Starting phenix.real_space_refine on Sat Dec 9 16:27:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c90_16497/12_2023/8c90_16497.pdb" } resolution = 3.15 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= 0.008 sd= 0.110 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 2219 5.49 5 S 48 5.16 5 C 31957 2.51 5 N 12080 2.21 5 O 18422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 64726 Number of models: 1 Model: "" Number of chains: 22 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 45129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2100, 45129 Classifications: {'RNA': 2100} Modifications used: {'rna2p_pur': 201, 'rna2p_pyr': 112, 'rna3p_pur': 1028, 'rna3p_pyr': 759} Link IDs: {'rna2p': 313, 'rna3p': 1786} Chain breaks: 8 Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1348 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1512 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 189} 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: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 824 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 913 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 108} 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: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} 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: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "2" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 349 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 528 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 25.53, per 1000 atoms: 0.39 Number of scatterers: 64726 At special positions: 0 Unit cell: (182.5, 236.25, 202.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 2219 15.00 O 18422 8.00 N 12080 7.00 C 31957 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: 28.71 Conformation dependent library (CDL) restraints added in 3.3 seconds 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 29 sheets defined 34.2% alpha, 19.8% beta 733 base pairs and 1048 stacking pairs defined. Time for finding SS restraints: 27.68 Creating SS restraints... Processing helix chain 'V' and resid 13 through 23 removed outlier: 3.774A pdb=" N SER V 17 " --> pdb=" O GLY V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.326A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.613A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.037A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 4.065A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) 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: 4.380A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 4.129A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 136 removed outlier: 4.537A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.634A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.179A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.606A pdb=" N ARG P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.899A 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: 4.127A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.589A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.655A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 25 No H-bonds generated for 'chain 'S' and resid 23 through 25' Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.697A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'T' and resid 3 through 10 Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.508A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.027A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 17 Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.292A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.947A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.594A pdb=" N TYR F 6 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.510A pdb=" N GLN F 26 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 23 through 27' Processing helix chain 'F' and resid 41 through 44 removed outlier: 3.765A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 45 through 60 removed outlier: 4.349A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.880A pdb=" N GLU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 removed outlier: 3.802A pdb=" N PHE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 137' Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.887A pdb=" N VAL F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'V' and resid 3 through 4 removed outlier: 5.525A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 169 through 175 removed outlier: 6.016A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.446A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.583A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.773A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.976A 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 76 removed outlier: 3.624A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.569A pdb=" N LEU K 8 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.046A 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: 3.902A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.645A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 121 through 123 removed outlier: 5.812A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.458A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 11 through 15 removed outlier: 7.204A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.750A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.090A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.620A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB9, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.792A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.519A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS U 23 " --> pdb=" O GLU U 36 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP U 80 " --> pdb=" O ILE U 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.646A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AC5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC6, first strand: chain 'O' and resid 47 through 52 removed outlier: 4.332A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.726A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU F 35 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC9, first strand: chain 'Z' and resid 35 through 38 removed outlier: 3.880A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.926A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.169A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1869 hydrogen bonds 2992 hydrogen bond angles 0 basepair planarities 733 basepair parallelities 1048 stacking parallelities Total time for adding SS restraints: 87.84 Time building geometry restraints manager: 31.02 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: 10573 1.33 - 1.45: 29482 1.45 - 1.57: 26079 1.57 - 1.69: 4428 1.69 - 1.81: 91 Bond restraints: 70653 Sorted by residual: bond pdb=" N MET T 1 " pdb=" CA MET T 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+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 3.04e+00 bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 ... (remaining 70648 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 13511 107.23 - 113.92: 44307 113.92 - 120.61: 25623 120.61 - 127.29: 18135 127.29 - 133.98: 4828 Bond angle restraints: 106404 Sorted by residual: angle pdb=" N GLU P 33 " pdb=" CA GLU P 33 " pdb=" C GLU P 33 " ideal model delta sigma weight residual 110.61 115.26 -4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CA GLU P 33 " pdb=" C GLU P 33 " pdb=" N SER P 35 " ideal model delta sigma weight residual 116.74 121.04 -4.30 1.42e+00 4.96e-01 9.17e+00 angle pdb=" C GLU P 33 " pdb=" N SER P 35 " pdb=" CA SER P 35 " ideal model delta sigma weight residual 121.70 127.05 -5.35 1.80e+00 3.09e-01 8.84e+00 angle pdb=" CA GLY L 28 " pdb=" C GLY L 28 " pdb=" N LYS L 29 " ideal model delta sigma weight residual 114.48 117.90 -3.42 1.19e+00 7.06e-01 8.25e+00 ... (remaining 106399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 38638 34.41 - 68.83: 4310 68.83 - 103.24: 611 103.24 - 137.66: 17 137.66 - 172.07: 7 Dihedral angle restraints: 43583 sinusoidal: 37372 harmonic: 6211 Sorted by residual: dihedral pdb=" O4' C A1675 " pdb=" C1' C A1675 " pdb=" N1 C A1675 " pdb=" C2 C A1675 " ideal model delta sinusoidal sigma weight residual 200.00 49.01 150.99 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual 232.00 61.15 170.85 1 1.70e+01 3.46e-03 6.60e+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 35.67 -163.67 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 43580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 10766 0.031 - 0.062: 2511 0.062 - 0.094: 226 0.094 - 0.125: 187 0.125 - 0.156: 26 Chirality restraints: 13716 Sorted by residual: chirality pdb=" CA VAL R 51 " pdb=" N VAL R 51 " pdb=" C VAL R 51 " pdb=" CB VAL R 51 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE T 2 " pdb=" N ILE T 2 " pdb=" C ILE T 2 " pdb=" CB ILE T 2 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 13713 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 418 " 0.004 2.00e-02 2.50e+03 1.82e-02 7.49e+00 pdb=" N1 C A 418 " 0.002 2.00e-02 2.50e+03 pdb=" C2 C A 418 " -0.045 2.00e-02 2.50e+03 pdb=" O2 C A 418 " 0.024 2.00e-02 2.50e+03 pdb=" N3 C A 418 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C A 418 " -0.013 2.00e-02 2.50e+03 pdb=" N4 C A 418 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C A 418 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C A 418 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 903 " 0.008 2.00e-02 2.50e+03 1.65e-02 6.10e+00 pdb=" N1 C A 903 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C A 903 " -0.041 2.00e-02 2.50e+03 pdb=" O2 C A 903 " 0.022 2.00e-02 2.50e+03 pdb=" N3 C A 903 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 903 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A 903 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C A 903 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A 903 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2264 " 0.006 2.00e-02 2.50e+03 1.52e-02 5.23e+00 pdb=" N1 C A2264 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C A2264 " -0.038 2.00e-02 2.50e+03 pdb=" O2 C A2264 " 0.023 2.00e-02 2.50e+03 pdb=" N3 C A2264 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C A2264 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A2264 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C A2264 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C A2264 " 0.002 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 380 2.47 - 3.08: 41191 3.08 - 3.69: 120566 3.69 - 4.29: 173139 4.29 - 4.90: 240223 Nonbonded interactions: 575499 Sorted by model distance: nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 1.866 2.440 nonbonded pdb=" O2' A A 905 " pdb=" O4' U A 906 " model vdw 1.917 2.440 nonbonded pdb=" OP2 U A 369 " pdb=" O2' U A 403 " model vdw 1.934 2.440 nonbonded pdb=" O2' C A1462 " pdb=" O2' G A2702 " model vdw 1.946 2.440 nonbonded pdb=" O2' U A 534 " pdb=" OD2 ASP Q 48 " model vdw 1.955 2.440 ... (remaining 575494 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 individual isotropic 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: 1.270 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: 0.050 Extract box with map and model: 7.970 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 219.760 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.033 70653 Z= 0.097 Angle : 0.383 6.690 106404 Z= 0.202 Chirality : 0.027 0.156 13716 Planarity : 0.002 0.030 5189 Dihedral : 21.866 172.073 39569 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.48 (0.19), residues: 2135 helix: 2.22 (0.22), residues: 662 sheet: 0.02 (0.27), residues: 414 loop : -0.80 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 60 HIS 0.004 0.001 HIS J 77 PHE 0.011 0.001 PHE S 75 TYR 0.015 0.001 TYR J 75 ARG 0.005 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.6310 time to fit residues: 317.6973 Evaluate side-chains 187 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 30.0000 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 205 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 40.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN E 62 GLN J 132 HIS K 5 GLN L 35 HIS P 9 GLN S 15 GLN T 92 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 70653 Z= 0.496 Angle : 0.730 9.349 106404 Z= 0.357 Chirality : 0.039 0.250 13716 Planarity : 0.006 0.060 5189 Dihedral : 22.612 177.220 35302 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.93 % Rotamer: Outliers : 2.42 % Allowed : 7.83 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.41 (0.18), residues: 2135 helix: 0.94 (0.20), residues: 673 sheet: -0.22 (0.27), residues: 401 loop : -1.07 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 30 HIS 0.010 0.002 HIS N 3 PHE 0.035 0.003 PHE S 75 TYR 0.028 0.003 TYR Q 23 ARG 0.013 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 28 residues processed: 232 average time/residue: 0.6629 time to fit residues: 268.7195 Evaluate side-chains 203 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.5041 time to fit residues: 30.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 393 optimal weight: 20.0000 chunk 424 optimal weight: 3.9990 chunk 350 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 12 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN F 20 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 70653 Z= 0.178 Angle : 0.501 12.325 106404 Z= 0.254 Chirality : 0.030 0.352 13716 Planarity : 0.004 0.042 5189 Dihedral : 22.497 175.563 35302 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 1.52 % Allowed : 11.94 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.24 (0.18), residues: 2135 helix: 1.27 (0.21), residues: 665 sheet: -0.37 (0.26), residues: 422 loop : -0.99 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 30 HIS 0.004 0.001 HIS V 44 PHE 0.022 0.001 PHE S 75 TYR 0.013 0.002 TYR F 7 ARG 0.010 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 230 average time/residue: 0.6189 time to fit residues: 247.1874 Evaluate side-chains 196 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 2.626 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4933 time to fit residues: 17.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 203 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 394 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 49 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 74 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 70653 Z= 0.460 Angle : 0.733 9.582 106404 Z= 0.363 Chirality : 0.040 0.240 13716 Planarity : 0.006 0.059 5189 Dihedral : 22.715 177.518 35302 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.90 % Rotamer: Outliers : 3.21 % Allowed : 14.87 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.85 (0.18), residues: 2135 helix: 0.55 (0.20), residues: 673 sheet: -0.65 (0.26), residues: 416 loop : -1.24 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 30 HIS 0.010 0.002 HIS Z 19 PHE 0.027 0.002 PHE S 75 TYR 0.023 0.002 TYR S 38 ARG 0.013 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 188 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 227 average time/residue: 0.6101 time to fit residues: 242.1256 Evaluate side-chains 209 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4619 time to fit residues: 33.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 30.0000 chunk 356 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 49 ASN E 195 GLN P 9 GLN P 74 GLN U 53 GLN O 38 GLN F 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 70653 Z= 0.285 Angle : 0.582 8.769 106404 Z= 0.294 Chirality : 0.034 0.264 13716 Planarity : 0.004 0.051 5189 Dihedral : 22.662 176.893 35302 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 1.92 % Allowed : 16.23 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.73 (0.18), residues: 2135 helix: 0.80 (0.21), residues: 668 sheet: -0.79 (0.25), residues: 439 loop : -1.18 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 30 HIS 0.006 0.001 HIS Z 19 PHE 0.024 0.002 PHE S 75 TYR 0.015 0.002 TYR S 38 ARG 0.010 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 210 average time/residue: 0.6441 time to fit residues: 236.2213 Evaluate side-chains 185 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 2.685 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5437 time to fit residues: 16.8242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 50.0000 chunk 376 optimal weight: 0.0000 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 138 optimal weight: 50.0000 chunk 219 optimal weight: 9.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN P 9 GLN P 74 GLN U 52 ASN 2 16 HIS O 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 70653 Z= 0.398 Angle : 0.677 9.194 106404 Z= 0.338 Chirality : 0.038 0.229 13716 Planarity : 0.005 0.056 5189 Dihedral : 22.777 176.585 35302 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 1.92 % Allowed : 18.37 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.03 (0.18), residues: 2135 helix: 0.49 (0.20), residues: 667 sheet: -0.82 (0.26), residues: 415 loop : -1.37 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 30 HIS 0.009 0.002 HIS Z 19 PHE 0.029 0.002 PHE S 75 TYR 0.018 0.002 TYR S 38 ARG 0.012 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 2.691 Fit side-chains outliers start: 34 outliers final: 19 residues processed: 208 average time/residue: 0.6193 time to fit residues: 224.9200 Evaluate side-chains 191 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4702 time to fit residues: 19.7500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 238 optimal weight: 0.0030 chunk 305 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 351 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 253 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN O 38 GLN F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 70653 Z= 0.199 Angle : 0.541 10.929 106404 Z= 0.275 Chirality : 0.032 0.244 13716 Planarity : 0.004 0.048 5189 Dihedral : 22.694 176.151 35302 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.24 % Allowed : 19.38 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.73 (0.18), residues: 2135 helix: 0.79 (0.21), residues: 670 sheet: -0.72 (0.26), residues: 415 loop : -1.20 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 30 HIS 0.004 0.001 HIS Z 19 PHE 0.023 0.001 PHE S 75 TYR 0.015 0.002 TYR F 6 ARG 0.009 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 2.666 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 200 average time/residue: 0.7011 time to fit residues: 242.2242 Evaluate side-chains 187 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5662 time to fit residues: 16.3679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 125 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN O 38 GLN F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 70653 Z= 0.402 Angle : 0.676 8.772 106404 Z= 0.337 Chirality : 0.038 0.275 13716 Planarity : 0.005 0.060 5189 Dihedral : 22.801 176.872 35302 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.58 % Allowed : 19.72 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.02 (0.18), residues: 2135 helix: 0.52 (0.20), residues: 665 sheet: -0.91 (0.25), residues: 417 loop : -1.33 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 30 HIS 0.008 0.002 HIS Z 19 PHE 0.027 0.002 PHE S 75 TYR 0.020 0.002 TYR F 6 ARG 0.013 0.001 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 2.677 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 195 average time/residue: 0.6637 time to fit residues: 225.8562 Evaluate side-chains 181 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 2.715 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5367 time to fit residues: 16.8266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 2.9990 chunk 398 optimal weight: 30.0000 chunk 363 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 350 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 386 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN U 52 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 70653 Z= 0.240 Angle : 0.565 10.040 106404 Z= 0.286 Chirality : 0.033 0.264 13716 Planarity : 0.004 0.052 5189 Dihedral : 22.733 176.637 35302 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.39 % Allowed : 20.56 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.85 (0.18), residues: 2135 helix: 0.72 (0.21), residues: 669 sheet: -0.86 (0.26), residues: 417 loop : -1.26 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 30 HIS 0.005 0.001 HIS Z 19 PHE 0.022 0.002 PHE S 75 TYR 0.016 0.002 TYR F 6 ARG 0.010 0.000 ARG O 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 2.724 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 186 average time/residue: 0.6723 time to fit residues: 217.0506 Evaluate side-chains 170 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4831 time to fit residues: 4.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 6.9990 chunk 410 optimal weight: 30.0000 chunk 250 optimal weight: 4.9990 chunk 194 optimal weight: 50.0000 chunk 285 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 396 optimal weight: 40.0000 chunk 342 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 GLN U 52 ASN ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 70653 Z= 0.343 Angle : 0.630 8.430 106404 Z= 0.316 Chirality : 0.036 0.311 13716 Planarity : 0.005 0.059 5189 Dihedral : 22.780 177.053 35302 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.62 % Allowed : 20.85 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.97 (0.18), residues: 2135 helix: 0.60 (0.20), residues: 669 sheet: -0.82 (0.26), residues: 398 loop : -1.37 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 30 HIS 0.007 0.001 HIS Z 19 PHE 0.025 0.002 PHE S 75 TYR 0.017 0.002 TYR F 6 ARG 0.012 0.001 ARG O 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4270 Ramachandran restraints generated. 2135 Oldfield, 0 Emsley, 2135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 2.694 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 0.6927 time to fit residues: 213.4458 Evaluate side-chains 174 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5019 time to fit residues: 10.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 30.0000 chunk 365 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 overall best weight: 6.1590 ------------------------------------------------------------------------------- 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** K 29 HIS ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.088483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062943 restraints weight = 272161.415| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.57 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 70653 Z= 0.321 Angle : 0.613 9.851 106404 Z= 0.308 Chirality : 0.035 0.307 13716 Planarity : 0.005 0.059 5189 Dihedral : 22.785 177.075 35302 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.39 % Allowed : 21.35 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.01 (0.18), residues: 2135 helix: 0.59 (0.20), residues: 670 sheet: -0.96 (0.25), residues: 416 loop : -1.35 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 30 HIS 0.007 0.001 HIS Z 19 PHE 0.020 0.002 PHE S 75 TYR 0.015 0.002 TYR F 6 ARG 0.010 0.001 ARG O 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8180.97 seconds wall clock time: 149 minutes 11.61 seconds (8951.61 seconds total)