Starting phenix.real_space_refine (version: dev) on Tue Apr 5 18:15:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/04_2022/7oug_13076_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.021 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: 15090 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 257, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 275, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "B" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 257, 'PCIS': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 275, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {'RLT': 1, ' ZN': 1, ' MG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {'RLT': 1, ' ZN': 1, ' MG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 105.427 119.943 25.979 1.00 64.43 S ATOM 260 SG CYS D 38 103.330 122.249 27.523 1.00 61.41 S ATOM 2296 SG CYS E 35 73.195 55.648 38.011 1.00 18.21 S ATOM 2317 SG CYS E 38 70.364 57.662 38.953 1.00 8.92 S ATOM 7744 SG CYS A 35 22.183 45.021 25.936 1.00 64.00 S ATOM 7765 SG CYS A 38 24.283 42.718 27.481 1.00 58.68 S ATOM 9801 SG CYS B 35 54.346 109.350 37.975 1.00 18.65 S ATOM 9822 SG CYS B 38 57.179 107.339 38.919 1.00 9.34 S Time building chain proxies: 9.24, per 1000 atoms: 0.61 Number of scatterers: 15090 At special positions: 0 Unit cell: (128.7, 166.1, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 2 9.00 O 2824 8.00 N 2710 7.00 C 9424 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: 6.35 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 6 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 12 sheets defined 46.0% alpha, 10.6% beta 20 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 174 removed outlier: 6.189A pdb=" N LEU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 38 through 49 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 Proline residue: F 93 - end of helix removed outlier: 3.986A pdb=" N VAL F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 213 Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 249 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 258 through 275 removed outlier: 4.556A pdb=" N SER F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS F 264 " --> pdb=" O SER F 261 " (cutoff:3.500A) Proline residue: F 265 - end of helix removed outlier: 4.187A pdb=" N LEU F 275 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix removed outlier: 3.618A pdb=" N LEU F 290 " --> pdb=" O MET F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET F 303 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 174 removed outlier: 6.190A pdb=" N LEU B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' 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 38 through 49 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 Proline residue: C 93 - end of helix removed outlier: 3.985A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 258 through 275 removed outlier: 4.555A pdb=" N SER C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 4.187A pdb=" N LEU C 275 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix removed outlier: 3.618A pdb=" N LEU C 290 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'D' and resid 89 through 94 removed outlier: 7.235A pdb=" N HIS D 118 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY D 64 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN D 120 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ILE D 66 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP D 122 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 14.810A pdb=" N HIS D 68 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 144 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= C, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.856A pdb=" N GLN D 250 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.081A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR E 144 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= F, first strand: chain 'E' and resid 255 through 259 Processing sheet with id= G, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.236A pdb=" N HIS A 118 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY A 64 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 120 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ILE A 66 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP A 122 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 14.811A pdb=" N HIS A 68 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR A 144 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.856A pdb=" N GLN A 250 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.080A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR B 144 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= L, first strand: chain 'B' and resid 255 through 259 540 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3564 1.33 - 1.45: 3583 1.45 - 1.57: 8311 1.57 - 1.69: 152 1.69 - 1.81: 62 Bond restraints: 15672 Sorted by residual: bond pdb=" CAU RLT E 304 " pdb=" NAR RLT E 304 " ideal model delta sigma weight residual 1.501 1.329 0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" CAU RLT B 304 " pdb=" NAR RLT B 304 " ideal model delta sigma weight residual 1.501 1.330 0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" CBC RLT E 304 " pdb=" NAQ RLT E 304 " ideal model delta sigma weight residual 1.511 1.362 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" CBC RLT B 304 " pdb=" NAQ RLT B 304 " ideal model delta sigma weight residual 1.511 1.363 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" CAV RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 1.458 1.324 0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 81.93 - 92.34: 4 92.34 - 102.76: 137 102.76 - 113.18: 9465 113.18 - 123.60: 11255 123.60 - 134.02: 817 Bond angle restraints: 21678 Sorted by residual: angle pdb=" CBC RLT B 304 " pdb=" CBF RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 109.28 81.93 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" CBC RLT E 304 " pdb=" CBF RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 109.28 82.19 27.09 3.00e+00 1.11e-01 8.16e+01 angle pdb=" CAD RLT E 304 " pdb=" CBF RLT E 304 " pdb=" CBC RLT E 304 " ideal model delta sigma weight residual 109.37 89.52 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" CAD RLT B 304 " pdb=" CBF RLT B 304 " pdb=" CBC RLT B 304 " ideal model delta sigma weight residual 109.37 89.57 19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" CAA RLT E 304 " pdb=" CAW RLT E 304 " pdb=" OAT RLT E 304 " ideal model delta sigma weight residual 133.86 115.25 18.61 3.00e+00 1.11e-01 3.85e+01 ... (remaining 21673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 7633 16.14 - 32.28: 838 32.28 - 48.43: 367 48.43 - 64.57: 160 64.57 - 80.71: 22 Dihedral angle restraints: 9020 sinusoidal: 4104 harmonic: 4916 Sorted by residual: dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N TYR E 231 " pdb=" CA TYR E 231 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 230 " pdb=" C TYR B 230 " pdb=" N TYR B 231 " pdb=" CA TYR B 231 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR D 230 " pdb=" C TYR D 230 " pdb=" N TYR D 231 " pdb=" CA TYR D 231 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1790 0.037 - 0.074: 432 0.074 - 0.110: 142 0.110 - 0.147: 40 0.147 - 0.184: 2 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CG LEU B 257 " pdb=" CB LEU B 257 " pdb=" CD1 LEU B 257 " pdb=" CD2 LEU B 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CG LEU E 257 " pdb=" CB LEU E 257 " pdb=" CD1 LEU E 257 " pdb=" CD2 LEU E 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2403 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAV RLT E 304 " 0.081 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" CBA RLT E 304 " -0.176 2.00e-02 2.50e+03 pdb=" CBF RLT E 304 " -0.307 2.00e-02 2.50e+03 pdb=" NAS RLT E 304 " 0.455 2.00e-02 2.50e+03 pdb=" OAF RLT E 304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAV RLT B 304 " 0.080 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" CBA RLT B 304 " -0.175 2.00e-02 2.50e+03 pdb=" CBF RLT B 304 " -0.305 2.00e-02 2.50e+03 pdb=" NAS RLT B 304 " 0.452 2.00e-02 2.50e+03 pdb=" OAF RLT B 304 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAN RLT B 304 " -0.158 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CAU RLT B 304 " 0.052 2.00e-02 2.50e+03 pdb=" CBB RLT B 304 " -0.120 2.00e-02 2.50e+03 pdb=" NAR RLT B 304 " 0.204 2.00e-02 2.50e+03 pdb=" OAE RLT B 304 " 0.022 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8167 3.02 - 3.65: 22423 3.65 - 4.27: 34225 4.27 - 4.90: 55631 Nonbonded interactions: 120497 Sorted by model distance: nonbonded pdb="MG MG B 303 " pdb=" OAE RLT B 304 " model vdw 1.769 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.777 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.785 2.170 nonbonded pdb="MG MG E 303 " pdb=" OAE RLT E 304 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.833 2.170 ... (remaining 120492 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 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'B' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) selection = (chain 'D' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'E' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9424 2.51 5 N 2710 2.21 5 O 2824 1.98 5 F 2 1.80 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.010 Extract box with map and model: 6.970 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.110 Process input model: 47.040 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.005 0.172 15672 Z= 0.279 Angle : 0.730 27.354 21678 Z= 0.332 Chirality : 0.039 0.184 2406 Planarity : 0.009 0.261 2466 Dihedral : 17.636 80.709 5808 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1640 helix: 1.16 (0.19), residues: 742 sheet: 0.36 (0.31), residues: 222 loop : -0.94 (0.24), residues: 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 477 time to evaluate : 1.554 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 outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.3362 time to fit residues: 218.4888 Evaluate side-chains 429 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 80 optimal weight: 0.0870 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 195 ASN D 206 GLN D 238 ASN E 21 HIS E 59 ASN E 93 HIS E 241 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN A 118 HIS A 134 HIS A 195 ASN A 238 ASN B 59 ASN B 161 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 15672 Z= 0.203 Angle : 0.601 13.668 21678 Z= 0.308 Chirality : 0.041 0.165 2406 Planarity : 0.006 0.125 2466 Dihedral : 19.065 83.827 2582 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1640 helix: 0.79 (0.19), residues: 758 sheet: 0.38 (0.32), residues: 222 loop : -0.84 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 434 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 444 average time/residue: 0.3378 time to fit residues: 203.3726 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 417 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1655 time to fit residues: 6.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 59 ASN E 93 HIS E 112 HIS A 238 ASN B 59 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 15672 Z= 0.237 Angle : 0.578 10.199 21678 Z= 0.297 Chirality : 0.041 0.145 2406 Planarity : 0.005 0.076 2466 Dihedral : 19.080 85.084 2582 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1640 helix: 0.73 (0.19), residues: 756 sheet: 0.45 (0.32), residues: 222 loop : -0.80 (0.24), residues: 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 441 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 447 average time/residue: 0.3530 time to fit residues: 214.9184 Evaluate side-chains 439 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 423 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1926 time to fit residues: 7.1092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 0.3980 chunk 80 optimal weight: 0.1980 chunk 145 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 59 ASN E 112 HIS F 233 ASN F 243 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN C 203 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 15672 Z= 0.235 Angle : 0.574 7.709 21678 Z= 0.297 Chirality : 0.041 0.175 2406 Planarity : 0.005 0.067 2466 Dihedral : 19.035 87.040 2582 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1640 helix: 0.66 (0.19), residues: 754 sheet: 0.37 (0.31), residues: 242 loop : -0.70 (0.24), residues: 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 433 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 13 residues processed: 444 average time/residue: 0.3433 time to fit residues: 207.4973 Evaluate side-chains 436 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 423 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1653 time to fit residues: 6.0573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.0570 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D 238 ASN E 59 ASN E 112 HIS E 118 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 41 ASN B 59 ASN B 112 HIS B 118 HIS B 195 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 15672 Z= 0.304 Angle : 0.616 9.794 21678 Z= 0.317 Chirality : 0.043 0.173 2406 Planarity : 0.006 0.105 2466 Dihedral : 19.117 88.631 2582 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1640 helix: 0.56 (0.18), residues: 752 sheet: 0.41 (0.31), residues: 242 loop : -0.85 (0.24), residues: 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 436 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 448 average time/residue: 0.3354 time to fit residues: 204.3873 Evaluate side-chains 432 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 419 time to evaluate : 1.667 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2128 time to fit residues: 6.6397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.3980 chunk 146 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 162 optimal weight: 0.2980 chunk 134 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 238 ASN E 41 ASN E 59 ASN E 112 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 15672 Z= 0.204 Angle : 0.603 11.899 21678 Z= 0.307 Chirality : 0.040 0.162 2406 Planarity : 0.006 0.113 2466 Dihedral : 19.035 89.317 2582 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1640 helix: 0.55 (0.19), residues: 756 sheet: 0.40 (0.31), residues: 242 loop : -0.66 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 416 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 423 average time/residue: 0.3431 time to fit residues: 196.6008 Evaluate side-chains 428 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 413 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2088 time to fit residues: 7.2958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 HIS D 238 ASN E 59 ASN E 112 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN B 112 HIS B 130 GLN B 134 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 15672 Z= 0.259 Angle : 0.612 13.007 21678 Z= 0.314 Chirality : 0.042 0.187 2406 Planarity : 0.006 0.112 2466 Dihedral : 19.022 89.735 2582 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1640 helix: 0.46 (0.18), residues: 754 sheet: 0.44 (0.31), residues: 242 loop : -0.75 (0.25), residues: 644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 412 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 420 average time/residue: 0.3538 time to fit residues: 202.8612 Evaluate side-chains 410 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 395 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2131 time to fit residues: 7.3223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS E 134 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN B 60 HIS B 112 HIS B 118 HIS C 203 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 15672 Z= 0.208 Angle : 0.624 13.128 21678 Z= 0.320 Chirality : 0.041 0.210 2406 Planarity : 0.006 0.114 2466 Dihedral : 18.960 89.899 2582 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1640 helix: 0.47 (0.19), residues: 758 sheet: 0.43 (0.31), residues: 242 loop : -0.68 (0.25), residues: 640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 420 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 424 average time/residue: 0.3459 time to fit residues: 198.7525 Evaluate side-chains 405 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 403 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1674 time to fit residues: 2.9320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.0020 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 0.0040 chunk 159 optimal weight: 0.5980 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 41 ASN E 59 ASN E 112 HIS E 134 HIS F 203 GLN A 238 ASN B 59 ASN B 112 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 15672 Z= 0.212 Angle : 0.623 12.554 21678 Z= 0.321 Chirality : 0.040 0.205 2406 Planarity : 0.006 0.119 2466 Dihedral : 18.885 89.983 2582 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1640 helix: 0.46 (0.19), residues: 764 sheet: 0.45 (0.31), residues: 242 loop : -0.58 (0.25), residues: 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 417 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 420 average time/residue: 0.3507 time to fit residues: 198.7153 Evaluate side-chains 415 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 408 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1522 time to fit residues: 4.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS E 134 HIS A 59 ASN A 238 ASN B 59 ASN B 112 HIS C 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 15672 Z= 0.240 Angle : 0.640 12.808 21678 Z= 0.329 Chirality : 0.041 0.235 2406 Planarity : 0.006 0.129 2466 Dihedral : 18.888 89.910 2582 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1640 helix: 0.50 (0.19), residues: 760 sheet: 0.47 (0.31), residues: 242 loop : -0.65 (0.25), residues: 638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 419 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 420 average time/residue: 0.3551 time to fit residues: 201.3721 Evaluate side-chains 410 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1438 time to fit residues: 2.9624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS A 238 ASN B 59 ASN B 112 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122068 restraints weight = 22681.831| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.24 r_work: 0.3495 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3468 rms_B_bonded: 2.09 restraints_weight: 0.1250 r_work: 0.3453 rms_B_bonded: 2.19 restraints_weight: 0.0625 r_work: 0.3436 rms_B_bonded: 2.33 restraints_weight: 0.0312 r_work: 0.3418 rms_B_bonded: 2.52 restraints_weight: 0.0156 r_work: 0.3398 rms_B_bonded: 2.75 restraints_weight: 0.0078 r_work: 0.3376 rms_B_bonded: 3.03 restraints_weight: 0.0039 r_work: 0.3352 rms_B_bonded: 3.37 restraints_weight: 0.0020 r_work: 0.3324 rms_B_bonded: 3.77 restraints_weight: 0.0010 r_work: 0.3292 rms_B_bonded: 4.25 restraints_weight: 0.0005 r_work: 0.3257 rms_B_bonded: 4.82 restraints_weight: 0.0002 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.126 15672 Z= 0.238 Angle : 0.640 12.373 21678 Z= 0.330 Chirality : 0.041 0.214 2406 Planarity : 0.006 0.130 2466 Dihedral : 18.876 89.851 2582 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1640 helix: 0.49 (0.18), residues: 766 sheet: 0.48 (0.31), residues: 242 loop : -0.71 (0.25), residues: 632 =============================================================================== Job complete usr+sys time: 4001.09 seconds wall clock time: 72 minutes 45.71 seconds (4365.71 seconds total)