Starting phenix.real_space_refine on Sun Dec 10 15:58:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/12_2023/6u96_20694_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.24, per 1000 atoms: 0.55 Number of scatterers: 14910 At special positions: 0 Unit cell: (87.74, 102.72, 204.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 110 16.00 P 10 15.00 O 2870 8.00 N 2510 7.00 C 9410 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 3.1 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 25 sheets defined 34.7% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.843A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.629A pdb=" N GLU A 117 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 118 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 122 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.978A pdb=" N TYR A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.725A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.989A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.586A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.529A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.009A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.547A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.566A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.868A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 373 removed outlier: 4.052A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.843A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.629A pdb=" N GLU B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 118 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 122 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.978A pdb=" N TYR B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.724A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.988A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.585A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.528A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 274 through 283 removed outlier: 4.009A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.546A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.566A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.869A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.051A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.843A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.629A pdb=" N GLU C 117 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS C 118 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 122 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.978A pdb=" N TYR C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.725A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.989A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.585A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 removed outlier: 3.528A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.010A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.547A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 317 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.566A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.868A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.051A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.843A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.629A pdb=" N GLU D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS D 118 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 122 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.978A pdb=" N TYR D 143 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.725A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.989A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.586A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 removed outlier: 3.529A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 261' Processing helix chain 'D' and resid 274 through 283 removed outlier: 4.009A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 No H-bonds generated for 'chain 'D' and resid 291 through 294' Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.547A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 removed outlier: 3.566A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.868A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.051A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.843A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.629A pdb=" N GLU E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS E 118 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE E 122 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 removed outlier: 3.978A pdb=" N TYR E 143 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.725A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.988A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 removed outlier: 3.585A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 removed outlier: 3.528A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 274 through 283 removed outlier: 4.009A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 310 through 319 removed outlier: 3.547A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE E 317 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.567A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.868A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 367 through 373 removed outlier: 4.051A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 149 through 151 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.564A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= H, first strand: chain 'B' and resid 149 through 151 Processing sheet with id= I, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 149 through 151 Processing sheet with id= N, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= P, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 105 through 107 Processing sheet with id= R, first strand: chain 'D' and resid 149 through 151 Processing sheet with id= S, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 105 through 107 Processing sheet with id= W, first strand: chain 'E' and resid 149 through 151 Processing sheet with id= X, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.692A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 238 through 241 275 hydrogen bonds defined for protein. 660 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: 3.78 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2486 1.31 - 1.44: 3934 1.44 - 1.57: 8615 1.57 - 1.70: 20 1.70 - 1.83: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" C CYS H 4 " pdb=" N HYP H 5 " ideal model delta sigma weight residual 1.329 1.488 -0.159 1.40e-02 5.10e+03 1.28e+02 bond pdb=" C CYS J 4 " pdb=" N HYP J 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS G 4 " pdb=" N HYP G 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS I 4 " pdb=" N HYP I 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS F 4 " pdb=" N HYP F 5 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.59: 461 105.59 - 113.23: 8349 113.23 - 120.88: 7413 120.88 - 128.52: 4329 128.52 - 136.16: 153 Bond angle restraints: 20705 Sorted by residual: angle pdb=" CD1 TRP F 7 " pdb=" NE1 TRP F 7 " pdb=" CE2 TRP F 7 " ideal model delta sigma weight residual 108.90 120.67 -11.77 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP H 7 " pdb=" NE1 TRP H 7 " pdb=" CE2 TRP H 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP J 7 " pdb=" NE1 TRP J 7 " pdb=" CE2 TRP J 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP I 7 " pdb=" NE1 TRP I 7 " pdb=" CE2 TRP I 7 " ideal model delta sigma weight residual 108.90 120.65 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CD1 TRP G 7 " pdb=" NE1 TRP G 7 " pdb=" CE2 TRP G 7 " ideal model delta sigma weight residual 108.90 120.62 -11.72 1.80e+00 3.09e-01 4.24e+01 ... (remaining 20700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 8920 24.43 - 48.87: 175 48.87 - 73.30: 15 73.30 - 97.74: 0 97.74 - 122.17: 5 Dihedral angle restraints: 9115 sinusoidal: 3655 harmonic: 5460 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.82 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.83 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.85 122.15 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 9112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2258 0.157 - 0.313: 42 0.313 - 0.470: 0 0.470 - 0.626: 0 0.626 - 0.783: 5 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA HIC E 73 " pdb=" N HIC E 73 " pdb=" C HIC E 73 " pdb=" CB HIC E 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA HIC D 73 " pdb=" N HIC D 73 " pdb=" C HIC D 73 " pdb=" CB HIC D 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA HIC A 73 " pdb=" N HIC A 73 " pdb=" C HIC A 73 " pdb=" CB HIC A 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 2302 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 69 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO E 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.036 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 40 2.45 - 3.06: 8383 3.06 - 3.68: 19989 3.68 - 4.29: 27513 4.29 - 4.90: 47034 Nonbonded interactions: 102959 Sorted by model distance: nonbonded pdb=" SG CYS I 4 " pdb=" CD1 TRP I 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS J 4 " pdb=" CD1 TRP J 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS G 4 " pdb=" CD1 TRP G 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS H 4 " pdb=" CD1 TRP H 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS F 4 " pdb=" CD1 TRP F 7 " model vdw 1.838 3.620 ... (remaining 102954 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.180 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 41.980 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 : 0.014 0.219 15245 Z= 0.893 Angle : 1.120 12.440 20705 Z= 0.579 Chirality : 0.071 0.783 2305 Planarity : 0.007 0.064 2630 Dihedral : 10.699 122.172 5615 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.63 % Allowed : 4.13 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.97 (0.15), residues: 1830 helix: -4.52 (0.09), residues: 580 sheet: -1.96 (0.26), residues: 385 loop : -2.97 (0.17), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 340 HIS 0.004 0.002 HIS D 40 PHE 0.016 0.003 PHE B 262 TYR 0.024 0.002 TYR D 294 ARG 0.005 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 240 average time/residue: 0.2944 time to fit residues: 101.4713 Evaluate side-chains 120 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1245 time to fit residues: 3.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 121 GLN B 137 GLN C 137 GLN D 360 GLN D 371 HIS E 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15245 Z= 0.339 Angle : 0.747 8.205 20705 Z= 0.362 Chirality : 0.051 0.224 2305 Planarity : 0.005 0.058 2630 Dihedral : 8.702 112.811 2120 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.21 % Allowed : 8.00 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.17), residues: 1830 helix: -3.29 (0.16), residues: 530 sheet: -1.56 (0.28), residues: 355 loop : -2.40 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.004 0.001 HIS D 371 PHE 0.008 0.001 PHE C 200 TYR 0.013 0.001 TYR E 294 ARG 0.004 0.001 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.919 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 143 average time/residue: 0.2802 time to fit residues: 61.1113 Evaluate side-chains 112 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1764 time to fit residues: 4.4426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 0.0980 chunk 114 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15245 Z= 0.270 Angle : 0.676 6.874 20705 Z= 0.322 Chirality : 0.049 0.168 2305 Planarity : 0.004 0.043 2630 Dihedral : 8.148 107.969 2120 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.35 % Allowed : 8.95 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.18), residues: 1830 helix: -2.52 (0.19), residues: 570 sheet: -1.54 (0.28), residues: 355 loop : -2.21 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS B 275 PHE 0.006 0.001 PHE A 21 TYR 0.013 0.001 TYR E 279 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.735 Fit side-chains outliers start: 37 outliers final: 9 residues processed: 141 average time/residue: 0.2722 time to fit residues: 59.0646 Evaluate side-chains 106 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1391 time to fit residues: 4.6333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 0.0980 chunk 113 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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: 0.8784 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15245 Z= 0.154 Angle : 0.611 7.275 20705 Z= 0.283 Chirality : 0.046 0.168 2305 Planarity : 0.004 0.034 2630 Dihedral : 7.646 99.856 2120 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.95 % Allowed : 10.35 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.98 (0.18), residues: 1830 helix: -2.02 (0.20), residues: 575 sheet: -1.55 (0.27), residues: 355 loop : -2.06 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.002 0.000 HIS B 275 PHE 0.005 0.001 PHE E 200 TYR 0.011 0.001 TYR A 279 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.807 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 124 average time/residue: 0.2491 time to fit residues: 48.6307 Evaluate side-chains 105 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1374 time to fit residues: 3.2430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- 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: 0.8826 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15245 Z= 0.254 Angle : 0.650 7.565 20705 Z= 0.303 Chirality : 0.048 0.160 2305 Planarity : 0.004 0.037 2630 Dihedral : 7.575 97.916 2120 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.02 % Allowed : 11.17 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.68 (0.18), residues: 1830 helix: -1.78 (0.21), residues: 545 sheet: -1.51 (0.27), residues: 355 loop : -1.83 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.003 0.001 HIS B 275 PHE 0.011 0.001 PHE E 200 TYR 0.010 0.001 TYR E 294 ARG 0.003 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.841 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 120 average time/residue: 0.2516 time to fit residues: 47.5733 Evaluate side-chains 102 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1399 time to fit residues: 3.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 0.0270 chunk 104 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 overall best weight: 7.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN E 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15245 Z= 0.330 Angle : 0.695 7.762 20705 Z= 0.330 Chirality : 0.050 0.172 2305 Planarity : 0.004 0.038 2630 Dihedral : 7.810 99.261 2120 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.95 % Allowed : 11.68 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.67 (0.18), residues: 1830 helix: -1.78 (0.21), residues: 540 sheet: -1.58 (0.27), residues: 355 loop : -1.78 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 340 HIS 0.004 0.001 HIS D 40 PHE 0.009 0.001 PHE E 200 TYR 0.017 0.001 TYR B 279 ARG 0.004 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 110 average time/residue: 0.2470 time to fit residues: 43.0239 Evaluate side-chains 101 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1476 time to fit residues: 4.1946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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: 0.8804 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15245 Z= 0.152 Angle : 0.594 7.020 20705 Z= 0.274 Chirality : 0.046 0.168 2305 Planarity : 0.004 0.032 2630 Dihedral : 7.333 95.437 2120 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.44 % Allowed : 11.87 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1830 helix: -1.36 (0.23), residues: 540 sheet: -1.52 (0.27), residues: 355 loop : -1.60 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.001 0.000 HIS C 173 PHE 0.008 0.001 PHE B 375 TYR 0.012 0.001 TYR B 279 ARG 0.002 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.822 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.2529 time to fit residues: 41.7145 Evaluate side-chains 98 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1384 time to fit residues: 3.1420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 0.0570 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 overall best weight: 5.8106 ------------------------------------------------------------------------------- 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: 0.8838 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15245 Z= 0.279 Angle : 0.648 8.747 20705 Z= 0.302 Chirality : 0.048 0.160 2305 Planarity : 0.004 0.035 2630 Dihedral : 7.412 97.047 2120 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.38 % Allowed : 12.57 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1830 helix: -1.33 (0.22), residues: 540 sheet: -1.53 (0.27), residues: 355 loop : -1.61 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 340 HIS 0.003 0.001 HIS D 40 PHE 0.008 0.001 PHE B 375 TYR 0.011 0.001 TYR B 279 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.810 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 0.2463 time to fit residues: 38.8005 Evaluate side-chains 97 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1494 time to fit residues: 2.8368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.4980 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 130 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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: 0.8813 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15245 Z= 0.185 Angle : 0.603 8.431 20705 Z= 0.277 Chirality : 0.046 0.165 2305 Planarity : 0.004 0.032 2630 Dihedral : 7.185 95.003 2120 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.51 % Allowed : 12.32 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.19), residues: 1830 helix: -1.11 (0.23), residues: 540 sheet: -1.48 (0.27), residues: 355 loop : -1.52 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 340 HIS 0.002 0.001 HIS D 40 PHE 0.016 0.001 PHE E 375 TYR 0.008 0.001 TYR E 240 ARG 0.003 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.789 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.2724 time to fit residues: 42.8208 Evaluate side-chains 99 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1605 time to fit residues: 4.0518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8824 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15245 Z= 0.224 Angle : 0.620 8.569 20705 Z= 0.286 Chirality : 0.047 0.161 2305 Planarity : 0.004 0.033 2630 Dihedral : 7.142 95.223 2120 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.13 % Allowed : 12.25 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.11 (0.19), residues: 1830 helix: -1.06 (0.23), residues: 540 sheet: -1.49 (0.27), residues: 355 loop : -1.50 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 340 HIS 0.002 0.001 HIS D 40 PHE 0.014 0.001 PHE E 375 TYR 0.009 0.001 TYR A 279 ARG 0.003 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 1.847 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.2544 time to fit residues: 40.1407 Evaluate side-chains 95 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.0980 chunk 44 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- 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 = 0.2834 r_free = 0.2834 target = 0.060194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.050370 restraints weight = 46277.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051971 restraints weight = 24447.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.053050 restraints weight = 15669.182| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15245 Z= 0.276 Angle : 0.649 8.584 20705 Z= 0.303 Chirality : 0.048 0.162 2305 Planarity : 0.004 0.035 2630 Dihedral : 7.244 97.053 2120 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.06 % Allowed : 12.63 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.29 (0.19), residues: 1830 helix: -1.35 (0.22), residues: 575 sheet: -1.53 (0.27), residues: 355 loop : -1.54 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 340 HIS 0.003 0.001 HIS D 40 PHE 0.014 0.001 PHE E 375 TYR 0.015 0.001 TYR D 279 ARG 0.005 0.000 ARG B 372 =============================================================================== Job complete usr+sys time: 2224.54 seconds wall clock time: 41 minutes 51.70 seconds (2511.70 seconds total)