Starting phenix.real_space_refine (version: dev) on Thu Apr 7 16:05:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqq_22441/04_2022/7jqq_22441_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 28416 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2698 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 315} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna3p_pur': 43, 'rna2p_pyr': 7, 'rna3p_pyr': 55} Link IDs: {'rna3p': 99, 'rna2p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 47, 'rna2p_pyr': 6, 'rna3p_pyr': 56} Link IDs: {'rna3p': 103, 'rna2p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 47, 'rna2p_pyr': 5, 'rna3p_pyr': 57} Link IDs: {'rna3p': 104, 'rna2p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 48, 'rna2p_pyr': 5, 'rna3p_pyr': 57} Link IDs: {'rna3p': 105, 'rna2p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "O" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2474 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 47, 'rna2p_pyr': 9, 'rna3p_pyr': 53} Link IDs: {'rna3p': 101, 'rna2p': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.75, per 1000 atoms: 0.55 Number of scatterers: 28416 At special positions: 0 Unit cell: (146.59, 150.87, 218.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 709 15.00 Mg 3 11.99 O 7351 8.00 N 4880 7.00 C 15415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.12 Conformation dependent library (CDL) restraints added in 2.1 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 16 sheets defined 33.1% alpha, 12.1% beta 251 base pairs and 313 stacking pairs defined. Time for finding SS restraints: 12.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 32 through 43 Proline residue: A 38 - end of helix Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.892A pdb=" N TYR A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 4.056A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.759A pdb=" N HIS A 298 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.527A pdb=" N TYR B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 60 through 64 removed outlier: 4.146A pdb=" N ASN B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 208 through 215 removed outlier: 4.122A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.774A pdb=" N ASN B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.191A pdb=" N TYR C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.706A pdb=" N TYR C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 38 - end of helix removed outlier: 3.939A pdb=" N LYS C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.105A pdb=" N VAL C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 69 " --> pdb=" O TYR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.483A pdb=" N ARG C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 300 through 307 Processing helix chain 'C' and resid 316 through 329 Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.949A pdb=" N TYR D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Proline residue: D 38 - end of helix Processing helix chain 'D' and resid 57 through 60 removed outlier: 4.001A pdb=" N ALA D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 69 through 72 No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 197 through 206 removed outlier: 4.622A pdb=" N LYS D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.920A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 28 through 45 removed outlier: 4.269A pdb=" N TYR E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.564A pdb=" N ALA E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.955A pdb=" N ALA E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLN E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 105 No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'E' and resid 133 through 144 removed outlier: 4.355A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.163A pdb=" N THR E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 204 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'E' and resid 317 through 327 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.487A pdb=" N CYS A 153 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 22 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N CYS A 155 " --> pdb=" O VAL A 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.707A pdb=" N PHE A 85 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 275 through 277 removed outlier: 8.504A pdb=" N TYR A 276 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER A 243 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS A 239 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 255 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 253 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.744A pdb=" N ILE B 23 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS B 153 " --> pdb=" O ASN B 20 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 22 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS B 155 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.671A pdb=" N TRP B 94 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 81 Processing sheet with id= G, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.031A pdb=" N MET B 262 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL B 255 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 240 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 180 through 182 removed outlier: 7.199A pdb=" N LEU C 19 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU C 189 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 21 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS C 153 " --> pdb=" O ASN C 20 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 22 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS C 155 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 50 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASP C 118 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL C 52 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG C 53 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C 85 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= J, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.395A pdb=" N LEU D 19 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU D 189 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE D 21 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS D 153 " --> pdb=" O ASN D 20 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL D 22 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N CYS D 155 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 50 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 118 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TRP D 94 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG D 53 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE D 96 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 78 through 81 Processing sheet with id= L, first strand: chain 'D' and resid 261 through 263 removed outlier: 3.665A pdb=" N PHE D 242 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 255 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE D 240 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 152 through 155 removed outlier: 7.960A pdb=" N ILE E 50 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE E 85 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 180 through 182 Processing sheet with id= O, first strand: chain 'E' and resid 243 through 246 Processing sheet with id= P, first strand: chain 'E' and resid 262 through 264 332 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 622 hydrogen bonds 1132 hydrogen bond angles 0 basepair planarities 251 basepair parallelities 313 stacking parallelities Total time for adding SS restraints: 11.70 Time building geometry restraints manager: 15.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7557 1.35 - 1.50: 13166 1.50 - 1.65: 9646 1.65 - 1.80: 66 1.80 - 1.95: 37 Bond restraints: 30472 Sorted by residual: bond pdb=" CA LEU C 299 " pdb=" CB LEU C 299 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.51e-02 4.39e+03 5.88e+00 bond pdb=" CA ASP B 118 " pdb=" CB ASP B 118 " ideal model delta sigma weight residual 1.531 1.561 -0.030 1.48e-02 4.57e+03 4.22e+00 bond pdb=" C2 C N 65 " pdb=" O2 C N 65 " ideal model delta sigma weight residual 1.240 1.204 0.036 2.00e-02 2.50e+03 3.23e+00 bond pdb=" C3' DA G 23 " pdb=" O3' DA G 23 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" O1B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.481 1.516 -0.035 2.00e-02 2.50e+03 3.05e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 97.34 - 105.15: 3344 105.15 - 112.96: 17090 112.96 - 120.76: 14346 120.76 - 128.57: 8922 128.57 - 136.38: 866 Bond angle restraints: 44568 Sorted by residual: angle pdb=" O4' A K 99 " pdb=" C1' A K 99 " pdb=" N9 A K 99 " ideal model delta sigma weight residual 108.20 114.58 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C3' G K 11 " pdb=" O3' G K 11 " pdb=" P G K 12 " ideal model delta sigma weight residual 120.20 126.55 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' G K 11 " pdb=" C3' G K 11 " pdb=" C2' G K 11 " ideal model delta sigma weight residual 109.50 115.85 -6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 112.98 107.90 5.08 1.25e+00 6.40e-01 1.65e+01 angle pdb=" C ARG D 200 " pdb=" N ARG D 201 " pdb=" CA ARG D 201 " ideal model delta sigma weight residual 122.06 114.66 7.40 1.86e+00 2.89e-01 1.58e+01 ... (remaining 44563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 14807 35.88 - 71.75: 1476 71.75 - 107.63: 153 107.63 - 143.51: 17 143.51 - 179.38: 13 Dihedral angle restraints: 16466 sinusoidal: 11616 harmonic: 4850 Sorted by residual: dihedral pdb=" O4' U O 69 " pdb=" C1' U O 69 " pdb=" N1 U O 69 " pdb=" C2 U O 69 " ideal model delta sinusoidal sigma weight residual -160.00 -26.11 -133.89 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U M 76 " pdb=" C1' U M 76 " pdb=" N1 U M 76 " pdb=" C2 U M 76 " ideal model delta sinusoidal sigma weight residual 232.00 88.30 143.70 1 1.70e+01 3.46e-03 6.00e+01 dihedral pdb=" O4' C K 18 " pdb=" C1' C K 18 " pdb=" N1 C K 18 " pdb=" C2 C K 18 " ideal model delta sinusoidal sigma weight residual -160.00 -61.46 -98.54 1 1.50e+01 4.44e-03 4.90e+01 ... (remaining 16463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4317 0.049 - 0.097: 823 0.097 - 0.146: 222 0.146 - 0.194: 35 0.194 - 0.243: 11 Chirality restraints: 5408 Sorted by residual: chirality pdb=" C1' U O 113 " pdb=" O4' U O 113 " pdb=" C2' U O 113 " pdb=" N1 U O 113 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' A N 46 " pdb=" O4' A N 46 " pdb=" C2' A N 46 " pdb=" N9 A N 46 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 5405 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C N 65 " 0.018 2.00e-02 2.50e+03 3.93e-02 3.47e+01 pdb=" N1 C N 65 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C N 65 " -0.095 2.00e-02 2.50e+03 pdb=" O2 C N 65 " 0.060 2.00e-02 2.50e+03 pdb=" N3 C N 65 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C N 65 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C5 C N 65 " 0.017 2.00e-02 2.50e+03 pdb=" C6 C N 65 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C L 65 " -0.010 2.00e-02 2.50e+03 3.73e-02 3.14e+01 pdb=" N1 C L 65 " 0.016 2.00e-02 2.50e+03 pdb=" C2 C L 65 " 0.088 2.00e-02 2.50e+03 pdb=" O2 C L 65 " -0.061 2.00e-02 2.50e+03 pdb=" N3 C L 65 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C L 65 " 0.008 2.00e-02 2.50e+03 pdb=" N4 C L 65 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C L 65 " -0.020 2.00e-02 2.50e+03 pdb=" C6 C L 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 65 " -0.007 2.00e-02 2.50e+03 3.61e-02 2.92e+01 pdb=" N1 C O 65 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C O 65 " -0.081 2.00e-02 2.50e+03 pdb=" O2 C O 65 " 0.066 2.00e-02 2.50e+03 pdb=" N3 C O 65 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C O 65 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C O 65 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C O 65 " 0.020 2.00e-02 2.50e+03 pdb=" C6 C O 65 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 11 2.08 - 2.79: 7078 2.79 - 3.49: 42401 3.49 - 4.20: 81640 4.20 - 4.90: 112357 Nonbonded interactions: 243487 Sorted by model distance: nonbonded pdb=" OG SER B 31 " pdb=" O1B AGS B 401 " model vdw 1.379 2.440 nonbonded pdb=" CB SER A 31 " pdb="MG MG A 402 " model vdw 1.888 2.570 nonbonded pdb=" O1B AGS A 401 " pdb=" O3G AGS A 401 " model vdw 1.940 2.440 nonbonded pdb=" CB SER C 31 " pdb="MG MG C 402 " model vdw 1.962 2.570 nonbonded pdb=" O6 G N 6 " pdb=" O4 U N 113 " model vdw 2.031 2.432 ... (remaining 243482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 330) selection = (chain 'B' and resid 4 through 330) selection = (chain 'C' and resid 4 through 330) selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 709 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 15415 2.51 5 N 4880 2.21 5 O 7351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.140 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.260 Process input model: 84.640 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 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 : 0.004 0.052 30472 Z= 0.237 Angle : 0.879 9.692 44568 Z= 0.449 Chirality : 0.044 0.243 5408 Planarity : 0.005 0.076 3128 Dihedral : 23.121 179.385 13346 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 0.00 % 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: -2.31 (0.20), residues: 1625 helix: -0.81 (0.22), residues: 514 sheet: -2.23 (0.33), residues: 229 loop : -1.77 (0.20), residues: 882 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3958 time to fit residues: 129.2233 Evaluate side-chains 152 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 50.0000 chunk 172 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 177 optimal weight: 40.0000 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 132 optimal weight: 0.8980 chunk 206 optimal weight: 50.0000 overall best weight: 10.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 268 HIS C 107 ASN C 132 ASN C 139 ASN C 259 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 30472 Z= 0.246 Angle : 0.834 9.102 44568 Z= 0.418 Chirality : 0.044 0.250 5408 Planarity : 0.005 0.051 3128 Dihedral : 24.826 178.552 10061 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer Outliers : 0.34 % 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: -2.24 (0.20), residues: 1625 helix: -0.67 (0.22), residues: 514 sheet: -2.15 (0.32), residues: 232 loop : -1.79 (0.20), residues: 879 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 196 average time/residue: 0.3480 time to fit residues: 113.4609 Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2327 time to fit residues: 2.8449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 171 optimal weight: 50.0000 chunk 140 optimal weight: 0.0980 chunk 56 optimal weight: 30.0000 chunk 206 optimal weight: 50.0000 chunk 223 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 204 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 overall best weight: 9.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 171 ASN B 268 HIS C 132 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 30472 Z= 0.225 Angle : 0.799 8.482 44568 Z= 0.401 Chirality : 0.042 0.253 5408 Planarity : 0.005 0.060 3128 Dihedral : 24.718 179.626 10061 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.20), residues: 1625 helix: -0.54 (0.22), residues: 509 sheet: -2.01 (0.34), residues: 215 loop : -1.78 (0.19), residues: 901 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.3645 time to fit residues: 120.2954 Evaluate side-chains 150 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2340 time to fit residues: 2.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 50.0000 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 98 optimal weight: 50.0000 chunk 138 optimal weight: 50.0000 chunk 207 optimal weight: 40.0000 chunk 219 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 196 optimal weight: 50.0000 chunk 59 optimal weight: 0.8980 overall best weight: 15.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 222 GLN B 259 GLN B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 30472 Z= 0.304 Angle : 0.892 9.610 44568 Z= 0.448 Chirality : 0.046 0.345 5408 Planarity : 0.006 0.069 3128 Dihedral : 24.923 179.301 10061 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 31.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1625 helix: -0.86 (0.22), residues: 511 sheet: -2.30 (0.34), residues: 197 loop : -1.98 (0.19), residues: 917 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.3717 time to fit residues: 117.6183 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2178 time to fit residues: 2.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 50.0000 chunk 124 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 163 optimal weight: 40.0000 chunk 90 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 112 optimal weight: 10.0000 chunk 196 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 HIS C 139 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30472 Z= 0.222 Angle : 0.809 8.689 44568 Z= 0.406 Chirality : 0.043 0.255 5408 Planarity : 0.005 0.062 3128 Dihedral : 24.773 179.693 10061 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.00 % 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: -2.33 (0.20), residues: 1625 helix: -0.73 (0.22), residues: 519 sheet: -2.20 (0.36), residues: 185 loop : -1.92 (0.19), residues: 921 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3722 time to fit residues: 121.7679 Evaluate side-chains 145 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 6.9990 chunk 197 optimal weight: 50.0000 chunk 43 optimal weight: 40.0000 chunk 128 optimal weight: 40.0000 chunk 54 optimal weight: 0.0770 chunk 219 optimal weight: 30.0000 chunk 182 optimal weight: 50.0000 chunk 101 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 115 optimal weight: 50.0000 overall best weight: 13.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN E 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 30472 Z= 0.274 Angle : 0.856 9.182 44568 Z= 0.430 Chirality : 0.044 0.368 5408 Planarity : 0.005 0.059 3128 Dihedral : 24.855 179.687 10061 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.19), residues: 1625 helix: -0.93 (0.22), residues: 532 sheet: -2.36 (0.36), residues: 185 loop : -2.01 (0.19), residues: 908 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.3488 time to fit residues: 108.4727 Evaluate side-chains 147 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 2.413 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2224 time to fit residues: 2.7857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 50.0000 chunk 24 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 160 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 184 optimal weight: 50.0000 chunk 122 optimal weight: 40.0000 chunk 218 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30472 Z= 0.194 Angle : 0.782 10.997 44568 Z= 0.392 Chirality : 0.041 0.252 5408 Planarity : 0.005 0.062 3128 Dihedral : 24.646 179.255 10061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % 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: -2.33 (0.20), residues: 1625 helix: -0.75 (0.22), residues: 523 sheet: -2.01 (0.36), residues: 197 loop : -1.95 (0.19), residues: 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3654 time to fit residues: 114.4441 Evaluate side-chains 151 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 65 optimal weight: 0.0270 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 50.0000 chunk 149 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 199 optimal weight: 50.0000 overall best weight: 2.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 30472 Z= 0.172 Angle : 0.745 9.796 44568 Z= 0.373 Chirality : 0.040 0.235 5408 Planarity : 0.005 0.070 3128 Dihedral : 24.328 176.697 10061 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.20), residues: 1625 helix: -0.63 (0.22), residues: 529 sheet: -1.82 (0.37), residues: 197 loop : -1.84 (0.19), residues: 899 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.3628 time to fit residues: 124.0868 Evaluate side-chains 156 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 20.0000 chunk 191 optimal weight: 50.0000 chunk 203 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 160 optimal weight: 50.0000 chunk 62 optimal weight: 8.9990 chunk 184 optimal weight: 50.0000 chunk 192 optimal weight: 50.0000 chunk 133 optimal weight: 1.9990 chunk 215 optimal weight: 30.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 ASN C 139 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 30472 Z= 0.212 Angle : 0.770 8.926 44568 Z= 0.386 Chirality : 0.041 0.238 5408 Planarity : 0.005 0.078 3128 Dihedral : 24.393 177.025 10061 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 0.00 % 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: -2.14 (0.20), residues: 1625 helix: -0.67 (0.22), residues: 522 sheet: -1.86 (0.39), residues: 179 loop : -1.80 (0.20), residues: 924 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.3635 time to fit residues: 111.2367 Evaluate side-chains 148 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 149 optimal weight: 40.0000 chunk 226 optimal weight: 40.0000 chunk 208 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 40.0000 chunk 143 optimal weight: 50.0000 chunk 191 optimal weight: 50.0000 overall best weight: 23.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 30472 Z= 0.440 Angle : 1.082 10.928 44568 Z= 0.541 Chirality : 0.052 0.319 5408 Planarity : 0.008 0.094 3128 Dihedral : 25.193 179.417 10061 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 40.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.35 % Favored : 86.58 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.06 % 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: -3.03 (0.19), residues: 1625 helix: -1.40 (0.22), residues: 502 sheet: -2.31 (0.35), residues: 199 loop : -2.36 (0.18), residues: 924 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.3640 time to fit residues: 102.8633 Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 26 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 180 optimal weight: 40.0000 chunk 75 optimal weight: 5.9990 chunk 185 optimal weight: 40.0000 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.099454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.094361 restraints weight = 189091.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.094526 restraints weight = 225378.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.094569 restraints weight = 140196.358| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30472 Z= 0.220 Angle : 0.825 10.502 44568 Z= 0.414 Chirality : 0.043 0.257 5408 Planarity : 0.005 0.075 3128 Dihedral : 24.680 178.554 10061 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer Outliers : 0.00 % 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 (0.20), residues: 1625 helix: -1.03 (0.22), residues: 512 sheet: -1.96 (0.36), residues: 210 loop : -2.09 (0.19), residues: 903 =============================================================================== Job complete usr+sys time: 3484.89 seconds wall clock time: 66 minutes 39.49 seconds (3999.49 seconds total)