Starting phenix.real_space_refine (version: dev) on Wed Dec 14 13:36:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/12_2022/6oll_20116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/12_2022/6oll_20116.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/6oll_20116/12_2022/6oll_20116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/12_2022/6oll_20116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/12_2022/6oll_20116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/12_2022/6oll_20116.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= 0.005 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10416 atoms to isotropic. 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "C" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "E" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "F" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Time building chain proxies: 6.97, per 1000 atoms: 0.67 Number of scatterers: 10426 At special positions: 0 Unit cell: (124.02, 121.9, 81.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2114 8.00 N 2114 7.00 C 6198 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: 4.94 Conformation dependent library (CDL) restraints added in 2.4 seconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 48.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.210A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.520A pdb=" N TYR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.163A pdb=" N ASP A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.543A pdb=" N PHE A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 113 through 120 removed outlier: 4.142A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.753A pdb=" N TYR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 113 through 120 removed outlier: 4.188A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.067A pdb=" N ASP C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 57 through 68 Processing helix chain 'D' and resid 113 through 120 removed outlier: 4.210A pdb=" N ARG D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 185 through 193 removed outlier: 3.511A pdb=" N TYR D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 4.167A pdb=" N ASP D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.542A pdb=" N PHE D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 333 through 341 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'E' and resid 57 through 68 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 113 through 120 removed outlier: 4.121A pdb=" N ARG E 117 " --> pdb=" O PRO E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 Processing helix chain 'E' and resid 185 through 193 removed outlier: 3.736A pdb=" N TYR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.025A pdb=" N ASP E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.547A pdb=" N VAL E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 288 through 297 Processing helix chain 'E' and resid 302 through 309 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 318 through 329 Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 57 through 68 Processing helix chain 'F' and resid 113 through 120 removed outlier: 4.202A pdb=" N ARG F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 194 through 197 removed outlier: 4.091A pdb=" N ASP F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 318 through 329 Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.551A pdb=" N LEU F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.653A pdb=" N GLN A 28 " --> pdb=" O HIS A 20 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 30 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 18 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 178 removed outlier: 6.519A pdb=" N ILE A 156 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 177 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 158 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS A 155 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 202 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 157 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY A 204 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 159 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 203 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 228 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 205 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 225 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 227 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 126 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 265 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 128 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 267 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 130 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU A 269 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.554A pdb=" N ASP B 18 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.543A pdb=" N ILE B 156 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ARG B 177 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 158 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS B 155 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 202 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 157 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY B 204 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 159 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 201 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR B 228 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL B 203 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 225 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 127 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA B 227 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 129 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 229 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 126 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 265 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 128 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN B 267 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR B 130 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 269 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.718A pdb=" N ASP C 18 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.242A pdb=" N VAL C 201 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 228 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL C 203 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 227 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 229 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 126 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 265 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 128 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN C 267 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR C 130 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C 269 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.646A pdb=" N GLN D 28 " --> pdb=" O HIS D 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 30 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP D 18 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.518A pdb=" N ILE D 156 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG D 177 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 158 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS D 155 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU D 202 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 157 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY D 204 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL D 159 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 203 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 228 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU D 205 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 225 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 227 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 126 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU D 265 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 128 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN D 267 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR D 130 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU D 269 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.631A pdb=" N ASP E 18 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.524A pdb=" N ILE E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ARG E 177 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR E 158 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS E 155 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU E 202 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 157 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 204 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL E 159 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 201 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 228 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL E 203 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS E 225 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 127 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA E 227 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 129 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 229 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 126 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 265 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU E 128 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN E 267 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR E 130 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU E 269 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.745A pdb=" N ASP F 18 " --> pdb=" O ARG F 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.208A pdb=" N VAL F 201 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR F 228 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL F 203 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 227 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 229 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU F 126 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU F 265 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU F 128 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN F 267 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR F 130 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU F 269 " --> pdb=" O THR F 130 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2114 1.29 - 1.36: 2102 1.36 - 1.42: 4 1.42 - 1.49: 2112 1.49 - 1.55: 4088 Bond restraints: 10420 Sorted by residual: bond pdb=" C ALA E 2 " pdb=" O ALA E 2 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.26e-02 6.30e+03 5.00e+00 bond pdb=" CA ALA E 2 " pdb=" C ALA E 2 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 3.02e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 ... (remaining 10415 not shown) Histogram of bond angle deviations from ideal: 96.56 - 103.50: 92 103.50 - 110.44: 2872 110.44 - 117.39: 4447 117.39 - 124.33: 6947 124.33 - 131.27: 134 Bond angle restraints: 14492 Sorted by residual: angle pdb=" C GLU F 160 " pdb=" N ASP F 161 " pdb=" CA ASP F 161 " ideal model delta sigma weight residual 122.56 130.62 -8.06 1.34e+00 5.57e-01 3.61e+01 angle pdb=" N ASP C 161 " pdb=" CA ASP C 161 " pdb=" C ASP C 161 " ideal model delta sigma weight residual 109.81 96.69 13.12 2.21e+00 2.05e-01 3.52e+01 angle pdb=" N LYS F 103 " pdb=" CA LYS F 103 " pdb=" C LYS F 103 " ideal model delta sigma weight residual 108.73 118.34 -9.61 1.63e+00 3.76e-01 3.47e+01 angle pdb=" N ASP F 161 " pdb=" CA ASP F 161 " pdb=" C ASP F 161 " ideal model delta sigma weight residual 107.91 96.56 11.35 2.05e+00 2.38e-01 3.07e+01 angle pdb=" N LYS C 103 " pdb=" CA LYS C 103 " pdb=" C LYS C 103 " ideal model delta sigma weight residual 109.24 118.08 -8.84 1.63e+00 3.76e-01 2.94e+01 ... (remaining 14487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6043 21.38 - 42.75: 1 42.75 - 64.13: 0 64.13 - 85.51: 0 85.51 - 106.88: 4 Dihedral angle restraints: 6048 sinusoidal: 0 harmonic: 6048 Sorted by residual: dihedral pdb=" CA ASP B 161 " pdb=" C ASP B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual -180.00 -73.12 -106.88 0 5.00e+00 4.00e-02 4.57e+02 dihedral pdb=" CA ASP E 161 " pdb=" C ASP E 161 " pdb=" N PRO E 162 " pdb=" CA PRO E 162 " ideal model delta harmonic sigma weight residual -180.00 -73.37 -106.63 0 5.00e+00 4.00e-02 4.55e+02 dihedral pdb=" CA ASP F 161 " pdb=" C ASP F 161 " pdb=" N PRO F 162 " pdb=" CA PRO F 162 " ideal model delta harmonic sigma weight residual -180.00 -84.19 -95.81 0 5.00e+00 4.00e-02 3.67e+02 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1656 0.076 - 0.151: 284 0.151 - 0.227: 28 0.227 - 0.303: 0 0.303 - 0.378: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO E 162 " pdb=" N PRO E 162 " pdb=" C PRO E 162 " pdb=" CB PRO E 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LEU F 294 " pdb=" N LEU F 294 " pdb=" C LEU F 294 " pdb=" CB LEU F 294 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1967 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 2 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ALA B 2 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA B 2 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 3 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 2 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ALA E 2 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA E 2 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN E 3 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 247 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C SER E 247 " -0.060 2.00e-02 2.50e+03 pdb=" O SER E 247 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR E 248 " 0.020 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4456 2.90 - 3.40: 9964 3.40 - 3.90: 14393 3.90 - 4.40: 14662 4.40 - 4.90: 24269 Nonbonded interactions: 67744 Sorted by model distance: nonbonded pdb=" N ALA E 273 " pdb=" O HIS E 331 " model vdw 2.400 2.520 nonbonded pdb=" N ALA B 273 " pdb=" O HIS B 331 " model vdw 2.434 2.520 nonbonded pdb=" O GLU E 160 " pdb=" N VAL E 179 " model vdw 2.456 2.520 nonbonded pdb=" N THR A 130 " pdb=" O LEU A 265 " model vdw 2.464 2.520 nonbonded pdb=" O GLU B 160 " pdb=" N VAL B 179 " model vdw 2.465 2.520 ... (remaining 67739 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 1 through 351) selection = chain 'B' selection = (chain 'C' and resid 1 through 351) selection = (chain 'D' and resid 1 through 351) selection = chain 'E' selection = (chain 'F' and resid 1 through 351) } 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: 3 Type Number sf(0) Gaussians C 6198 2.51 5 N 2114 2.21 5 O 2114 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 4.630 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 33.660 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.050 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 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 0.086 10420 Z= 0.329 Angle : 1.052 13.117 14492 Z= 0.702 Chirality : 0.056 0.378 1970 Planarity : 0.005 0.044 2108 Dihedral : 6.943 106.883 2108 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.05 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.51 (0.17), residues: 2102 helix: -0.57 (0.14), residues: 990 sheet: 0.99 (0.25), residues: 456 loop : -0.66 (0.22), residues: 656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0931 time to fit residues: 13.0713 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10420 Z= 0.201 Angle : 0.585 8.309 14492 Z= 0.373 Chirality : 0.046 0.180 1970 Planarity : 0.004 0.024 2108 Dihedral : 5.939 47.769 2108 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.10 % 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: 0.12 (0.18), residues: 2102 helix: 0.22 (0.16), residues: 998 sheet: 0.79 (0.26), residues: 460 loop : -0.44 (0.23), residues: 644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.161 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0898 time to fit residues: 12.7712 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 206 optimal weight: 30.0000 chunk 170 optimal weight: 50.0000 chunk 189 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 overall best weight: 5.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 10420 Z= 0.307 Angle : 0.654 5.440 14492 Z= 0.427 Chirality : 0.047 0.173 1970 Planarity : 0.004 0.020 2108 Dihedral : 6.720 32.121 2108 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2102 helix: -1.12 (0.15), residues: 964 sheet: 0.16 (0.25), residues: 450 loop : -1.57 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0926 time to fit residues: 13.1294 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 99 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 191 optimal weight: 0.0970 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.026 10420 Z= 0.110 Angle : 0.421 5.345 14492 Z= 0.271 Chirality : 0.044 0.143 1970 Planarity : 0.002 0.009 2108 Dihedral : 5.038 27.169 2108 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.57 (0.18), residues: 2102 helix: 0.22 (0.16), residues: 964 sheet: 0.22 (0.26), residues: 426 loop : -1.47 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0920 time to fit residues: 13.0495 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 50.0000 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 0.0050 chunk 83 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 10420 Z= 0.275 Angle : 0.608 4.966 14492 Z= 0.401 Chirality : 0.046 0.148 1970 Planarity : 0.004 0.019 2108 Dihedral : 6.248 25.737 2108 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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 (0.17), residues: 2102 helix: -1.17 (0.15), residues: 972 sheet: -0.19 (0.27), residues: 402 loop : -2.33 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0943 time to fit residues: 13.2381 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 168 optimal weight: 40.0000 chunk 94 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10420 Z= 0.194 Angle : 0.492 4.348 14492 Z= 0.324 Chirality : 0.044 0.139 1970 Planarity : 0.003 0.013 2108 Dihedral : 5.299 20.621 2108 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.06 (0.18), residues: 2102 helix: -0.81 (0.15), residues: 966 sheet: -0.38 (0.28), residues: 366 loop : -2.48 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0960 time to fit residues: 13.5703 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 10420 Z= 0.337 Angle : 0.681 5.377 14492 Z= 0.451 Chirality : 0.047 0.170 1970 Planarity : 0.005 0.033 2108 Dihedral : 6.917 31.846 2108 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.65 % Favored : 86.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.15 (0.17), residues: 2102 helix: -2.10 (0.14), residues: 920 sheet: -0.49 (0.28), residues: 386 loop : -2.75 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1001 time to fit residues: 13.8894 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10420 Z= 0.198 Angle : 0.522 4.526 14492 Z= 0.344 Chirality : 0.045 0.133 1970 Planarity : 0.003 0.012 2108 Dihedral : 5.856 21.704 2108 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.86 (0.17), residues: 2102 helix: -1.52 (0.15), residues: 932 sheet: -0.78 (0.27), residues: 376 loop : -2.80 (0.22), residues: 794 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0957 time to fit residues: 13.4006 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.8389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10420 Z= 0.236 Angle : 0.556 4.942 14492 Z= 0.368 Chirality : 0.045 0.144 1970 Planarity : 0.003 0.014 2108 Dihedral : 5.878 25.063 2108 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.94 (0.17), residues: 2102 helix: -1.58 (0.15), residues: 932 sheet: -0.92 (0.27), residues: 396 loop : -2.84 (0.23), residues: 774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0925 time to fit residues: 13.0504 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 20.0000 chunk 121 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.8218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.015 10420 Z= 0.103 Angle : 0.411 3.845 14492 Z= 0.267 Chirality : 0.043 0.131 1970 Planarity : 0.002 0.009 2108 Dihedral : 4.706 17.948 2108 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -1.90 (0.18), residues: 2102 helix: -0.29 (0.16), residues: 964 sheet: -0.97 (0.28), residues: 360 loop : -2.59 (0.23), residues: 778 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.304 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1041 time to fit residues: 14.6481 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 51 optimal weight: 40.0000 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 171 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.156169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.131480 restraints weight = 35081.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.132775 restraints weight = 26482.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.133493 restraints weight = 21545.093| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.8567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10420 Z= 0.219 Angle : 0.516 4.686 14492 Z= 0.342 Chirality : 0.045 0.136 1970 Planarity : 0.003 0.013 2108 Dihedral : 5.427 22.886 2108 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -2.32 (0.18), residues: 2102 helix: -0.77 (0.16), residues: 954 sheet: -0.94 (0.27), residues: 396 loop : -2.78 (0.24), residues: 752 =============================================================================== Job complete usr+sys time: 1371.83 seconds wall clock time: 25 minutes 31.19 seconds (1531.19 seconds total)