Starting phenix.real_space_refine on Mon Sep 30 10:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppk_20441/09_2024/6ppk_20441.cif" } resolution = 4.4 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= 0.001 sd= 0.005 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 2773 5.49 5 S 65 5.16 5 C 39667 2.51 5 N 14963 2.21 5 O 22983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 80451 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 57112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2658, 57112 Classifications: {'RNA': 2658} Modifications used: {'rna2p_pur': 253, 'rna2p_pyr': 132, 'rna3p_pur': 1302, 'rna3p_pyr': 971} Link IDs: {'rna2p': 385, 'rna3p': 2272} Chain breaks: 14 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "C" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2010 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 16, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1511 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain breaks: 3 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 829 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 904 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 947 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 775 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 3 Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 691 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 2 Chain: "V" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 604 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1958 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 239} Chain breaks: 4 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.94, per 1000 atoms: 0.40 Number of scatterers: 80451 At special positions: 0 Unit cell: (203, 210.25, 217.5, 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 65 16.00 P 2773 15.00 O 22983 8.00 N 14963 7.00 C 39667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 58212 O4' U B 54 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.60 Conformation dependent library (CDL) restraints added in 3.1 seconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4890 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 40 sheets defined 28.2% alpha, 14.2% beta 645 base pairs and 1304 stacking pairs defined. Time for finding SS restraints: 31.31 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.785A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.918A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.666A pdb=" N VAL C 224 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.703A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.591A pdb=" N GLY D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.609A pdb=" N MET E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.625A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 removed outlier: 4.268A pdb=" N GLY E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.716A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL E 187 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 11 through 16 Processing helix chain 'F' and resid 94 through 107 removed outlier: 4.027A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.609A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 82 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.737A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA G 146 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 38 Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 97 through 110 removed outlier: 3.712A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 121 removed outlier: 3.569A pdb=" N LYS J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'L' and resid 92 through 99 removed outlier: 4.015A pdb=" N GLU L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 137 removed outlier: 3.783A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 3.624A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU N 17 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 20 " --> pdb=" O MET N 16 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 52 removed outlier: 4.832A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 64 removed outlier: 3.523A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 removed outlier: 3.623A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER N 85 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR N 89 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 21 Processing helix chain 'O' and resid 73 through 77 removed outlier: 3.766A pdb=" N LYS O 76 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 85 through 88 removed outlier: 3.591A pdb=" N LYS O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 85 through 88' Processing helix chain 'O' and resid 104 through 116 Processing helix chain 'P' and resid 6 through 16 removed outlier: 4.234A pdb=" N ASP P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU P 14 " --> pdb=" O ASP P 10 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN P 15 " --> pdb=" O ILE P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 60 removed outlier: 3.767A pdb=" N GLU P 60 " --> pdb=" O GLY P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.646A pdb=" N LEU P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 115 Processing helix chain 'Q' and resid 8 through 20 removed outlier: 3.784A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.048A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 38 through 73 removed outlier: 3.849A pdb=" N ASN Q 44 " --> pdb=" O MET Q 40 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 removed outlier: 3.918A pdb=" N LEU Q 85 " --> pdb=" O HIS Q 81 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER Q 86 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 97 Processing helix chain 'Q' and resid 106 through 115 removed outlier: 3.585A pdb=" N ALA Q 110 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP Q 111 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 22 removed outlier: 3.600A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.104A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 63 removed outlier: 3.768A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'S' and resid 88 through 92 Processing helix chain 'T' and resid 14 through 20 removed outlier: 3.656A pdb=" N ALA T 18 " --> pdb=" O THR T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.542A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 17 removed outlier: 4.343A pdb=" N ASP U 16 " --> pdb=" O SER U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.532A pdb=" N VAL Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 4.258A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.325A pdb=" N HIS b 19 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS b 21 " --> pdb=" O THR b 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.978A pdb=" N GLN Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS Y 17 " --> pdb=" O GLU Y 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER Y 20 " --> pdb=" O GLN Y 16 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 65 removed outlier: 3.994A pdb=" N ARG Y 47 " --> pdb=" O ILE Y 43 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.597A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 18 removed outlier: 3.509A pdb=" N GLU W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 21 No H-bonds generated for 'chain 'W' and resid 19 through 21' Processing helix chain 'W' and resid 36 through 40 removed outlier: 3.663A pdb=" N ARG W 40 " --> pdb=" O MET W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 48 removed outlier: 3.714A pdb=" N ILE W 47 " --> pdb=" O MET W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 77 Processing helix chain 'W' and resid 98 through 103 Processing helix chain 'W' and resid 104 through 108 removed outlier: 3.852A pdb=" N PHE W 108 " --> pdb=" O GLN W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 193 removed outlier: 3.566A pdb=" N THR W 192 " --> pdb=" O LEU W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 216 removed outlier: 3.857A pdb=" N ALA W 206 " --> pdb=" O LEU W 202 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG W 211 " --> pdb=" O VAL W 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE W 212 " --> pdb=" O PHE W 208 " (cutoff:3.500A) Processing helix chain 'W' and resid 217 through 219 No H-bonds generated for 'chain 'W' and resid 217 through 219' Processing helix chain 'W' and resid 220 through 225 removed outlier: 4.382A pdb=" N ARG W 224 " --> pdb=" O ARG W 220 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR W 225 " --> pdb=" O LEU W 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 220 through 225' Processing helix chain 'W' and resid 235 through 246 removed outlier: 3.818A pdb=" N ASP W 239 " --> pdb=" O ALA W 235 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS W 244 " --> pdb=" O ALA W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 255 through 268 removed outlier: 3.508A pdb=" N THR W 259 " --> pdb=" O ASN W 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE W 263 " --> pdb=" O THR W 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP W 266 " --> pdb=" O VAL W 262 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG W 268 " --> pdb=" O ILE W 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.583A pdb=" N LYS C 4 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.628A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.761A pdb=" N LEU C 165 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 182 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 181 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 168 through 174 removed outlier: 5.611A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 174 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 28 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AA9, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.999A pdb=" N PHE D 53 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.665A pdb=" N ILE E 194 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67 removed outlier: 4.156A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 122 through 125 Processing sheet with id=AB4, first strand: chain 'G' and resid 104 through 105 removed outlier: 3.512A pdb=" N LEU G 104 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 123 through 125 removed outlier: 3.585A pdb=" N ASN J 124 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU J 17 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE J 58 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL J 19 " --> pdb=" O ILE J 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.932A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL K 19 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR K 21 " --> pdb=" O CYS K 41 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS K 41 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.540A pdb=" N SER K 78 " --> pdb=" O GLU P 74 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE P 67 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N GLU P 47 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR P 28 " --> pdb=" O VAL P 90 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS P 86 " --> pdb=" O HIS P 32 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 75 through 77 removed outlier: 3.955A pdb=" N LYS L 110 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 77 " --> pdb=" O LYS L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 124 through 125 removed outlier: 3.734A pdb=" N ALA L 125 " --> pdb=" O GLU L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'N' and resid 29 through 33 removed outlier: 3.717A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET N 102 " --> pdb=" O ILE N 116 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU N 118 " --> pdb=" O ARG N 100 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG N 100 " --> pdb=" O GLU N 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 70 through 72 removed outlier: 3.725A pdb=" N GLN N 77 " --> pdb=" O ASN N 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 30 through 31 removed outlier: 3.629A pdb=" N ILE O 45 " --> pdb=" O ARG O 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'P' and resid 93 through 94 removed outlier: 4.556A pdb=" N ILE P 116 " --> pdb=" O LYS P 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 22 removed outlier: 4.108A pdb=" N GLY R 66 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 71 through 76 removed outlier: 3.687A pdb=" N ILE R 71 " --> pdb=" O HIS R 88 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 3 through 6 removed outlier: 6.698A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'S' and resid 84 through 86 removed outlier: 3.681A pdb=" N ARG S 86 " --> pdb=" O SER S 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 94 " --> pdb=" O ARG S 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 25 through 29 removed outlier: 3.581A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 9 through 10 Processing sheet with id=AD6, first strand: chain 'U' and resid 23 through 27 Processing sheet with id=AD7, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.525A pdb=" N GLN U 59 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.709A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG V 47 " --> pdb=" O GLY V 30 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 54 through 55 removed outlier: 5.390A pdb=" N TYR V 54 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL V 89 " --> pdb=" O TYR V 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 35 through 38 removed outlier: 3.768A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 27 through 28 Processing sheet with id=AE3, first strand: chain 'W' and resid 81 through 82 removed outlier: 4.351A pdb=" N ARG W 81 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN W 58 " --> pdb=" O VAL W 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 248 through 250 removed outlier: 6.682A pdb=" N LEU W 253 " --> pdb=" O MET W 249 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1520 hydrogen bonds 2308 hydrogen bond angles 0 basepair planarities 645 basepair parallelities 1304 stacking parallelities Total time for adding SS restraints: 119.91 Time building geometry restraints manager: 16.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8834 1.32 - 1.44: 38759 1.44 - 1.56: 34598 1.56 - 1.69: 5530 1.69 - 1.81: 124 Bond restraints: 87845 Sorted by residual: bond pdb=" C GLN d 6 " pdb=" N PRO d 7 " ideal model delta sigma weight residual 1.335 1.285 0.050 8.70e-03 1.32e+04 3.25e+01 bond pdb=" O2B GNP W 301 " pdb=" PB GNP W 301 " ideal model delta sigma weight residual 1.505 1.610 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C4 GNP W 301 " pdb=" C5 GNP W 301 " ideal model delta sigma weight residual 1.382 1.470 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O2G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O3G GNP W 301 " pdb=" PG GNP W 301 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 87840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.21: 131829 5.21 - 10.43: 485 10.43 - 15.64: 21 15.64 - 20.86: 5 20.86 - 26.07: 2 Bond angle restraints: 132342 Sorted by residual: angle pdb=" C ILE K 2 " pdb=" CA ILE K 2 " pdb=" CB ILE K 2 " ideal model delta sigma weight residual 111.49 137.56 -26.07 1.38e+00 5.25e-01 3.57e+02 angle pdb=" C ARG V 82 " pdb=" CA ARG V 82 " pdb=" CB ARG V 82 " ideal model delta sigma weight residual 111.26 134.21 -22.95 1.66e+00 3.63e-01 1.91e+02 angle pdb=" N ARG V 82 " pdb=" CA ARG V 82 " pdb=" C ARG V 82 " ideal model delta sigma weight residual 112.12 95.34 16.78 1.34e+00 5.57e-01 1.57e+02 angle pdb=" N ILE K 2 " pdb=" CA ILE K 2 " pdb=" C ILE K 2 " ideal model delta sigma weight residual 109.45 92.19 17.26 1.39e+00 5.18e-01 1.54e+02 angle pdb=" N LYS U 84 " pdb=" CA LYS U 84 " pdb=" C LYS U 84 " ideal model delta sigma weight residual 112.93 127.69 -14.76 1.33e+00 5.65e-01 1.23e+02 ... (remaining 132337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 47655 35.96 - 71.93: 7660 71.93 - 107.89: 891 107.89 - 143.86: 31 143.86 - 179.82: 51 Dihedral angle restraints: 56288 sinusoidal: 48692 harmonic: 7596 Sorted by residual: dihedral pdb=" O4' C A1281 " pdb=" C1' C A1281 " pdb=" N1 C A1281 " pdb=" C2 C A1281 " ideal model delta sinusoidal sigma weight residual -160.00 19.45 -179.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1515 " pdb=" C1' C A1515 " pdb=" N1 C A1515 " pdb=" C2 C A1515 " ideal model delta sinusoidal sigma weight residual 200.00 46.15 153.85 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C A 482 " pdb=" C1' C A 482 " pdb=" N1 C A 482 " pdb=" C2 C A 482 " ideal model delta sinusoidal sigma weight residual 200.00 47.90 152.10 1 1.50e+01 4.44e-03 8.04e+01 ... (remaining 56285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 16497 0.123 - 0.247: 521 0.247 - 0.370: 36 0.370 - 0.493: 7 0.493 - 0.617: 5 Chirality restraints: 17066 Sorted by residual: chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" CA SER D 103 " pdb=" N SER D 103 " pdb=" C SER D 103 " pdb=" CB SER D 103 " both_signs ideal model delta sigma weight residual False 2.51 3.09 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA LEU P 29 " pdb=" N LEU P 29 " pdb=" C LEU P 29 " pdb=" CB LEU P 29 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 17063 not shown) Planarity restraints: 6406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 50 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO R 51 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 51 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 51 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 4 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO J 5 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO J 5 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 5 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 248 " 0.049 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO C 249 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.040 5.00e-02 4.00e+02 ... (remaining 6403 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 36 1.90 - 2.65: 5138 2.65 - 3.40: 110636 3.40 - 4.15: 268388 4.15 - 4.90: 353433 Nonbonded interactions: 737631 Sorted by model distance: nonbonded pdb=" CD LYS F 33 " pdb=" NH2 ARG F 92 " model vdw 1.150 3.520 nonbonded pdb=" O4' A B 55 " pdb=" OE1 GLN F 27 " model vdw 1.152 3.040 nonbonded pdb=" OD2 ASP D 54 " pdb=" NH1 ARG D 78 " model vdw 1.177 3.120 nonbonded pdb=" OD1 ASP U 72 " pdb=" NE2 GLN U 99 " model vdw 1.245 3.120 nonbonded pdb=" O2 C B 41 " pdb=" CD ARG F 92 " model vdw 1.329 3.440 ... (remaining 737626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.060 Extract box with map and model: 2.160 Check model and map are aligned: 0.460 Set scattering table: 0.550 Process input model: 235.580 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.250 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: 243.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.008 0.134 87845 Z= 0.500 Angle : 1.080 26.069 132342 Z= 0.548 Chirality : 0.054 0.617 17066 Planarity : 0.006 0.079 6406 Dihedral : 26.185 179.820 51398 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.81 % Favored : 87.54 % Rotamer: Outliers : 8.03 % Allowed : 13.19 % Favored : 78.78 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.28 (0.13), residues: 2608 helix: -3.33 (0.14), residues: 587 sheet: -2.46 (0.24), residues: 396 loop : -2.87 (0.13), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 16 HIS 0.014 0.002 HIS J 54 PHE 0.044 0.002 PHE Q 57 TYR 0.022 0.002 TYR J 97 ARG 0.023 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 785 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 MET cc_start: 0.8494 (ppp) cc_final: 0.7536 (ppp) REVERT: C 156 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: C 188 CYS cc_start: 0.8253 (m) cc_final: 0.8001 (m) REVERT: C 247 MET cc_start: 0.5812 (ttm) cc_final: 0.5172 (ttm) REVERT: D 36 LEU cc_start: 0.9147 (mt) cc_final: 0.8713 (mp) REVERT: D 95 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: D 153 ARG cc_start: 0.8473 (ptt90) cc_final: 0.8022 (ptm-80) REVERT: D 155 PHE cc_start: 0.8370 (m-10) cc_final: 0.8163 (m-80) REVERT: D 159 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (mt) REVERT: D 201 THR cc_start: 0.8701 (m) cc_final: 0.8406 (p) REVERT: E 35 ASP cc_start: 0.8656 (t70) cc_final: 0.8251 (t70) REVERT: E 48 THR cc_start: 0.8957 (p) cc_final: 0.8564 (p) REVERT: E 150 LYS cc_start: 0.9179 (mppt) cc_final: 0.8729 (mttp) REVERT: E 158 ASP cc_start: 0.8530 (p0) cc_final: 0.7950 (p0) REVERT: E 165 LEU cc_start: 0.8891 (mm) cc_final: 0.8463 (tp) REVERT: F 12 ILE cc_start: 0.4784 (OUTLIER) cc_final: 0.4550 (mp) REVERT: G 66 HIS cc_start: 0.5839 (t-90) cc_final: 0.5230 (t70) REVERT: G 73 LEU cc_start: 0.8615 (mt) cc_final: 0.8227 (mt) REVERT: G 78 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: G 90 LEU cc_start: 0.6201 (mt) cc_final: 0.5940 (mp) REVERT: J 50 ASP cc_start: 0.8131 (t70) cc_final: 0.6784 (t70) REVERT: J 109 MET cc_start: 0.8600 (mmp) cc_final: 0.8205 (mmp) REVERT: J 121 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7618 (pttm) REVERT: J 139 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7928 (mp0) REVERT: K 7 ARG cc_start: 0.8752 (ttm170) cc_final: 0.8269 (mmt90) REVERT: K 122 ILE cc_start: 0.8142 (mt) cc_final: 0.7646 (mt) REVERT: L 36 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7202 (mmtm) REVERT: L 74 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.4058 (m-80) REVERT: L 89 THR cc_start: 0.6165 (OUTLIER) cc_final: 0.5438 (p) REVERT: L 90 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: L 106 ASN cc_start: 0.9019 (m-40) cc_final: 0.8788 (t0) REVERT: L 109 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7267 (p) REVERT: L 120 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6728 (pttp) REVERT: L 137 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: N 26 ILE cc_start: 0.9021 (mt) cc_final: 0.8511 (mt) REVERT: N 92 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8877 (tm-30) REVERT: O 41 TYR cc_start: 0.8121 (m-10) cc_final: 0.7905 (m-10) REVERT: O 61 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.5703 (ptmm) REVERT: O 96 ASP cc_start: 0.8751 (m-30) cc_final: 0.8433 (m-30) REVERT: O 102 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.5200 (t80) REVERT: O 107 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7925 (mtpp) REVERT: O 111 ASP cc_start: 0.7506 (m-30) cc_final: 0.7176 (m-30) REVERT: P 6 LYS cc_start: 0.8623 (tttt) cc_final: 0.8355 (tttt) REVERT: P 28 THR cc_start: 0.8830 (p) cc_final: 0.8189 (p) REVERT: P 44 GLN cc_start: 0.7962 (pt0) cc_final: 0.7421 (pp30) REVERT: P 51 ILE cc_start: 0.9624 (mt) cc_final: 0.9391 (mm) REVERT: P 52 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8164 (mmmt) REVERT: P 87 ILE cc_start: 0.9133 (mt) cc_final: 0.8686 (mm) REVERT: Q 40 MET cc_start: 0.9261 (ttm) cc_final: 0.8926 (ttm) REVERT: Q 41 LYS cc_start: 0.9516 (tptt) cc_final: 0.9139 (tppp) REVERT: Q 49 ASP cc_start: 0.8882 (t0) cc_final: 0.8422 (t0) REVERT: Q 92 ARG cc_start: 0.8349 (tpt90) cc_final: 0.8008 (tpp80) REVERT: R 11 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6290 (mt0) REVERT: R 16 GLU cc_start: 0.7448 (tt0) cc_final: 0.6687 (mt-10) REVERT: R 36 GLU cc_start: 0.8538 (tp30) cc_final: 0.8230 (tp30) REVERT: R 63 GLU cc_start: 0.8538 (tt0) cc_final: 0.8165 (mm-30) REVERT: R 76 TYR cc_start: 0.9123 (p90) cc_final: 0.8352 (p90) REVERT: S 31 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7662 (mm-30) REVERT: S 63 GLU cc_start: 0.7753 (mp0) cc_final: 0.7252 (mp0) REVERT: S 64 MET cc_start: 0.5899 (mmt) cc_final: 0.5441 (mtt) REVERT: S 78 GLU cc_start: 0.8554 (pt0) cc_final: 0.8132 (pt0) REVERT: S 100 THR cc_start: 0.9152 (m) cc_final: 0.8906 (p) REVERT: T 33 ARG cc_start: 0.8442 (ptp90) cc_final: 0.7977 (tpt170) REVERT: T 35 ASN cc_start: 0.9232 (m-40) cc_final: 0.8917 (m-40) REVERT: T 56 ILE cc_start: 0.9365 (mt) cc_final: 0.8916 (tt) REVERT: T 60 LYS cc_start: 0.8968 (mttt) cc_final: 0.8718 (mtpt) REVERT: U 31 ASP cc_start: 0.8534 (m-30) cc_final: 0.8145 (m-30) REVERT: U 59 GLN cc_start: 0.8641 (mt0) cc_final: 0.8084 (mt0) REVERT: V 27 LYS cc_start: 0.8418 (mttt) cc_final: 0.8147 (pttt) REVERT: V 28 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7740 (mmt-90) REVERT: V 46 TYR cc_start: 0.8233 (t80) cc_final: 0.7888 (t80) REVERT: V 48 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: V 65 ASP cc_start: 0.8630 (t0) cc_final: 0.8415 (t0) REVERT: Z 6 ILE cc_start: 0.8249 (mm) cc_final: 0.7387 (tp) REVERT: Z 8 LEU cc_start: 0.8825 (mt) cc_final: 0.8057 (mp) REVERT: Z 17 GLU cc_start: 0.6960 (pm20) cc_final: 0.6481 (pm20) REVERT: Z 20 ARG cc_start: 0.8581 (mtt180) cc_final: 0.8362 (mtp180) REVERT: Z 24 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8206 (tpt90) REVERT: Z 25 THR cc_start: 0.9033 (p) cc_final: 0.8813 (p) REVERT: Z 28 LEU cc_start: 0.7850 (mt) cc_final: 0.7632 (mt) REVERT: b 6 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: b 11 MET cc_start: 0.8921 (ttt) cc_final: 0.8703 (ttt) REVERT: b 14 ARG cc_start: 0.9488 (mtt180) cc_final: 0.9145 (mtp85) REVERT: b 27 MET cc_start: 0.8579 (mtm) cc_final: 0.7694 (mtm) REVERT: b 42 VAL cc_start: 0.8528 (t) cc_final: 0.8250 (t) REVERT: Y 5 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6612 (mm-30) REVERT: Y 28 LEU cc_start: 0.9394 (tp) cc_final: 0.9156 (tp) REVERT: Y 31 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8805 (mp10) REVERT: Y 43 ILE cc_start: 0.8908 (mt) cc_final: 0.8574 (mt) REVERT: Y 53 MET cc_start: 0.8946 (mtm) cc_final: 0.8702 (mmm) REVERT: Y 65 ASN cc_start: 0.7978 (t0) cc_final: 0.7455 (m110) REVERT: W 15 ARG cc_start: 0.5446 (ttt90) cc_final: 0.4986 (tpt-90) REVERT: W 58 ASN cc_start: 0.7473 (p0) cc_final: 0.7086 (p0) REVERT: W 177 TRP cc_start: 0.6139 (OUTLIER) cc_final: 0.5546 (m-10) REVERT: W 201 ASN cc_start: 0.6302 (t0) cc_final: 0.5685 (m-40) REVERT: W 271 LYS cc_start: 0.7911 (mttt) cc_final: 0.7209 (ttmt) REVERT: W 277 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6155 (m-80) outliers start: 179 outliers final: 39 residues processed: 890 average time/residue: 0.8436 time to fit residues: 1238.0066 Evaluate side-chains 578 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 519 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 451 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 225 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 419 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 254 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 485 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 135 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS J 96 ASN J 124 ASN L 78 ASN N 61 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN P 32 HIS P 44 GLN Q 37 GLN Q 44 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 60 HIS U 20 GLN U 67 ASN V 48 GLN ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 HIS W 78 GLN W 130 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 87845 Z= 0.315 Angle : 0.815 9.579 132342 Z= 0.403 Chirality : 0.042 0.291 17066 Planarity : 0.006 0.072 6406 Dihedral : 26.491 178.709 46042 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.09 % Favored : 90.84 % Rotamer: Outliers : 0.22 % Allowed : 6.01 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.15), residues: 2608 helix: -1.95 (0.18), residues: 654 sheet: -1.92 (0.24), residues: 414 loop : -2.51 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 213 HIS 0.013 0.002 HIS J 54 PHE 0.028 0.003 PHE Q 47 TYR 0.037 0.003 TYR C 171 ARG 0.014 0.001 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 667 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 MET cc_start: 0.8558 (ppp) cc_final: 0.7897 (tmm) REVERT: C 247 MET cc_start: 0.5679 (ttm) cc_final: 0.4992 (ttm) REVERT: D 153 ARG cc_start: 0.8492 (ptt90) cc_final: 0.6196 (ptt90) REVERT: D 154 VAL cc_start: 0.9408 (t) cc_final: 0.9117 (p) REVERT: D 168 GLN cc_start: 0.9257 (mt0) cc_final: 0.8922 (mt0) REVERT: D 201 THR cc_start: 0.8684 (m) cc_final: 0.8303 (p) REVERT: E 35 ASP cc_start: 0.8636 (t70) cc_final: 0.8172 (t70) REVERT: E 83 TRP cc_start: 0.9460 (m-10) cc_final: 0.9041 (m-10) REVERT: E 165 LEU cc_start: 0.8522 (mm) cc_final: 0.7985 (tp) REVERT: G 90 LEU cc_start: 0.6896 (mt) cc_final: 0.6463 (mp) REVERT: J 20 ASP cc_start: 0.8680 (t70) cc_final: 0.8439 (t70) REVERT: J 92 GLU cc_start: 0.9092 (tp30) cc_final: 0.8685 (tp30) REVERT: J 102 LEU cc_start: 0.9043 (tp) cc_final: 0.8807 (tp) REVERT: J 109 MET cc_start: 0.8929 (mmp) cc_final: 0.8517 (mmp) REVERT: J 139 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7874 (mp0) REVERT: K 7 ARG cc_start: 0.8764 (ttm170) cc_final: 0.8312 (mmt90) REVERT: K 22 ILE cc_start: 0.9102 (mt) cc_final: 0.8399 (mp) REVERT: K 41 CYS cc_start: 0.7787 (p) cc_final: 0.7298 (m) REVERT: K 112 MET cc_start: 0.8893 (mpp) cc_final: 0.8590 (mpp) REVERT: L 10 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8280 (tm-30) REVERT: L 106 ASN cc_start: 0.8816 (m-40) cc_final: 0.8455 (t0) REVERT: L 122 THR cc_start: 0.8892 (p) cc_final: 0.8621 (t) REVERT: N 26 ILE cc_start: 0.9491 (mt) cc_final: 0.8690 (tt) REVERT: N 34 GLU cc_start: 0.9164 (pp20) cc_final: 0.8673 (pp20) REVERT: N 69 GLU cc_start: 0.8706 (mp0) cc_final: 0.8390 (mp0) REVERT: N 92 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8900 (tm-30) REVERT: O 32 ASN cc_start: 0.8194 (p0) cc_final: 0.7882 (p0) REVERT: O 79 GLU cc_start: 0.8416 (tp30) cc_final: 0.8073 (tp30) REVERT: P 6 LYS cc_start: 0.8600 (tttt) cc_final: 0.8285 (tttt) REVERT: P 19 ASP cc_start: 0.6877 (t0) cc_final: 0.6590 (t0) REVERT: P 92 TYR cc_start: 0.8427 (m-80) cc_final: 0.8211 (m-80) REVERT: Q 40 MET cc_start: 0.8820 (ttm) cc_final: 0.8400 (ttm) REVERT: Q 49 ASP cc_start: 0.8768 (t0) cc_final: 0.8269 (t0) REVERT: Q 65 ILE cc_start: 0.9504 (mt) cc_final: 0.9293 (tt) REVERT: Q 94 MET cc_start: 0.8835 (ttt) cc_final: 0.8366 (ttt) REVERT: R 31 GLU cc_start: 0.6065 (mp0) cc_final: 0.5752 (mp0) REVERT: R 36 GLU cc_start: 0.8240 (tp30) cc_final: 0.7826 (tp30) REVERT: R 48 VAL cc_start: 0.6786 (OUTLIER) cc_final: 0.6406 (p) REVERT: R 52 THR cc_start: 0.8972 (m) cc_final: 0.8583 (t) REVERT: R 63 GLU cc_start: 0.8843 (tt0) cc_final: 0.8199 (mm-30) REVERT: R 76 TYR cc_start: 0.9041 (p90) cc_final: 0.8524 (p90) REVERT: S 61 ASN cc_start: 0.8339 (m-40) cc_final: 0.7911 (m-40) REVERT: S 78 GLU cc_start: 0.8345 (pt0) cc_final: 0.8096 (pt0) REVERT: S 102 HIS cc_start: 0.7996 (m170) cc_final: 0.7523 (m-70) REVERT: T 33 ARG cc_start: 0.8551 (ptp90) cc_final: 0.8101 (tpt170) REVERT: T 56 ILE cc_start: 0.9291 (mt) cc_final: 0.8793 (tt) REVERT: U 31 ASP cc_start: 0.8403 (m-30) cc_final: 0.7768 (m-30) REVERT: U 59 GLN cc_start: 0.8123 (mt0) cc_final: 0.7291 (mp10) REVERT: V 28 ARG cc_start: 0.8360 (mmt90) cc_final: 0.7832 (mmt-90) REVERT: V 46 TYR cc_start: 0.8422 (t80) cc_final: 0.8124 (t80) REVERT: V 48 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8371 (mm-40) REVERT: V 85 LYS cc_start: 0.8133 (mttm) cc_final: 0.7494 (mttt) REVERT: Z 8 LEU cc_start: 0.9319 (mt) cc_final: 0.9035 (mp) REVERT: Z 9 LYS cc_start: 0.9351 (mmpt) cc_final: 0.8981 (mmmm) REVERT: Z 19 GLN cc_start: 0.8178 (mp10) cc_final: 0.7688 (mp10) REVERT: Z 20 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8116 (mmm160) REVERT: Z 26 LEU cc_start: 0.9155 (tt) cc_final: 0.8773 (tt) REVERT: Z 46 MET cc_start: 0.9040 (mtp) cc_final: 0.8044 (mmt) REVERT: b 27 MET cc_start: 0.8559 (mtm) cc_final: 0.7924 (mtm) REVERT: Y 15 GLU cc_start: 0.7155 (tp30) cc_final: 0.6875 (tp30) REVERT: Y 31 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8947 (mm-40) REVERT: Y 39 ASN cc_start: 0.6955 (t0) cc_final: 0.6729 (m-40) REVERT: Y 53 MET cc_start: 0.9242 (mtm) cc_final: 0.8794 (mmm) REVERT: Y 65 ASN cc_start: 0.7878 (t0) cc_final: 0.7439 (m110) REVERT: d 22 MET cc_start: 0.9348 (mmm) cc_final: 0.9080 (mmm) REVERT: W 15 ARG cc_start: 0.5504 (ttt180) cc_final: 0.4889 (tpt-90) REVERT: W 55 MET cc_start: 0.7299 (mtt) cc_final: 0.7044 (mtp) REVERT: W 71 TRP cc_start: 0.5264 (m100) cc_final: 0.5028 (m100) REVERT: W 81 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7533 (ttt180) REVERT: W 135 THR cc_start: 0.8359 (t) cc_final: 0.8004 (t) REVERT: W 136 LEU cc_start: 0.9062 (tp) cc_final: 0.8792 (tp) REVERT: W 138 ASN cc_start: 0.8912 (p0) cc_final: 0.8590 (p0) REVERT: W 201 ASN cc_start: 0.5881 (t0) cc_final: 0.5041 (m-40) REVERT: W 264 ILE cc_start: 0.7866 (pt) cc_final: 0.7624 (pt) outliers start: 5 outliers final: 2 residues processed: 672 average time/residue: 0.8409 time to fit residues: 964.3189 Evaluate side-chains 496 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 493 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 270 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 486 optimal weight: 0.0070 chunk 525 optimal weight: 7.9990 chunk 433 optimal weight: 0.0000 chunk 482 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 overall best weight: 4.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 50 GLN D 191 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN P 15 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN U 67 ASN Z 37 HIS b 40 HIS Y 4 ASN ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 216 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 87845 Z= 0.237 Angle : 0.709 9.346 132342 Z= 0.355 Chirality : 0.038 0.313 17066 Planarity : 0.005 0.093 6406 Dihedral : 26.286 178.740 46042 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.14 % Rotamer: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.15), residues: 2608 helix: -1.26 (0.19), residues: 660 sheet: -1.72 (0.24), residues: 432 loop : -2.15 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 213 HIS 0.009 0.001 HIS J 41 PHE 0.023 0.002 PHE E 90 TYR 0.019 0.002 TYR J 126 ARG 0.009 0.001 ARG N 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 607 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8039 (mt-10) REVERT: C 188 CYS cc_start: 0.8174 (m) cc_final: 0.7427 (m) REVERT: C 247 MET cc_start: 0.5944 (ttm) cc_final: 0.5226 (ttm) REVERT: D 12 MET cc_start: 0.7372 (mmm) cc_final: 0.7037 (mmm) REVERT: D 36 LEU cc_start: 0.8873 (mt) cc_final: 0.8627 (mp) REVERT: D 140 HIS cc_start: 0.8991 (p90) cc_final: 0.8732 (p90) REVERT: D 146 MET cc_start: 0.7829 (mmp) cc_final: 0.7600 (mmp) REVERT: D 154 VAL cc_start: 0.9386 (t) cc_final: 0.9032 (p) REVERT: D 168 GLN cc_start: 0.9233 (mt0) cc_final: 0.8903 (mt0) REVERT: D 201 THR cc_start: 0.8730 (m) cc_final: 0.8465 (p) REVERT: E 83 TRP cc_start: 0.9360 (m-10) cc_final: 0.9117 (m-10) REVERT: E 165 LEU cc_start: 0.8623 (mm) cc_final: 0.8055 (tp) REVERT: F 96 MET cc_start: 0.7057 (mpp) cc_final: 0.6805 (mpp) REVERT: F 132 ILE cc_start: 0.3059 (mp) cc_final: 0.2338 (mt) REVERT: G 84 PHE cc_start: 0.4592 (m-80) cc_final: 0.4044 (m-10) REVERT: G 90 LEU cc_start: 0.5835 (mt) cc_final: 0.5613 (mp) REVERT: J 56 ILE cc_start: 0.9374 (pt) cc_final: 0.9096 (mm) REVERT: J 92 GLU cc_start: 0.8984 (tp30) cc_final: 0.8505 (tp30) REVERT: J 109 MET cc_start: 0.8834 (mmp) cc_final: 0.7194 (mmm) REVERT: J 110 LEU cc_start: 0.9377 (mt) cc_final: 0.9068 (tp) REVERT: J 121 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8037 (pttm) REVERT: J 139 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7778 (mp0) REVERT: K 4 GLN cc_start: 0.8879 (tp40) cc_final: 0.8608 (tp-100) REVERT: K 7 ARG cc_start: 0.8945 (ttm170) cc_final: 0.8033 (mmt90) REVERT: K 18 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6710 (mt-10) REVERT: K 41 CYS cc_start: 0.7833 (p) cc_final: 0.7472 (m) REVERT: K 104 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.7053 (tmm-80) REVERT: K 112 MET cc_start: 0.8853 (mpp) cc_final: 0.8431 (mpp) REVERT: L 23 ILE cc_start: 0.9429 (mm) cc_final: 0.9082 (tp) REVERT: L 94 GLU cc_start: 0.8355 (mp0) cc_final: 0.8113 (mp0) REVERT: L 106 ASN cc_start: 0.8954 (m-40) cc_final: 0.8343 (t0) REVERT: N 26 ILE cc_start: 0.9521 (mt) cc_final: 0.9164 (mt) REVERT: O 32 ASN cc_start: 0.7818 (p0) cc_final: 0.7426 (p0) REVERT: O 34 PHE cc_start: 0.7769 (t80) cc_final: 0.7266 (t80) REVERT: O 41 TYR cc_start: 0.7756 (m-80) cc_final: 0.6484 (m-80) REVERT: O 43 GLN cc_start: 0.5513 (mp10) cc_final: 0.5119 (mp10) REVERT: O 95 PHE cc_start: 0.8467 (t80) cc_final: 0.8217 (t80) REVERT: P 6 LYS cc_start: 0.8525 (tttt) cc_final: 0.8302 (tttt) REVERT: P 92 TYR cc_start: 0.8398 (m-80) cc_final: 0.8182 (m-80) REVERT: Q 40 MET cc_start: 0.8795 (ttm) cc_final: 0.8225 (ttm) REVERT: Q 49 ASP cc_start: 0.8775 (t0) cc_final: 0.8178 (t0) REVERT: Q 80 MET cc_start: 0.8249 (mtt) cc_final: 0.8030 (mtp) REVERT: Q 94 MET cc_start: 0.8849 (ttt) cc_final: 0.8346 (ttt) REVERT: R 16 GLU cc_start: 0.7779 (tp30) cc_final: 0.7052 (tp30) REVERT: R 31 GLU cc_start: 0.6073 (mp0) cc_final: 0.5760 (mp0) REVERT: R 36 GLU cc_start: 0.8295 (tp30) cc_final: 0.7832 (tp30) REVERT: R 52 THR cc_start: 0.8771 (m) cc_final: 0.8361 (t) REVERT: R 63 GLU cc_start: 0.8986 (tt0) cc_final: 0.8438 (mm-30) REVERT: R 76 TYR cc_start: 0.8453 (p90) cc_final: 0.8213 (p90) REVERT: R 89 ARG cc_start: 0.9005 (ttt180) cc_final: 0.8618 (ttt180) REVERT: R 98 GLU cc_start: 0.8701 (tt0) cc_final: 0.8498 (mt-10) REVERT: S 61 ASN cc_start: 0.8225 (m-40) cc_final: 0.7949 (m-40) REVERT: S 78 GLU cc_start: 0.8323 (pt0) cc_final: 0.7901 (pt0) REVERT: S 100 THR cc_start: 0.8778 (p) cc_final: 0.8568 (p) REVERT: S 102 HIS cc_start: 0.7912 (m170) cc_final: 0.7435 (m-70) REVERT: T 56 ILE cc_start: 0.9044 (mt) cc_final: 0.8556 (tt) REVERT: U 31 ASP cc_start: 0.8338 (m-30) cc_final: 0.7627 (m-30) REVERT: V 28 ARG cc_start: 0.8387 (mmt90) cc_final: 0.7849 (mmt-90) REVERT: Z 8 LEU cc_start: 0.9294 (mt) cc_final: 0.8815 (mt) REVERT: Z 9 LYS cc_start: 0.9315 (mmpt) cc_final: 0.8657 (mmtm) REVERT: Z 19 GLN cc_start: 0.8365 (mp10) cc_final: 0.7966 (mp10) REVERT: b 27 MET cc_start: 0.8442 (mtm) cc_final: 0.8015 (ptp) REVERT: b 37 LYS cc_start: 0.8580 (pptt) cc_final: 0.8200 (pptt) REVERT: Y 15 GLU cc_start: 0.6871 (tp30) cc_final: 0.6451 (tp30) REVERT: Y 29 ARG cc_start: 0.9102 (mtt180) cc_final: 0.8698 (tpp80) REVERT: Y 31 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8813 (mm-40) REVERT: Y 53 MET cc_start: 0.9289 (mtm) cc_final: 0.8926 (mmp) REVERT: d 22 MET cc_start: 0.9437 (mmm) cc_final: 0.9097 (mmm) REVERT: W 15 ARG cc_start: 0.5590 (ttt180) cc_final: 0.5022 (ttt90) REVERT: W 77 ASN cc_start: 0.8706 (m110) cc_final: 0.8491 (m110) REVERT: W 81 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7616 (ttt180) REVERT: W 135 THR cc_start: 0.8383 (t) cc_final: 0.8035 (t) REVERT: W 136 LEU cc_start: 0.9088 (tp) cc_final: 0.8809 (tp) REVERT: W 138 ASN cc_start: 0.8861 (p0) cc_final: 0.8598 (p0) REVERT: W 201 ASN cc_start: 0.6161 (t0) cc_final: 0.5583 (m-40) REVERT: W 271 LYS cc_start: 0.8185 (mttt) cc_final: 0.7857 (ttmt) outliers start: 4 outliers final: 0 residues processed: 610 average time/residue: 0.7957 time to fit residues: 833.2158 Evaluate side-chains 491 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 480 optimal weight: 5.9990 chunk 365 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 232 optimal weight: 30.0000 chunk 326 optimal weight: 10.0000 chunk 488 optimal weight: 9.9990 chunk 517 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 462 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 197 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS d 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 87845 Z= 0.322 Angle : 0.780 9.730 132342 Z= 0.387 Chirality : 0.041 0.422 17066 Planarity : 0.006 0.072 6406 Dihedral : 26.355 179.212 46042 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.39 % Favored : 90.57 % Rotamer: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2608 helix: -1.07 (0.19), residues: 666 sheet: -1.68 (0.25), residues: 415 loop : -2.14 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 213 HIS 0.021 0.002 HIS J 54 PHE 0.035 0.002 PHE Q 57 TYR 0.017 0.002 TYR V 46 ARG 0.008 0.001 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 564 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 MET cc_start: 0.8154 (tmm) cc_final: 0.7912 (tmm) REVERT: C 188 CYS cc_start: 0.8201 (m) cc_final: 0.7922 (m) REVERT: C 197 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8169 (t0) REVERT: C 247 MET cc_start: 0.5779 (ttm) cc_final: 0.5266 (ttm) REVERT: D 153 ARG cc_start: 0.8407 (ptt90) cc_final: 0.7951 (ptt90) REVERT: D 168 GLN cc_start: 0.9234 (mt0) cc_final: 0.8916 (mt0) REVERT: D 201 THR cc_start: 0.8777 (m) cc_final: 0.8375 (p) REVERT: E 35 ASP cc_start: 0.8645 (t70) cc_final: 0.8302 (t70) REVERT: E 83 TRP cc_start: 0.9281 (m-10) cc_final: 0.8947 (m-10) REVERT: E 165 LEU cc_start: 0.8549 (mm) cc_final: 0.8069 (tp) REVERT: F 9 ASN cc_start: 0.5812 (m110) cc_final: 0.5547 (t0) REVERT: G 141 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8902 (tpp80) REVERT: J 50 ASP cc_start: 0.8174 (t70) cc_final: 0.6615 (t70) REVERT: J 81 HIS cc_start: 0.8649 (m-70) cc_final: 0.8365 (m-70) REVERT: J 89 THR cc_start: 0.8877 (m) cc_final: 0.8646 (p) REVERT: J 92 GLU cc_start: 0.9070 (tp30) cc_final: 0.8674 (tp30) REVERT: J 102 LEU cc_start: 0.9144 (tp) cc_final: 0.8924 (tp) REVERT: J 109 MET cc_start: 0.9016 (mmp) cc_final: 0.8714 (mmp) REVERT: J 110 LEU cc_start: 0.9448 (mt) cc_final: 0.9086 (tp) REVERT: J 139 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7927 (mp0) REVERT: K 4 GLN cc_start: 0.8845 (tp40) cc_final: 0.8551 (tp-100) REVERT: K 7 ARG cc_start: 0.8885 (ttm170) cc_final: 0.7885 (tpp80) REVERT: K 8 LEU cc_start: 0.9575 (tp) cc_final: 0.9348 (tp) REVERT: K 18 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7108 (mt-10) REVERT: K 41 CYS cc_start: 0.7736 (p) cc_final: 0.7299 (m) REVERT: K 112 MET cc_start: 0.8941 (mpp) cc_final: 0.8451 (mpp) REVERT: L 23 ILE cc_start: 0.9420 (mm) cc_final: 0.9071 (tp) REVERT: L 106 ASN cc_start: 0.8809 (m-40) cc_final: 0.8212 (t0) REVERT: L 122 THR cc_start: 0.8950 (p) cc_final: 0.8643 (p) REVERT: N 26 ILE cc_start: 0.9512 (mt) cc_final: 0.9170 (tt) REVERT: N 59 ARG cc_start: 0.8956 (mtt180) cc_final: 0.8214 (mtp85) REVERT: O 41 TYR cc_start: 0.7694 (m-80) cc_final: 0.7365 (m-80) REVERT: O 43 GLN cc_start: 0.4864 (mp10) cc_final: 0.4217 (mp10) REVERT: O 95 PHE cc_start: 0.8502 (t80) cc_final: 0.7395 (t80) REVERT: P 6 LYS cc_start: 0.8647 (tttt) cc_final: 0.8393 (tttt) REVERT: P 19 ASP cc_start: 0.6766 (t0) cc_final: 0.6453 (t0) REVERT: Q 49 ASP cc_start: 0.8773 (t0) cc_final: 0.8272 (t0) REVERT: R 16 GLU cc_start: 0.7752 (tp30) cc_final: 0.7528 (tp30) REVERT: R 31 GLU cc_start: 0.6336 (mp0) cc_final: 0.5936 (mp0) REVERT: R 36 GLU cc_start: 0.8211 (tp30) cc_final: 0.7887 (tp30) REVERT: R 52 THR cc_start: 0.8722 (m) cc_final: 0.8308 (t) REVERT: R 63 GLU cc_start: 0.8874 (tt0) cc_final: 0.8305 (mm-30) REVERT: S 48 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6555 (tm-30) REVERT: S 60 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8129 (t-170) REVERT: S 78 GLU cc_start: 0.8431 (pt0) cc_final: 0.7984 (pt0) REVERT: S 100 THR cc_start: 0.8946 (p) cc_final: 0.8668 (p) REVERT: S 102 HIS cc_start: 0.7840 (m170) cc_final: 0.7403 (m90) REVERT: T 56 ILE cc_start: 0.9085 (mt) cc_final: 0.8630 (tt) REVERT: U 31 ASP cc_start: 0.8428 (m-30) cc_final: 0.7757 (m-30) REVERT: U 58 ASN cc_start: 0.8693 (m-40) cc_final: 0.8308 (m-40) REVERT: V 28 ARG cc_start: 0.8439 (mmt90) cc_final: 0.7775 (mmt-90) REVERT: V 48 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7453 (mm-40) REVERT: V 49 ARG cc_start: 0.8355 (mmt180) cc_final: 0.7466 (mmt180) REVERT: Z 8 LEU cc_start: 0.9382 (mt) cc_final: 0.9065 (mp) REVERT: Z 9 LYS cc_start: 0.9442 (mmpt) cc_final: 0.8714 (mmtm) REVERT: Z 19 GLN cc_start: 0.8431 (mp10) cc_final: 0.8075 (mp10) REVERT: Z 50 VAL cc_start: 0.9037 (t) cc_final: 0.8785 (m) REVERT: b 27 MET cc_start: 0.8425 (mtm) cc_final: 0.8093 (ptp) REVERT: b 37 LYS cc_start: 0.8583 (pptt) cc_final: 0.8239 (pptt) REVERT: Y 15 GLU cc_start: 0.6933 (tp30) cc_final: 0.6573 (tp30) REVERT: Y 22 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8226 (mtmt) REVERT: Y 31 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8761 (mm110) REVERT: Y 53 MET cc_start: 0.9270 (mtm) cc_final: 0.9007 (mmp) REVERT: W 15 ARG cc_start: 0.5700 (ttt180) cc_final: 0.5399 (ttt180) REVERT: W 81 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7761 (ttt180) REVERT: W 135 THR cc_start: 0.8275 (t) cc_final: 0.7841 (t) REVERT: W 136 LEU cc_start: 0.9112 (tp) cc_final: 0.8824 (tp) REVERT: W 138 ASN cc_start: 0.8934 (p0) cc_final: 0.8653 (p0) REVERT: W 147 LYS cc_start: 0.7668 (mttt) cc_final: 0.6826 (pttt) REVERT: W 201 ASN cc_start: 0.6325 (t0) cc_final: 0.5700 (m-40) REVERT: W 231 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7514 (Cg_exo) REVERT: W 249 MET cc_start: 0.6998 (ptm) cc_final: 0.6738 (ptm) REVERT: W 269 THR cc_start: 0.6827 (t) cc_final: 0.6522 (m) outliers start: 3 outliers final: 1 residues processed: 567 average time/residue: 0.7951 time to fit residues: 772.3135 Evaluate side-chains 441 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 438 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 430 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 213 optimal weight: 30.0000 chunk 441 optimal weight: 1.9990 chunk 357 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 129 GLN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN J 124 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 ASN Y 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 87845 Z= 0.333 Angle : 0.783 9.478 132342 Z= 0.389 Chirality : 0.041 0.331 17066 Planarity : 0.006 0.077 6406 Dihedral : 26.369 179.415 46042 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.16 % Favored : 90.80 % Rotamer: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 2608 helix: -0.99 (0.19), residues: 665 sheet: -1.53 (0.26), residues: 369 loop : -2.16 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 65 HIS 0.022 0.002 HIS J 54 PHE 0.038 0.003 PHE Q 57 TYR 0.021 0.003 TYR Q 24 ARG 0.012 0.001 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 579 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 MET cc_start: 0.8498 (ppp) cc_final: 0.7876 (tmm) REVERT: C 24 ILE cc_start: 0.9294 (mp) cc_final: 0.9026 (mt) REVERT: C 117 MET cc_start: 0.8376 (tmm) cc_final: 0.8076 (tmm) REVERT: C 188 CYS cc_start: 0.8318 (m) cc_final: 0.7980 (m) REVERT: C 247 MET cc_start: 0.5771 (ttm) cc_final: 0.5379 (ttm) REVERT: D 152 ASN cc_start: 0.8996 (m-40) cc_final: 0.8549 (m110) REVERT: D 160 LEU cc_start: 0.8932 (tp) cc_final: 0.8625 (tp) REVERT: D 168 GLN cc_start: 0.9250 (mt0) cc_final: 0.8939 (mt0) REVERT: D 170 THR cc_start: 0.9008 (m) cc_final: 0.8674 (p) REVERT: D 201 THR cc_start: 0.8586 (m) cc_final: 0.8207 (p) REVERT: E 35 ASP cc_start: 0.8453 (t70) cc_final: 0.8115 (t0) REVERT: E 83 TRP cc_start: 0.9313 (m-10) cc_final: 0.8929 (m-10) REVERT: E 158 ASP cc_start: 0.8536 (p0) cc_final: 0.8085 (p0) REVERT: E 165 LEU cc_start: 0.8679 (mm) cc_final: 0.8130 (tp) REVERT: F 9 ASN cc_start: 0.5755 (m110) cc_final: 0.5482 (t0) REVERT: G 107 ASN cc_start: 0.2127 (m-40) cc_final: 0.1455 (p0) REVERT: G 150 ARG cc_start: 0.8041 (ttt-90) cc_final: 0.7419 (tpp80) REVERT: J 81 HIS cc_start: 0.8597 (m-70) cc_final: 0.8285 (m-70) REVERT: J 89 THR cc_start: 0.8932 (m) cc_final: 0.8639 (p) REVERT: J 92 GLU cc_start: 0.9151 (tp30) cc_final: 0.8774 (tp30) REVERT: J 102 LEU cc_start: 0.9149 (tp) cc_final: 0.8938 (tp) REVERT: J 109 MET cc_start: 0.8974 (mmp) cc_final: 0.7211 (mmm) REVERT: J 110 LEU cc_start: 0.9470 (mt) cc_final: 0.9114 (tp) REVERT: J 121 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8627 (mtmm) REVERT: J 139 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8033 (mp0) REVERT: K 4 GLN cc_start: 0.8887 (tp40) cc_final: 0.8618 (tp-100) REVERT: K 8 LEU cc_start: 0.9458 (tp) cc_final: 0.8652 (tp) REVERT: K 18 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7029 (mt-10) REVERT: K 41 CYS cc_start: 0.7553 (p) cc_final: 0.6973 (m) REVERT: K 112 MET cc_start: 0.8906 (mpp) cc_final: 0.8338 (mpp) REVERT: L 23 ILE cc_start: 0.9400 (mm) cc_final: 0.9168 (tp) REVERT: L 106 ASN cc_start: 0.8901 (m-40) cc_final: 0.8128 (t0) REVERT: N 26 ILE cc_start: 0.9613 (mt) cc_final: 0.9130 (tt) REVERT: N 34 GLU cc_start: 0.8870 (pp20) cc_final: 0.8486 (pp20) REVERT: O 43 GLN cc_start: 0.4796 (mp10) cc_final: 0.4182 (mp10) REVERT: O 95 PHE cc_start: 0.8499 (t80) cc_final: 0.7839 (t80) REVERT: Q 40 MET cc_start: 0.9131 (ttm) cc_final: 0.8457 (ttm) REVERT: Q 49 ASP cc_start: 0.8783 (t0) cc_final: 0.8320 (t0) REVERT: R 16 GLU cc_start: 0.7915 (tp30) cc_final: 0.7653 (tp30) REVERT: R 31 GLU cc_start: 0.6532 (mp0) cc_final: 0.6077 (mp0) REVERT: R 36 GLU cc_start: 0.8359 (tp30) cc_final: 0.7936 (tp30) REVERT: R 50 ASN cc_start: 0.8483 (p0) cc_final: 0.8265 (p0) REVERT: R 52 THR cc_start: 0.8775 (m) cc_final: 0.8309 (t) REVERT: R 63 GLU cc_start: 0.8750 (tt0) cc_final: 0.8249 (mm-30) REVERT: R 76 TYR cc_start: 0.8508 (p90) cc_final: 0.8153 (p90) REVERT: R 89 ARG cc_start: 0.9107 (ttt180) cc_final: 0.8596 (ttt180) REVERT: S 48 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6632 (tm-30) REVERT: S 78 GLU cc_start: 0.8487 (pt0) cc_final: 0.8013 (pt0) REVERT: S 100 THR cc_start: 0.8960 (p) cc_final: 0.8723 (p) REVERT: S 102 HIS cc_start: 0.7881 (m170) cc_final: 0.7403 (m-70) REVERT: T 56 ILE cc_start: 0.9067 (mt) cc_final: 0.8682 (tt) REVERT: U 5 LYS cc_start: 0.8248 (ttpt) cc_final: 0.8003 (tptp) REVERT: U 31 ASP cc_start: 0.8347 (m-30) cc_final: 0.7813 (m-30) REVERT: U 58 ASN cc_start: 0.8405 (m-40) cc_final: 0.8065 (m-40) REVERT: V 28 ARG cc_start: 0.8443 (mmt90) cc_final: 0.7768 (mmt-90) REVERT: V 48 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7537 (mm-40) REVERT: V 49 ARG cc_start: 0.8411 (mmt180) cc_final: 0.7494 (mmt180) REVERT: Z 8 LEU cc_start: 0.9440 (mt) cc_final: 0.9092 (mt) REVERT: Z 9 LYS cc_start: 0.9408 (mmpt) cc_final: 0.8735 (mmtm) REVERT: Z 19 GLN cc_start: 0.8452 (mp10) cc_final: 0.7737 (mp10) REVERT: Z 24 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8315 (tpt170) REVERT: b 27 MET cc_start: 0.8266 (mtm) cc_final: 0.7832 (mtm) REVERT: b 36 MET cc_start: 0.7932 (tmm) cc_final: 0.7418 (tmm) REVERT: b 37 LYS cc_start: 0.8645 (pptt) cc_final: 0.8215 (pptt) REVERT: Y 15 GLU cc_start: 0.7446 (tp30) cc_final: 0.7009 (tp30) REVERT: Y 22 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8264 (mtmt) REVERT: Y 31 GLN cc_start: 0.9371 (mm-40) cc_final: 0.8676 (mm110) REVERT: Y 53 MET cc_start: 0.9268 (mtm) cc_final: 0.9048 (mmp) REVERT: W 15 ARG cc_start: 0.5903 (ttt180) cc_final: 0.5572 (ttt180) REVERT: W 81 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7655 (ttt180) REVERT: W 135 THR cc_start: 0.8613 (t) cc_final: 0.8090 (t) REVERT: W 136 LEU cc_start: 0.9199 (tp) cc_final: 0.8890 (tp) REVERT: W 138 ASN cc_start: 0.8881 (p0) cc_final: 0.8639 (p0) REVERT: W 147 LYS cc_start: 0.7602 (mttt) cc_final: 0.6731 (pttt) REVERT: W 201 ASN cc_start: 0.6262 (t0) cc_final: 0.5647 (m-40) REVERT: W 231 PRO cc_start: 0.7668 (Cg_exo) cc_final: 0.7218 (Cg_exo) REVERT: W 249 MET cc_start: 0.6907 (ptm) cc_final: 0.6645 (ptm) REVERT: W 269 THR cc_start: 0.6796 (t) cc_final: 0.6512 (m) outliers start: 3 outliers final: 2 residues processed: 582 average time/residue: 0.7861 time to fit residues: 787.1224 Evaluate side-chains 443 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 441 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 173 optimal weight: 10.0000 chunk 465 optimal weight: 0.0060 chunk 102 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 429 optimal weight: 0.9990 chunk 239 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 overall best weight: 6.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 129 GLN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 ASN Q 52 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 87845 Z= 0.295 Angle : 0.748 9.177 132342 Z= 0.373 Chirality : 0.040 0.356 17066 Planarity : 0.005 0.063 6406 Dihedral : 26.319 179.151 46042 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.09 % Favored : 90.87 % Rotamer: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 2608 helix: -0.77 (0.19), residues: 662 sheet: -1.59 (0.25), residues: 397 loop : -2.11 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 16 HIS 0.011 0.002 HIS J 41 PHE 0.032 0.002 PHE Q 57 TYR 0.025 0.002 TYR Q 32 ARG 0.012 0.001 ARG P 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 566 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 MET cc_start: 0.8500 (ppp) cc_final: 0.7842 (tmm) REVERT: C 24 ILE cc_start: 0.9306 (mp) cc_final: 0.9008 (mt) REVERT: C 188 CYS cc_start: 0.8211 (m) cc_final: 0.7798 (m) REVERT: C 247 MET cc_start: 0.5725 (ttm) cc_final: 0.5502 (ttm) REVERT: D 150 ASP cc_start: 0.8780 (t70) cc_final: 0.8548 (t70) REVERT: D 152 ASN cc_start: 0.8952 (m-40) cc_final: 0.8429 (m110) REVERT: D 160 LEU cc_start: 0.8876 (tp) cc_final: 0.8640 (tp) REVERT: D 168 GLN cc_start: 0.9191 (mt0) cc_final: 0.8903 (mt0) REVERT: D 201 THR cc_start: 0.8763 (m) cc_final: 0.8509 (p) REVERT: E 35 ASP cc_start: 0.8553 (t70) cc_final: 0.8152 (t0) REVERT: E 158 ASP cc_start: 0.8480 (p0) cc_final: 0.8048 (p0) REVERT: E 165 LEU cc_start: 0.8800 (mm) cc_final: 0.8205 (tp) REVERT: F 8 TYR cc_start: 0.7472 (p90) cc_final: 0.7247 (p90) REVERT: F 63 GLN cc_start: 0.4964 (mm-40) cc_final: 0.4637 (mm-40) REVERT: F 132 ILE cc_start: 0.4438 (pt) cc_final: 0.4106 (pt) REVERT: G 150 ARG cc_start: 0.8020 (ttt-90) cc_final: 0.7453 (tpp80) REVERT: J 50 ASP cc_start: 0.8195 (t70) cc_final: 0.6701 (t70) REVERT: J 81 HIS cc_start: 0.8583 (m-70) cc_final: 0.8209 (m-70) REVERT: J 89 THR cc_start: 0.8911 (m) cc_final: 0.8589 (p) REVERT: J 93 MET cc_start: 0.8719 (ttm) cc_final: 0.8505 (ttm) REVERT: J 102 LEU cc_start: 0.9087 (tp) cc_final: 0.8850 (tp) REVERT: J 110 LEU cc_start: 0.9452 (mt) cc_final: 0.9116 (tp) REVERT: J 121 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8727 (mtmm) REVERT: J 139 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7889 (mp0) REVERT: K 4 GLN cc_start: 0.8857 (tp40) cc_final: 0.8575 (tp-100) REVERT: K 8 LEU cc_start: 0.9525 (tp) cc_final: 0.8813 (tp) REVERT: K 18 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7000 (mt-10) REVERT: K 41 CYS cc_start: 0.7509 (p) cc_final: 0.6948 (m) REVERT: K 66 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8690 (tppp) REVERT: K 89 ASP cc_start: 0.7719 (p0) cc_final: 0.7452 (p0) REVERT: K 112 MET cc_start: 0.8970 (mpp) cc_final: 0.8474 (mpp) REVERT: L 23 ILE cc_start: 0.9330 (mm) cc_final: 0.9122 (tp) REVERT: L 35 HIS cc_start: 0.7854 (m90) cc_final: 0.7333 (m90) REVERT: L 106 ASN cc_start: 0.9024 (m-40) cc_final: 0.7949 (t0) REVERT: N 26 ILE cc_start: 0.9550 (mt) cc_final: 0.9309 (tt) REVERT: O 32 ASN cc_start: 0.7981 (p0) cc_final: 0.7549 (p0) REVERT: O 41 TYR cc_start: 0.7756 (m-80) cc_final: 0.6768 (m-80) REVERT: O 43 GLN cc_start: 0.4759 (mp10) cc_final: 0.4151 (mp10) REVERT: P 74 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7219 (mm-30) REVERT: P 117 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7746 (mtt-85) REVERT: Q 40 MET cc_start: 0.8934 (ttm) cc_final: 0.8472 (ttm) REVERT: Q 49 ASP cc_start: 0.8649 (t0) cc_final: 0.7834 (t0) REVERT: Q 65 ILE cc_start: 0.9551 (mt) cc_final: 0.9348 (mm) REVERT: R 16 GLU cc_start: 0.7864 (tp30) cc_final: 0.7611 (tp30) REVERT: R 31 GLU cc_start: 0.6540 (mp0) cc_final: 0.6281 (mp0) REVERT: R 36 GLU cc_start: 0.8340 (tp30) cc_final: 0.7955 (tp30) REVERT: R 52 THR cc_start: 0.8829 (m) cc_final: 0.8338 (t) REVERT: R 63 GLU cc_start: 0.8918 (tt0) cc_final: 0.8451 (mm-30) REVERT: R 76 TYR cc_start: 0.8612 (p90) cc_final: 0.8351 (p90) REVERT: R 89 ARG cc_start: 0.9042 (ttt180) cc_final: 0.8655 (ttt180) REVERT: S 78 GLU cc_start: 0.8489 (pt0) cc_final: 0.8048 (pt0) REVERT: S 102 HIS cc_start: 0.7876 (m170) cc_final: 0.7496 (m90) REVERT: T 38 GLU cc_start: 0.8550 (tt0) cc_final: 0.8183 (tt0) REVERT: T 56 ILE cc_start: 0.9039 (mt) cc_final: 0.8588 (tt) REVERT: U 5 LYS cc_start: 0.8256 (ttpt) cc_final: 0.7915 (tptp) REVERT: U 10 MET cc_start: 0.8729 (tpp) cc_final: 0.8417 (tpp) REVERT: U 31 ASP cc_start: 0.8359 (m-30) cc_final: 0.7822 (m-30) REVERT: U 58 ASN cc_start: 0.8371 (m-40) cc_final: 0.7918 (m-40) REVERT: V 28 ARG cc_start: 0.8434 (mmt90) cc_final: 0.7767 (mmt-90) REVERT: V 49 ARG cc_start: 0.8433 (mmt180) cc_final: 0.7417 (mmt180) REVERT: Z 9 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9161 (mmmm) REVERT: Z 19 GLN cc_start: 0.8443 (mp10) cc_final: 0.7910 (mp10) REVERT: Z 24 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8358 (tpt90) REVERT: b 27 MET cc_start: 0.8284 (mtm) cc_final: 0.7842 (mtm) REVERT: b 37 LYS cc_start: 0.8637 (pptt) cc_final: 0.8272 (pptt) REVERT: Y 15 GLU cc_start: 0.7099 (tp30) cc_final: 0.6631 (tp30) REVERT: Y 31 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8690 (mm110) REVERT: W 15 ARG cc_start: 0.5813 (ttt180) cc_final: 0.5514 (ttt180) REVERT: W 81 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7512 (ttt180) REVERT: W 135 THR cc_start: 0.8604 (t) cc_final: 0.8172 (t) REVERT: W 136 LEU cc_start: 0.9234 (tp) cc_final: 0.8991 (tp) REVERT: W 138 ASN cc_start: 0.8845 (p0) cc_final: 0.8564 (p0) REVERT: W 147 LYS cc_start: 0.7530 (mttt) cc_final: 0.6688 (pttt) REVERT: W 201 ASN cc_start: 0.6192 (t0) cc_final: 0.5593 (m-40) REVERT: W 249 MET cc_start: 0.6972 (ptm) cc_final: 0.6687 (ptm) REVERT: W 269 THR cc_start: 0.6902 (t) cc_final: 0.6571 (m) outliers start: 2 outliers final: 0 residues processed: 567 average time/residue: 0.8289 time to fit residues: 814.4286 Evaluate side-chains 432 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 499 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 435 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 515 optimal weight: 30.0000 chunk 322 optimal weight: 0.2980 chunk 314 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 overall best weight: 5.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 129 GLN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 ASN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 87845 Z= 0.276 Angle : 0.731 9.179 132342 Z= 0.365 Chirality : 0.039 0.339 17066 Planarity : 0.005 0.070 6406 Dihedral : 26.287 179.184 46042 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.05 % Favored : 90.91 % Rotamer: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 2608 helix: -0.71 (0.19), residues: 670 sheet: -1.64 (0.25), residues: 388 loop : -2.06 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP W 71 HIS 0.013 0.002 HIS J 54 PHE 0.022 0.002 PHE S 75 TYR 0.019 0.002 TYR Q 24 ARG 0.011 0.001 ARG J 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 556 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.9300 (mp) cc_final: 0.9000 (mt) REVERT: C 188 CYS cc_start: 0.8190 (m) cc_final: 0.7905 (m) REVERT: C 247 MET cc_start: 0.5709 (ttm) cc_final: 0.5462 (ttm) REVERT: D 133 MET cc_start: 0.7427 (tpt) cc_final: 0.7156 (tpp) REVERT: D 152 ASN cc_start: 0.8963 (m-40) cc_final: 0.8443 (m110) REVERT: D 160 LEU cc_start: 0.8883 (tp) cc_final: 0.8612 (tp) REVERT: D 168 GLN cc_start: 0.9227 (mt0) cc_final: 0.8941 (pt0) REVERT: D 201 THR cc_start: 0.8750 (m) cc_final: 0.8486 (p) REVERT: E 35 ASP cc_start: 0.8479 (t70) cc_final: 0.8082 (t0) REVERT: E 39 MET cc_start: 0.8809 (tmm) cc_final: 0.8606 (tmm) REVERT: E 158 ASP cc_start: 0.8465 (p0) cc_final: 0.8015 (p0) REVERT: E 165 LEU cc_start: 0.8766 (mm) cc_final: 0.8140 (tp) REVERT: F 63 GLN cc_start: 0.4664 (mm-40) cc_final: 0.4247 (mt0) REVERT: F 89 VAL cc_start: 0.7572 (t) cc_final: 0.7336 (t) REVERT: J 16 TRP cc_start: 0.7298 (m100) cc_final: 0.6838 (m100) REVERT: J 33 VAL cc_start: 0.9752 (t) cc_final: 0.9548 (p) REVERT: J 89 THR cc_start: 0.8925 (m) cc_final: 0.8586 (p) REVERT: J 102 LEU cc_start: 0.9070 (tp) cc_final: 0.8851 (tp) REVERT: J 110 LEU cc_start: 0.9451 (mt) cc_final: 0.9145 (tp) REVERT: J 121 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8703 (mtmm) REVERT: J 139 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7915 (mp0) REVERT: K 4 GLN cc_start: 0.8830 (tp40) cc_final: 0.8540 (tp-100) REVERT: K 8 LEU cc_start: 0.9330 (tp) cc_final: 0.8685 (tp) REVERT: K 18 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6980 (mt-10) REVERT: K 41 CYS cc_start: 0.7444 (p) cc_final: 0.6949 (m) REVERT: K 66 LYS cc_start: 0.9144 (ttmm) cc_final: 0.8657 (tppp) REVERT: K 89 ASP cc_start: 0.7718 (p0) cc_final: 0.7432 (p0) REVERT: K 112 MET cc_start: 0.8956 (mpp) cc_final: 0.8455 (mpp) REVERT: L 6 LEU cc_start: 0.7938 (tp) cc_final: 0.7678 (tp) REVERT: L 36 LYS cc_start: 0.8546 (mmtm) cc_final: 0.7344 (pttp) REVERT: L 106 ASN cc_start: 0.9005 (m-40) cc_final: 0.8040 (t0) REVERT: N 21 THR cc_start: 0.9281 (t) cc_final: 0.9074 (t) REVERT: N 26 ILE cc_start: 0.9541 (mt) cc_final: 0.9268 (tt) REVERT: N 102 MET cc_start: 0.7824 (mmm) cc_final: 0.7540 (tpp) REVERT: N 114 MET cc_start: 0.7946 (tpt) cc_final: 0.7443 (tpp) REVERT: O 41 TYR cc_start: 0.7609 (m-80) cc_final: 0.6789 (m-80) REVERT: O 43 GLN cc_start: 0.4760 (mp10) cc_final: 0.4059 (mp10) REVERT: P 74 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7538 (mm-30) REVERT: Q 40 MET cc_start: 0.8887 (ttm) cc_final: 0.8319 (ttm) REVERT: Q 49 ASP cc_start: 0.8597 (t0) cc_final: 0.7921 (t70) REVERT: Q 65 ILE cc_start: 0.9496 (mt) cc_final: 0.9258 (mm) REVERT: R 16 GLU cc_start: 0.7883 (tp30) cc_final: 0.7274 (tp30) REVERT: R 31 GLU cc_start: 0.6634 (mp0) cc_final: 0.6384 (mp0) REVERT: R 36 GLU cc_start: 0.8451 (tp30) cc_final: 0.8088 (tp30) REVERT: R 52 THR cc_start: 0.8652 (m) cc_final: 0.8266 (t) REVERT: R 63 GLU cc_start: 0.8949 (tt0) cc_final: 0.8465 (mm-30) REVERT: R 76 TYR cc_start: 0.8572 (p90) cc_final: 0.8309 (p90) REVERT: R 89 ARG cc_start: 0.9177 (ttt180) cc_final: 0.8724 (ttt180) REVERT: S 78 GLU cc_start: 0.8486 (pt0) cc_final: 0.8036 (pt0) REVERT: S 102 HIS cc_start: 0.8079 (m170) cc_final: 0.7494 (m-70) REVERT: T 56 ILE cc_start: 0.9036 (mt) cc_final: 0.8629 (tt) REVERT: U 10 MET cc_start: 0.8625 (tpp) cc_final: 0.8369 (tpp) REVERT: U 31 ASP cc_start: 0.8414 (m-30) cc_final: 0.7993 (m-30) REVERT: U 58 ASN cc_start: 0.8409 (m-40) cc_final: 0.7992 (m-40) REVERT: V 28 ARG cc_start: 0.8420 (mmt90) cc_final: 0.7734 (mmt-90) REVERT: V 49 ARG cc_start: 0.8624 (mmt180) cc_final: 0.7551 (mmt180) REVERT: Z 9 LYS cc_start: 0.9358 (mmpt) cc_final: 0.9081 (mmmm) REVERT: Z 19 GLN cc_start: 0.8494 (mp10) cc_final: 0.7945 (mp10) REVERT: Z 24 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8348 (tpt90) REVERT: Z 38 GLU cc_start: 0.8433 (pt0) cc_final: 0.8198 (pm20) REVERT: b 28 THR cc_start: 0.8159 (p) cc_final: 0.7736 (p) REVERT: b 37 LYS cc_start: 0.8541 (pptt) cc_final: 0.7698 (pptt) REVERT: Y 15 GLU cc_start: 0.6935 (tp30) cc_final: 0.6539 (tp30) REVERT: Y 31 GLN cc_start: 0.9358 (mm-40) cc_final: 0.8679 (mm110) REVERT: W 15 ARG cc_start: 0.5835 (ttt180) cc_final: 0.5551 (ttt180) REVERT: W 81 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7378 (ttt180) REVERT: W 135 THR cc_start: 0.8639 (t) cc_final: 0.8274 (t) REVERT: W 147 LYS cc_start: 0.7487 (mttt) cc_final: 0.6692 (pttt) REVERT: W 201 ASN cc_start: 0.6304 (t0) cc_final: 0.5632 (m-40) REVERT: W 249 MET cc_start: 0.6924 (ptm) cc_final: 0.6652 (ptm) REVERT: W 269 THR cc_start: 0.6785 (t) cc_final: 0.6504 (m) outliers start: 1 outliers final: 0 residues processed: 556 average time/residue: 0.7645 time to fit residues: 731.5243 Evaluate side-chains 429 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 319 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 307 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 351 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 405 optimal weight: 0.9980 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 129 GLN J 96 ASN N 12 GLN P 32 HIS ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 87845 Z= 0.206 Angle : 0.668 9.303 132342 Z= 0.336 Chirality : 0.037 0.351 17066 Planarity : 0.005 0.065 6406 Dihedral : 26.146 179.324 46042 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.28 % Favored : 91.68 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2608 helix: -0.54 (0.20), residues: 673 sheet: -1.61 (0.25), residues: 387 loop : -1.91 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 83 HIS 0.010 0.001 HIS J 54 PHE 0.026 0.002 PHE Q 57 TYR 0.014 0.002 TYR Q 32 ARG 0.004 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 570 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.9318 (mp) cc_final: 0.8996 (mt) REVERT: C 188 CYS cc_start: 0.8080 (m) cc_final: 0.7830 (m) REVERT: C 247 MET cc_start: 0.5622 (ttm) cc_final: 0.5361 (ttm) REVERT: D 133 MET cc_start: 0.7316 (tpt) cc_final: 0.7056 (tpp) REVERT: D 150 ASP cc_start: 0.8558 (t70) cc_final: 0.8355 (t70) REVERT: D 152 ASN cc_start: 0.8849 (m-40) cc_final: 0.8314 (m110) REVERT: D 160 LEU cc_start: 0.8831 (tp) cc_final: 0.8599 (tp) REVERT: D 168 GLN cc_start: 0.9202 (mt0) cc_final: 0.8756 (pt0) REVERT: D 170 THR cc_start: 0.9031 (m) cc_final: 0.8487 (p) REVERT: D 201 THR cc_start: 0.8797 (m) cc_final: 0.8283 (p) REVERT: E 35 ASP cc_start: 0.8564 (t70) cc_final: 0.7993 (t0) REVERT: E 39 MET cc_start: 0.8801 (tmm) cc_final: 0.8559 (tmm) REVERT: E 158 ASP cc_start: 0.8409 (p0) cc_final: 0.7945 (p0) REVERT: E 165 LEU cc_start: 0.8694 (mm) cc_final: 0.8081 (tp) REVERT: F 63 GLN cc_start: 0.4681 (mm-40) cc_final: 0.4118 (mm-40) REVERT: G 132 VAL cc_start: 0.5916 (t) cc_final: 0.5607 (t) REVERT: J 20 ASP cc_start: 0.8233 (t70) cc_final: 0.7992 (t0) REVERT: J 33 VAL cc_start: 0.9713 (t) cc_final: 0.9504 (p) REVERT: J 89 THR cc_start: 0.8898 (m) cc_final: 0.8648 (p) REVERT: J 102 LEU cc_start: 0.9028 (tp) cc_final: 0.8774 (tp) REVERT: J 110 LEU cc_start: 0.9421 (mt) cc_final: 0.9110 (tp) REVERT: J 139 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7988 (mp0) REVERT: J 144 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7697 (mmt180) REVERT: K 4 GLN cc_start: 0.8843 (tp40) cc_final: 0.8553 (tp-100) REVERT: K 8 LEU cc_start: 0.9283 (tp) cc_final: 0.8606 (tp) REVERT: K 18 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7110 (mt-10) REVERT: K 41 CYS cc_start: 0.7393 (p) cc_final: 0.6995 (m) REVERT: K 66 LYS cc_start: 0.9111 (ttmm) cc_final: 0.8615 (tppp) REVERT: K 89 ASP cc_start: 0.7812 (p0) cc_final: 0.7517 (p0) REVERT: K 112 MET cc_start: 0.8883 (mpp) cc_final: 0.8389 (mpp) REVERT: L 25 SER cc_start: 0.9252 (p) cc_final: 0.8747 (t) REVERT: L 36 LYS cc_start: 0.8634 (mmtm) cc_final: 0.7368 (pttp) REVERT: L 106 ASN cc_start: 0.9026 (m-40) cc_final: 0.7962 (t0) REVERT: N 16 MET cc_start: 0.9009 (ttm) cc_final: 0.6724 (ttm) REVERT: N 114 MET cc_start: 0.7624 (tpt) cc_final: 0.7273 (tpp) REVERT: O 32 ASN cc_start: 0.7816 (p0) cc_final: 0.7349 (p0) REVERT: O 41 TYR cc_start: 0.7620 (m-80) cc_final: 0.6560 (m-80) REVERT: O 43 GLN cc_start: 0.5629 (mp10) cc_final: 0.5304 (mp10) REVERT: P 74 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7523 (mm-30) REVERT: P 102 TYR cc_start: 0.9023 (p90) cc_final: 0.8389 (p90) REVERT: P 105 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8607 (mm-30) REVERT: Q 40 MET cc_start: 0.8751 (ttm) cc_final: 0.8258 (ttm) REVERT: Q 49 ASP cc_start: 0.8539 (t0) cc_final: 0.7774 (t70) REVERT: R 16 GLU cc_start: 0.8047 (tp30) cc_final: 0.7481 (tp30) REVERT: R 31 GLU cc_start: 0.6656 (mp0) cc_final: 0.6385 (mp0) REVERT: R 36 GLU cc_start: 0.8418 (tp30) cc_final: 0.8188 (tp30) REVERT: R 52 THR cc_start: 0.8532 (m) cc_final: 0.8166 (t) REVERT: R 63 GLU cc_start: 0.8916 (tt0) cc_final: 0.8376 (mm-30) REVERT: R 76 TYR cc_start: 0.8490 (p90) cc_final: 0.8251 (p90) REVERT: S 68 ASN cc_start: 0.8554 (m-40) cc_final: 0.8199 (t0) REVERT: S 78 GLU cc_start: 0.8384 (pt0) cc_final: 0.7935 (pt0) REVERT: S 102 HIS cc_start: 0.8070 (m170) cc_final: 0.7460 (m-70) REVERT: T 20 LEU cc_start: 0.8734 (mt) cc_final: 0.8473 (mt) REVERT: T 35 ASN cc_start: 0.9178 (m-40) cc_final: 0.8955 (m-40) REVERT: T 56 ILE cc_start: 0.8940 (mt) cc_final: 0.8563 (tt) REVERT: U 10 MET cc_start: 0.8586 (tpp) cc_final: 0.8377 (tpp) REVERT: U 31 ASP cc_start: 0.8312 (m-30) cc_final: 0.7909 (t0) REVERT: U 58 ASN cc_start: 0.8557 (m-40) cc_final: 0.7830 (m-40) REVERT: U 64 HIS cc_start: 0.8262 (t-90) cc_final: 0.7663 (t-90) REVERT: U 69 MET cc_start: 0.8446 (ttm) cc_final: 0.7610 (ttt) REVERT: V 28 ARG cc_start: 0.8435 (mmt90) cc_final: 0.7760 (mmt-90) REVERT: V 49 ARG cc_start: 0.8594 (mmt180) cc_final: 0.7554 (mmt180) REVERT: V 78 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7886 (mm-30) REVERT: Z 6 ILE cc_start: 0.8392 (tt) cc_final: 0.7983 (tt) REVERT: Z 9 LYS cc_start: 0.9243 (mmpt) cc_final: 0.8976 (mmmm) REVERT: Z 19 GLN cc_start: 0.8448 (mp10) cc_final: 0.8099 (mp10) REVERT: Z 24 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8419 (tpt90) REVERT: Y 29 ARG cc_start: 0.9089 (mtt180) cc_final: 0.8750 (tpp80) REVERT: Y 31 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8602 (mm110) REVERT: W 15 ARG cc_start: 0.5984 (ttt180) cc_final: 0.5712 (ttt180) REVERT: W 81 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7522 (ttt180) REVERT: W 138 ASN cc_start: 0.8999 (p0) cc_final: 0.8719 (p0) REVERT: W 147 LYS cc_start: 0.7440 (mttt) cc_final: 0.6719 (pttt) REVERT: W 201 ASN cc_start: 0.5975 (t0) cc_final: 0.5438 (m-40) REVERT: W 249 MET cc_start: 0.6899 (ptm) cc_final: 0.6617 (ptm) REVERT: W 269 THR cc_start: 0.6735 (t) cc_final: 0.6405 (m) REVERT: W 271 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7586 (mtpt) outliers start: 1 outliers final: 0 residues processed: 571 average time/residue: 0.7902 time to fit residues: 771.1143 Evaluate side-chains 436 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 469 optimal weight: 30.0000 chunk 494 optimal weight: 8.9990 chunk 450 optimal weight: 3.9990 chunk 480 optimal weight: 0.1980 chunk 493 optimal weight: 20.0000 chunk 289 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 434 optimal weight: 0.3980 chunk 454 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN D 33 ASN D 50 GLN E 40 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 87845 Z= 0.156 Angle : 0.622 9.411 132342 Z= 0.313 Chirality : 0.035 0.337 17066 Planarity : 0.004 0.061 6406 Dihedral : 25.948 179.286 46042 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2608 helix: -0.40 (0.20), residues: 671 sheet: -1.42 (0.25), residues: 391 loop : -1.81 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP Q 61 HIS 0.009 0.001 HIS P 32 PHE 0.042 0.002 PHE V 80 TYR 0.043 0.002 TYR O 102 ARG 0.008 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.9257 (mp) cc_final: 0.8854 (mt) REVERT: C 156 ARG cc_start: 0.8605 (ttm170) cc_final: 0.8204 (ttm170) REVERT: C 203 ILE cc_start: 0.9065 (mt) cc_final: 0.8857 (mt) REVERT: C 247 MET cc_start: 0.5586 (ttm) cc_final: 0.5134 (ttm) REVERT: D 133 MET cc_start: 0.7282 (tpt) cc_final: 0.7015 (tpp) REVERT: D 153 ARG cc_start: 0.8247 (ptt90) cc_final: 0.6252 (ptt90) REVERT: D 154 VAL cc_start: 0.9208 (t) cc_final: 0.8887 (p) REVERT: D 160 LEU cc_start: 0.8802 (tp) cc_final: 0.8556 (tp) REVERT: D 168 GLN cc_start: 0.9243 (mt0) cc_final: 0.8772 (pt0) REVERT: D 170 THR cc_start: 0.9066 (m) cc_final: 0.8758 (p) REVERT: E 35 ASP cc_start: 0.8611 (t70) cc_final: 0.8180 (t0) REVERT: E 39 MET cc_start: 0.8845 (tmm) cc_final: 0.8558 (tmm) REVERT: E 83 TRP cc_start: 0.9213 (m-10) cc_final: 0.8932 (m-10) REVERT: E 161 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7692 (pm20) REVERT: E 165 LEU cc_start: 0.8641 (mm) cc_final: 0.7739 (tp) REVERT: F 83 MET cc_start: 0.4861 (pmm) cc_final: 0.4527 (pmm) REVERT: G 78 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6147 (tp30) REVERT: G 150 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7480 (ttm-80) REVERT: J 89 THR cc_start: 0.8815 (m) cc_final: 0.8542 (p) REVERT: J 110 LEU cc_start: 0.9306 (mt) cc_final: 0.9060 (mt) REVERT: J 121 LYS cc_start: 0.8763 (mtmt) cc_final: 0.7858 (mttt) REVERT: J 139 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7980 (mp0) REVERT: J 144 ARG cc_start: 0.8203 (mmt180) cc_final: 0.7654 (mmt180) REVERT: K 4 GLN cc_start: 0.8834 (tp40) cc_final: 0.8559 (tp-100) REVERT: K 8 LEU cc_start: 0.9288 (tp) cc_final: 0.8632 (tp) REVERT: K 18 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6985 (mt-10) REVERT: K 41 CYS cc_start: 0.7522 (p) cc_final: 0.7174 (m) REVERT: K 66 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8596 (ttmt) REVERT: K 91 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7781 (mmmt) REVERT: K 112 MET cc_start: 0.8794 (mpp) cc_final: 0.8274 (mpp) REVERT: L 25 SER cc_start: 0.9224 (p) cc_final: 0.8715 (t) REVERT: L 36 LYS cc_start: 0.8535 (mmtm) cc_final: 0.7420 (pttp) REVERT: N 48 ILE cc_start: 0.9611 (mm) cc_final: 0.9102 (mm) REVERT: N 91 TYR cc_start: 0.8393 (m-80) cc_final: 0.7428 (m-80) REVERT: N 102 MET cc_start: 0.7871 (mmm) cc_final: 0.7520 (tpt) REVERT: N 114 MET cc_start: 0.7656 (tpt) cc_final: 0.7275 (tpp) REVERT: O 102 TYR cc_start: 0.6356 (t80) cc_final: 0.4878 (t80) REVERT: O 107 LYS cc_start: 0.9139 (tttm) cc_final: 0.8666 (tptp) REVERT: P 102 TYR cc_start: 0.8951 (p90) cc_final: 0.8309 (p90) REVERT: Q 32 TYR cc_start: 0.9042 (t80) cc_final: 0.8644 (t80) REVERT: Q 40 MET cc_start: 0.8685 (ttm) cc_final: 0.8227 (ttm) REVERT: Q 49 ASP cc_start: 0.8399 (t0) cc_final: 0.7542 (t70) REVERT: Q 61 TRP cc_start: 0.8278 (m-10) cc_final: 0.8076 (m-10) REVERT: R 16 GLU cc_start: 0.8078 (tp30) cc_final: 0.7771 (tp30) REVERT: R 31 GLU cc_start: 0.6750 (mp0) cc_final: 0.6439 (mp0) REVERT: R 36 GLU cc_start: 0.8403 (tp30) cc_final: 0.8176 (tp30) REVERT: R 52 THR cc_start: 0.8476 (m) cc_final: 0.8094 (t) REVERT: R 63 GLU cc_start: 0.8866 (tt0) cc_final: 0.8377 (mm-30) REVERT: R 89 ARG cc_start: 0.9020 (ttt180) cc_final: 0.8688 (ttt-90) REVERT: S 31 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7641 (tp30) REVERT: S 48 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6340 (tm-30) REVERT: S 68 ASN cc_start: 0.8415 (m-40) cc_final: 0.8194 (t0) REVERT: S 78 GLU cc_start: 0.8421 (pt0) cc_final: 0.7965 (pt0) REVERT: S 102 HIS cc_start: 0.7812 (m170) cc_final: 0.7276 (m-70) REVERT: T 56 ILE cc_start: 0.8828 (mt) cc_final: 0.8511 (tt) REVERT: U 31 ASP cc_start: 0.8192 (m-30) cc_final: 0.7868 (t0) REVERT: U 64 HIS cc_start: 0.8227 (t-90) cc_final: 0.7581 (t-90) REVERT: V 28 ARG cc_start: 0.8356 (mmt90) cc_final: 0.7705 (mmt-90) REVERT: V 48 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7345 (mm-40) REVERT: V 49 ARG cc_start: 0.8440 (mmt180) cc_final: 0.7531 (mmt180) REVERT: Z 6 ILE cc_start: 0.8509 (tt) cc_final: 0.8066 (tp) REVERT: Z 9 LYS cc_start: 0.9305 (mmpt) cc_final: 0.9095 (mmmt) REVERT: Z 19 GLN cc_start: 0.8290 (mp10) cc_final: 0.7891 (mp10) REVERT: b 27 MET cc_start: 0.8132 (mtm) cc_final: 0.7925 (mtp) REVERT: b 37 LYS cc_start: 0.8139 (pptt) cc_final: 0.7723 (pptt) REVERT: Y 29 ARG cc_start: 0.8991 (mtt180) cc_final: 0.8500 (tpp80) REVERT: Y 31 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8759 (mm110) REVERT: W 15 ARG cc_start: 0.5881 (ttt180) cc_final: 0.5618 (ttt180) REVERT: W 81 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7524 (ttt180) REVERT: W 138 ASN cc_start: 0.8979 (p0) cc_final: 0.8777 (p0) REVERT: W 147 LYS cc_start: 0.7380 (mttt) cc_final: 0.6740 (pttt) REVERT: W 201 ASN cc_start: 0.5904 (t0) cc_final: 0.5305 (m-40) REVERT: W 223 GLU cc_start: 0.8569 (tp30) cc_final: 0.7956 (mp0) REVERT: W 269 THR cc_start: 0.6672 (t) cc_final: 0.6331 (m) REVERT: W 271 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7535 (mtpt) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.8011 time to fit residues: 781.4308 Evaluate side-chains 442 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 478 optimal weight: 20.0000 chunk 315 optimal weight: 9.9990 chunk 508 optimal weight: 7.9990 chunk 310 optimal weight: 0.0470 chunk 241 optimal weight: 30.0000 chunk 353 optimal weight: 40.0000 chunk 532 optimal weight: 6.9990 chunk 490 optimal weight: 10.0000 chunk 424 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 327 optimal weight: 8.9990 overall best weight: 6.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN N 12 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 87845 Z= 0.309 Angle : 0.748 8.996 132342 Z= 0.371 Chirality : 0.039 0.353 17066 Planarity : 0.005 0.059 6406 Dihedral : 26.125 178.719 46042 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.16), residues: 2608 helix: -0.67 (0.19), residues: 681 sheet: -1.48 (0.26), residues: 387 loop : -1.92 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP J 16 HIS 0.038 0.002 HIS J 54 PHE 0.033 0.002 PHE Q 57 TYR 0.029 0.002 TYR O 102 ARG 0.008 0.001 ARG N 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 526 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ILE cc_start: 0.9293 (mp) cc_final: 0.9011 (mt) REVERT: C 156 ARG cc_start: 0.8692 (ttm170) cc_final: 0.7969 (ttp80) REVERT: C 188 CYS cc_start: 0.8128 (m) cc_final: 0.7845 (m) REVERT: C 247 MET cc_start: 0.5775 (ttm) cc_final: 0.5511 (ttm) REVERT: D 133 MET cc_start: 0.7602 (tpt) cc_final: 0.7259 (tpp) REVERT: D 152 ASN cc_start: 0.9033 (m-40) cc_final: 0.8547 (m-40) REVERT: D 153 ARG cc_start: 0.8435 (ptt90) cc_final: 0.6441 (ptt90) REVERT: D 160 LEU cc_start: 0.8812 (tp) cc_final: 0.8575 (tp) REVERT: D 168 GLN cc_start: 0.9198 (mt0) cc_final: 0.8791 (pt0) REVERT: D 170 THR cc_start: 0.9055 (m) cc_final: 0.8621 (p) REVERT: E 35 ASP cc_start: 0.8510 (t70) cc_final: 0.8012 (t0) REVERT: E 39 MET cc_start: 0.8852 (tmm) cc_final: 0.8645 (tmm) REVERT: E 158 ASP cc_start: 0.8393 (p0) cc_final: 0.7918 (p0) REVERT: E 161 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7861 (pm20) REVERT: E 165 LEU cc_start: 0.8742 (mm) cc_final: 0.7888 (tp) REVERT: F 83 MET cc_start: 0.5474 (pmm) cc_final: 0.5270 (pmm) REVERT: F 153 ASP cc_start: 0.1952 (t0) cc_final: 0.1714 (t70) REVERT: G 78 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6019 (tp30) REVERT: J 6 MET cc_start: 0.8683 (mpp) cc_final: 0.8479 (mpp) REVERT: J 50 ASP cc_start: 0.8239 (t70) cc_final: 0.6881 (t70) REVERT: J 89 THR cc_start: 0.8887 (m) cc_final: 0.8657 (p) REVERT: J 99 GLU cc_start: 0.9095 (mp0) cc_final: 0.8798 (mp0) REVERT: J 102 LEU cc_start: 0.9032 (tp) cc_final: 0.8765 (tp) REVERT: J 103 GLU cc_start: 0.8503 (tt0) cc_final: 0.8009 (tp30) REVERT: J 110 LEU cc_start: 0.9372 (mt) cc_final: 0.9135 (tp) REVERT: J 121 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8247 (pttm) REVERT: J 139 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7992 (mp0) REVERT: K 4 GLN cc_start: 0.8834 (tp40) cc_final: 0.8545 (tp-100) REVERT: K 8 LEU cc_start: 0.9338 (tp) cc_final: 0.8728 (tp) REVERT: K 18 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7325 (mt-10) REVERT: K 41 CYS cc_start: 0.7698 (p) cc_final: 0.7261 (m) REVERT: K 66 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8700 (ttmt) REVERT: K 91 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8018 (mmtm) REVERT: L 25 SER cc_start: 0.9323 (p) cc_final: 0.8962 (t) REVERT: L 36 LYS cc_start: 0.8562 (mmtm) cc_final: 0.7348 (pttp) REVERT: L 106 ASN cc_start: 0.9078 (m-40) cc_final: 0.7833 (t0) REVERT: N 48 ILE cc_start: 0.9402 (mm) cc_final: 0.9020 (mm) REVERT: O 41 TYR cc_start: 0.7943 (m-80) cc_final: 0.7395 (m-80) REVERT: O 95 PHE cc_start: 0.8573 (t80) cc_final: 0.7697 (t80) REVERT: Q 40 MET cc_start: 0.8854 (ttm) cc_final: 0.8325 (ttp) REVERT: Q 49 ASP cc_start: 0.8685 (t0) cc_final: 0.7922 (t70) REVERT: Q 80 MET cc_start: 0.8464 (mtp) cc_final: 0.8081 (mtp) REVERT: R 16 GLU cc_start: 0.8057 (tp30) cc_final: 0.7801 (tp30) REVERT: R 31 GLU cc_start: 0.6778 (mp0) cc_final: 0.6439 (mp0) REVERT: R 36 GLU cc_start: 0.8444 (tp30) cc_final: 0.8223 (tp30) REVERT: R 52 THR cc_start: 0.8521 (m) cc_final: 0.8167 (t) REVERT: R 63 GLU cc_start: 0.8756 (tt0) cc_final: 0.8240 (mm-30) REVERT: S 48 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6543 (tm-30) REVERT: S 78 GLU cc_start: 0.8382 (pt0) cc_final: 0.7941 (pt0) REVERT: S 102 HIS cc_start: 0.8079 (m170) cc_final: 0.7256 (m170) REVERT: T 56 ILE cc_start: 0.9007 (mt) cc_final: 0.8633 (tt) REVERT: U 31 ASP cc_start: 0.8384 (m-30) cc_final: 0.7924 (m-30) REVERT: U 34 LEU cc_start: 0.8854 (mm) cc_final: 0.8608 (mm) REVERT: U 58 ASN cc_start: 0.8517 (m-40) cc_final: 0.8046 (m-40) REVERT: U 69 MET cc_start: 0.8589 (ttp) cc_final: 0.8288 (ptp) REVERT: V 28 ARG cc_start: 0.8353 (mmt90) cc_final: 0.7799 (mmt-90) REVERT: V 49 ARG cc_start: 0.8646 (mmt180) cc_final: 0.7559 (mmt180) REVERT: Z 6 ILE cc_start: 0.8529 (tt) cc_final: 0.8237 (tp) REVERT: Z 9 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8971 (mmmt) REVERT: Z 19 GLN cc_start: 0.8432 (mp10) cc_final: 0.8004 (mp10) REVERT: Z 29 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8044 (mtmt) REVERT: Y 22 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8572 (mtmt) REVERT: Y 29 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8656 (tpp80) REVERT: Y 31 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8731 (mm110) REVERT: Y 53 MET cc_start: 0.9056 (mmp) cc_final: 0.8788 (mmp) REVERT: W 15 ARG cc_start: 0.6151 (ttt180) cc_final: 0.5891 (ttt180) REVERT: W 81 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7376 (ttt180) REVERT: W 147 LYS cc_start: 0.7450 (mttt) cc_final: 0.6839 (pttt) REVERT: W 201 ASN cc_start: 0.6117 (t0) cc_final: 0.5544 (m-40) REVERT: W 269 THR cc_start: 0.6737 (t) cc_final: 0.6411 (m) REVERT: W 271 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7609 (mtpt) outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.7828 time to fit residues: 711.8002 Evaluate side-chains 421 residues out of total 2242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 260 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 452 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 425 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 436 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** J 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059528 restraints weight = 349452.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.061029 restraints weight = 131558.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061919 restraints weight = 74540.256| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 87845 Z= 0.261 Angle : 0.705 9.155 132342 Z= 0.353 Chirality : 0.038 0.353 17066 Planarity : 0.005 0.056 6406 Dihedral : 26.117 178.959 46042 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.74 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2608 helix: -0.68 (0.19), residues: 680 sheet: -1.48 (0.26), residues: 394 loop : -1.89 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP J 16 HIS 0.026 0.002 HIS J 54 PHE 0.028 0.002 PHE Q 57 TYR 0.035 0.002 TYR O 102 ARG 0.006 0.001 ARG J 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13599.60 seconds wall clock time: 242 minutes 7.76 seconds (14527.76 seconds total)