues: 1913 helix: -1.31 (0.17), residues: 702 sheet: -1.36 (0.26), residues: 340 loop : -2.94 (0.18), residues: 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 431 time to evaluate : 3.095 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 outliers start: 98 outliers final: 62 residues processed: 484 average time/residue: 0.6915 time to fit residues: 523.2743 Evaluate side-chains 449 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 387 time to evaluate : 2.847 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4516 time to fit residues: 54.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 304 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 138 GLN D 74 ASN D 131 ASN D 140 ASN D 164 GLN F 52 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 36 GLN I 80 HIS J 70 HIS K 15 GLN M 104 ASN N 3 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 52058 Z= 0.235 Angle : 0.662 10.114 77812 Z= 0.337 Chirality : 0.038 0.282 9933 Planarity : 0.005 0.086 4217 Dihedral : 15.252 175.880 20401 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.22 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.48 (0.18), residues: 1913 helix: -0.66 (0.19), residues: 696 sheet: -1.05 (0.27), residues: 340 loop : -2.74 (0.18), residues: 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 408 time to evaluate : 2.854 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: 50 outliers final: 23 residues processed: 442 average time/residue: 0.6849 time to fit residues: 470.5824 Evaluate side-chains 391 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 368 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4121 time to fit residues: 20.9638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 325 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 138 GLN D 40 GLN D 74 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 3 ASN I 36 GLN M 104 ASN N 34 ASN N 70 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 52058 Z= 0.212 Angle : 0.641 9.863 77812 Z= 0.326 Chirality : 0.037 0.247 9933 Planarity : 0.005 0.085 4217 Dihedral : 15.186 176.110 20401 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.30 % Favored : 90.54 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.18 (0.18), residues: 1913 helix: -0.32 (0.19), residues: 704 sheet: -0.94 (0.27), residues: 331 loop : -2.64 (0.19), residues: 878 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 387 time to evaluate : 2.868 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: 72 outliers final: 43 residues processed: 432 average time/residue: 0.6714 time to fit residues: 456.7290 Evaluate side-chains 409 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 366 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4030 time to fit residues: 36.2152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 242 optimal weight: 0.0970 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 225 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 166 optimal weight: 0.2980 chunk 292 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN D 41 HIS D 74 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN M 13 HIS M 104 ASN R 52 GLN S 42 ASN T 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 52058 Z= 0.144 Angle : 0.555 9.637 77812 Z= 0.284 Chirality : 0.033 0.225 9933 Planarity : 0.005 0.115 4217 Dihedral : 14.851 177.421 20401 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.00 % Favored : 92.84 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1913 helix: 0.13 (0.19), residues: 711 sheet: -0.78 (0.28), residues: 329 loop : -2.43 (0.19), residues: 873 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 397 time to evaluate : 2.842 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 outliers start: 28 outliers final: 11 residues processed: 415 average time/residue: 0.6800 time to fit residues: 440.9818 Evaluate side-chains 376 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 365 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4130 time to fit residues: 11.6443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 326 optimal weight: 0.6980 chunk 270 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 4 GLN J 64 GLN M 104 ASN R 52 GLN T 61 GLN T 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 52058 Z= 0.301 Angle : 0.763 9.920 77812 Z= 0.384 Chirality : 0.042 0.268 9933 Planarity : 0.006 0.108 4217 Dihedral : 15.597 174.800 20401 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.82 % Favored : 89.02 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.19 (0.18), residues: 1913 helix: -0.28 (0.19), residues: 704 sheet: -1.02 (0.27), residues: 325 loop : -2.65 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 381 time to evaluate : 3.061 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: 67 outliers final: 36 residues processed: 421 average time/residue: 0.7007 time to fit residues: 472.2723 Evaluate side-chains 399 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 363 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4512 time to fit residues: 33.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 324 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN J 64 GLN M 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 52058 Z= 0.159 Angle : 0.587 9.802 77812 Z= 0.300 Chirality : 0.034 0.313 9933 Planarity : 0.005 0.111 4217 Dihedral : 15.043 176.091 20401 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.63 % Favored : 92.21 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.74 (0.19), residues: 1913 helix: 0.19 (0.20), residues: 702 sheet: -0.85 (0.28), residues: 324 loop : -2.45 (0.19), residues: 887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 383 time to evaluate : 3.139 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 outliers start: 26 outliers final: 13 residues processed: 396 average time/residue: 0.6649 time to fit residues: 418.7108 Evaluate side-chains 375 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 362 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5042 time to fit residues: 14.5545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 160 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 0.1980 overall best weight: 2.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN J 64 GLN Q 9 GLN T 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 52058 Z= 0.232 Angle : 0.658 9.875 77812 Z= 0.333 Chirality : 0.037 0.364 9933 Planarity : 0.006 0.120 4217 Dihedral : 15.241 177.341 20401 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.56 % Favored : 89.28 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 1913 helix: 0.06 (0.19), residues: 698 sheet: -0.83 (0.28), residues: 321 loop : -2.51 (0.19), residues: 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 376 time to evaluate : 3.003 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 outliers start: 29 outliers final: 18 residues processed: 391 average time/residue: 0.6919 time to fit residues: 425.6496 Evaluate side-chains 379 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 361 time to evaluate : 2.899 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4291 time to fit residues: 17.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 283 optimal weight: 0.9980 chunk 302 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 273 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN J 64 GLN Q 9 GLN T 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.423 52058 Z= 0.247 Angle : 0.700 73.800 77812 Z= 0.346 Chirality : 0.035 0.322 9933 Planarity : 0.007 0.179 4217 Dihedral : 15.207 176.926 20401 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.83 % Favored : 90.02 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.18), residues: 1913 helix: 0.12 (0.19), residues: 699 sheet: -0.75 (0.28), residues: 319 loop : -2.51 (0.19), residues: 895 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 365 time to evaluate : 3.031 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 outliers start: 16 outliers final: 9 residues processed: 373 average time/residue: 0.6731 time to fit residues: 396.4038 Evaluate side-chains 367 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 358 time to evaluate : 2.780 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4078 time to fit residues: 9.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.2980 chunk 320 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 267 optimal weight: 0.0070 chunk 27 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN T 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.550 52058 Z= 0.276 Angle : 0.714 73.794 77812 Z= 0.359 Chirality : 0.035 0.322 9933 Planarity : 0.007 0.181 4217 Dihedral : 15.207 176.926 20401 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.83 % Favored : 90.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.18), residues: 1913 helix: 0.12 (0.19), residues: 699 sheet: -0.75 (0.28), residues: 319 loop : -2.51 (0.19), residues: 895 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.539 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 outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.6819 time to fit residues: 385.5982 Evaluate side-chains 358 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 267 optimal weight: 0.0020 chunk 112 optimal weight: 9.9990 chunk 274 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN T 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.148510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.138779 restraints weight = 142501.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140350 restraints weight = 59763.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141281 restraints weight = 31615.230| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.549 52058 Z= 0.276 Angle : 0.714 73.786 77812 Z= 0.359 Chirality : 0.035 0.322 9933 Planarity : 0.007 0.181 4217 Dihedral : 15.207 176.926 20401 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.83 % Favored : 90.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.18), residues: 1913 helix: 0.12 (0.19), residues: 699 sheet: -0.75 (0.28), residues: 319 loop : -2.51 (0.19), residues: 895 =============================================================================== Job complete usr+sys time: 8506.48 seconds wall clock time: 156 minutes 29.33 seconds (9389.33 seconds total)