Starting phenix.real_space_refine on Fri Feb 16 09:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/02_2024/6u96_20694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/02_2024/6u96_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_20694/02_2024/6u96_20694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/02_2024/6u96_20694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/02_2024/6u96_20694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/02_2024/6u96_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-dev-5238/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 Unresolved non-hydrogen dihedrals: 4 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 Unresolved non-hydrogen dihedrals: 4 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 Unresolved non-hydrogen dihedrals: 4 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 Unresolved non-hydrogen dihedrals: 4 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 Unresolved non-hydrogen dihedrals: 4 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: 8.15, 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: 5.36 Conformation dependent library (CDL) restraints added in 2.9 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: 2.82 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: 3.75 Time building geometry restraints manager: 5.80 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: 8975 24.43 - 48.87: 190 48.87 - 73.30: 15 73.30 - 97.74: 10 97.74 - 122.17: 5 Dihedral angle restraints: 9195 sinusoidal: 3735 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 9192 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: 0.280 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: 2.110 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.770 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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: 0.010 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: 46.490 ------------------------------------------------------------------------------- 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 : 11.419 122.172 5695 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 : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 THR cc_start: 0.9112 (p) cc_final: 0.8887 (t) REVERT: E 216 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8524 (pp) outliers start: 10 outliers final: 4 residues processed: 240 average time/residue: 0.2902 time to fit residues: 99.6747 Evaluate side-chains 122 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU 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: B 121 GLN B 137 GLN D 360 GLN D 371 HIS E 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2127 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= 0.338 Angle : 0.737 7.447 20705 Z= 0.359 Chirality : 0.050 0.192 2305 Planarity : 0.005 0.061 2630 Dihedral : 10.568 112.150 2210 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.46 % Allowed : 7.56 % Favored : 90.98 % 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: -3.78 (0.17), residues: 1830 helix: -3.30 (0.16), residues: 530 sheet: -1.55 (0.28), residues: 355 loop : -2.39 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.005 0.001 HIS D 88 PHE 0.008 0.001 PHE A 375 TYR 0.013 0.001 TYR E 294 ARG 0.005 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 152 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.687 Fit side-chains REVERT: A 283 MET cc_start: 0.9102 (tpp) cc_final: 0.8737 (tpp) REVERT: A 325 MET cc_start: 0.8692 (mtt) cc_final: 0.8467 (mtt) REVERT: B 208 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9111 (mt) REVERT: B 355 MET cc_start: 0.8539 (mmm) cc_final: 0.8080 (mtp) REVERT: E 283 MET cc_start: 0.9114 (tpp) cc_final: 0.8700 (tpp) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 0.2725 time to fit residues: 60.8761 Evaluate side-chains 117 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 HIS C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15245 Z= 0.330 Angle : 0.707 6.874 20705 Z= 0.339 Chirality : 0.050 0.169 2305 Planarity : 0.005 0.045 2630 Dihedral : 10.001 109.558 2210 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.98 % Allowed : 8.83 % Favored : 88.19 % 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: -3.36 (0.18), residues: 1830 helix: -2.52 (0.19), residues: 565 sheet: -1.59 (0.27), residues: 355 loop : -2.26 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 340 HIS 0.004 0.001 HIS B 275 PHE 0.008 0.001 PHE B 21 TYR 0.013 0.001 TYR E 294 ARG 0.004 0.001 ARG C 256 *********************** 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 154 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 107 time to evaluate : 1.627 Fit side-chains REVERT: A 82 MET cc_start: 0.9136 (tpp) cc_final: 0.8913 (mmm) REVERT: A 244 ASP cc_start: 0.7974 (t0) cc_final: 0.7687 (t0) REVERT: A 283 MET cc_start: 0.8934 (tpp) cc_final: 0.8686 (tpp) REVERT: A 325 MET cc_start: 0.8575 (mtt) cc_final: 0.8366 (mtt) REVERT: B 283 MET cc_start: 0.8874 (tpp) cc_final: 0.8133 (mpp) REVERT: B 349 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 355 MET cc_start: 0.8576 (mmm) cc_final: 0.8198 (mtp) REVERT: C 349 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8678 (mp) REVERT: D 325 MET cc_start: 0.9313 (mmm) cc_final: 0.9086 (mmt) REVERT: E 236 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8758 (pt) REVERT: E 283 MET cc_start: 0.9050 (tpp) cc_final: 0.8590 (tpp) outliers start: 47 outliers final: 21 residues processed: 150 average time/residue: 0.2368 time to fit residues: 54.7159 Evaluate side-chains 122 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.8805 moved from start: 0.2909 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= 0.180 Angle : 0.617 6.383 20705 Z= 0.289 Chirality : 0.047 0.169 2305 Planarity : 0.004 0.036 2630 Dihedral : 9.483 102.007 2210 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.65 % Allowed : 10.67 % 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: -3.01 (0.18), residues: 1830 helix: -2.01 (0.20), residues: 570 sheet: -1.58 (0.27), residues: 355 loop : -2.11 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.002 0.001 HIS B 275 PHE 0.005 0.001 PHE C 200 TYR 0.008 0.001 TYR E 294 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 129 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.756 Fit side-chains REVERT: A 82 MET cc_start: 0.9144 (tpp) cc_final: 0.8918 (mmm) REVERT: A 208 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8951 (mt) REVERT: A 244 ASP cc_start: 0.7936 (t0) cc_final: 0.7536 (t0) REVERT: B 82 MET cc_start: 0.8846 (tpp) cc_final: 0.8640 (mmm) REVERT: B 269 MET cc_start: 0.8877 (ttm) cc_final: 0.8584 (ttm) REVERT: B 349 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8652 (mp) REVERT: B 355 MET cc_start: 0.8514 (mmm) cc_final: 0.8159 (mtp) REVERT: C 49 GLN cc_start: 0.8647 (pp30) cc_final: 0.8373 (tm-30) REVERT: D 82 MET cc_start: 0.8802 (mmm) cc_final: 0.8405 (tpt) REVERT: E 236 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8721 (pt) REVERT: E 283 MET cc_start: 0.8979 (tpp) cc_final: 0.8684 (tpp) outliers start: 26 outliers final: 13 residues processed: 126 average time/residue: 0.2428 time to fit residues: 47.9544 Evaluate side-chains 114 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 374 CYS 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: 9.9990 chunk 2 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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: 0.8885 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15245 Z= 0.443 Angle : 0.765 7.193 20705 Z= 0.368 Chirality : 0.053 0.188 2305 Planarity : 0.005 0.045 2630 Dihedral : 9.806 106.396 2210 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.29 % Allowed : 10.60 % Favored : 87.11 % 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: -2.99 (0.18), residues: 1830 helix: -2.09 (0.20), residues: 535 sheet: -1.71 (0.27), residues: 355 loop : -1.98 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 340 HIS 0.005 0.002 HIS D 40 PHE 0.011 0.002 PHE E 200 TYR 0.015 0.002 TYR A 279 ARG 0.005 0.001 ARG A 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 134 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.620 Fit side-chains REVERT: A 49 GLN cc_start: 0.8619 (pt0) cc_final: 0.8406 (tm-30) REVERT: A 82 MET cc_start: 0.9205 (tpp) cc_final: 0.8949 (mmm) REVERT: A 208 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9075 (mt) REVERT: A 244 ASP cc_start: 0.8068 (t0) cc_final: 0.7661 (t0) REVERT: A 283 MET cc_start: 0.8735 (tpp) cc_final: 0.8488 (mpp) REVERT: B 244 ASP cc_start: 0.7661 (t0) cc_final: 0.7359 (m-30) REVERT: B 283 MET cc_start: 0.8805 (tpp) cc_final: 0.8179 (mpp) REVERT: B 349 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8694 (mp) REVERT: C 349 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8745 (mp) REVERT: E 49 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: E 236 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8748 (pt) outliers start: 36 outliers final: 18 residues processed: 132 average time/residue: 0.2284 time to fit residues: 48.0023 Evaluate side-chains 122 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3281 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= 0.226 Angle : 0.630 6.476 20705 Z= 0.297 Chirality : 0.047 0.170 2305 Planarity : 0.004 0.036 2630 Dihedral : 9.320 102.029 2210 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.71 % Allowed : 11.37 % Favored : 86.92 % 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: -1.66 (0.22), residues: 535 sheet: -1.65 (0.27), residues: 355 loop : -1.84 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.002 0.001 HIS B 371 PHE 0.005 0.001 PHE E 200 TYR 0.012 0.001 TYR E 279 ARG 0.003 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 127 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.721 Fit side-chains REVERT: A 244 ASP cc_start: 0.8094 (t0) cc_final: 0.7709 (t0) REVERT: A 283 MET cc_start: 0.8768 (tpp) cc_final: 0.8479 (tpp) REVERT: B 244 ASP cc_start: 0.7547 (t0) cc_final: 0.7338 (m-30) REVERT: B 269 MET cc_start: 0.8971 (ttm) cc_final: 0.8724 (ttm) REVERT: B 349 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 355 MET cc_start: 0.8528 (mmm) cc_final: 0.8176 (mtt) REVERT: C 349 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8808 (mp) REVERT: E 236 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8683 (pt) REVERT: E 283 MET cc_start: 0.8871 (tpp) cc_final: 0.8500 (tpp) outliers start: 27 outliers final: 15 residues processed: 126 average time/residue: 0.2292 time to fit residues: 45.5658 Evaluate side-chains 113 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.0470 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 178 optimal weight: 0.0170 chunk 111 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 0.0980 overall best weight: 1.3918 ------------------------------------------------------------------------------- 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: 0.8793 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15245 Z= 0.128 Angle : 0.577 6.664 20705 Z= 0.266 Chirality : 0.045 0.168 2305 Planarity : 0.003 0.029 2630 Dihedral : 8.653 91.917 2210 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.08 % Allowed : 11.87 % 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: -2.26 (0.19), residues: 1830 helix: -1.22 (0.23), residues: 540 sheet: -1.53 (0.27), residues: 355 loop : -1.58 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.001 0.000 HIS C 173 PHE 0.005 0.001 PHE B 255 TYR 0.009 0.001 TYR E 240 ARG 0.003 0.000 ARG C 290 *********************** 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 115 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.753 Fit side-chains REVERT: A 82 MET cc_start: 0.8884 (mmm) cc_final: 0.8659 (tpt) REVERT: A 244 ASP cc_start: 0.7898 (t0) cc_final: 0.7618 (t0) REVERT: A 283 MET cc_start: 0.8634 (tpp) cc_final: 0.8381 (tpp) REVERT: B 244 ASP cc_start: 0.7622 (t0) cc_final: 0.7387 (m-30) REVERT: B 269 MET cc_start: 0.8909 (ttm) cc_final: 0.8660 (ttm) REVERT: B 355 MET cc_start: 0.8471 (mmm) cc_final: 0.8227 (mtp) REVERT: D 82 MET cc_start: 0.8697 (mmm) cc_final: 0.8290 (tpt) REVERT: E 236 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8660 (pt) REVERT: E 283 MET cc_start: 0.8859 (tpp) cc_final: 0.8155 (mpp) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.2324 time to fit residues: 41.7076 Evaluate side-chains 108 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR 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: 10.0000 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 113 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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: 0.8809 moved from start: 0.3500 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= 0.168 Angle : 0.586 6.691 20705 Z= 0.270 Chirality : 0.046 0.162 2305 Planarity : 0.003 0.030 2630 Dihedral : 8.547 89.913 2210 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.46 % Allowed : 11.81 % Favored : 86.73 % 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: -1.00 (0.23), residues: 545 sheet: -1.48 (0.27), residues: 355 loop : -1.54 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 340 HIS 0.002 0.001 HIS B 275 PHE 0.006 0.001 PHE C 200 TYR 0.009 0.001 TYR E 240 ARG 0.003 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 120 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.617 Fit side-chains REVERT: A 124 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: A 244 ASP cc_start: 0.7915 (t0) cc_final: 0.7671 (t0) REVERT: A 283 MET cc_start: 0.8658 (tpp) cc_final: 0.8369 (tpp) REVERT: B 132 MET cc_start: 0.8427 (ptm) cc_final: 0.8199 (ptt) REVERT: B 244 ASP cc_start: 0.7677 (t0) cc_final: 0.7414 (m-30) REVERT: B 269 MET cc_start: 0.8928 (ttm) cc_final: 0.8663 (ttm) REVERT: B 283 MET cc_start: 0.8721 (tpp) cc_final: 0.8438 (tpp) REVERT: B 355 MET cc_start: 0.8471 (mmm) cc_final: 0.8219 (mtp) REVERT: D 82 MET cc_start: 0.8717 (mmm) cc_final: 0.8310 (tpt) REVERT: E 236 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8648 (pt) REVERT: E 283 MET cc_start: 0.8832 (tpp) cc_final: 0.8066 (mpp) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.2159 time to fit residues: 40.7749 Evaluate side-chains 112 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 0.0570 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- 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: 0.8822 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15245 Z= 0.202 Angle : 0.601 6.702 20705 Z= 0.278 Chirality : 0.047 0.162 2305 Planarity : 0.004 0.031 2630 Dihedral : 8.520 91.024 2210 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.46 % Allowed : 11.75 % Favored : 86.79 % 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: -2.00 (0.19), residues: 1830 helix: -0.93 (0.23), residues: 540 sheet: -1.45 (0.27), residues: 355 loop : -1.45 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 340 HIS 0.002 0.001 HIS B 275 PHE 0.006 0.001 PHE C 200 TYR 0.009 0.001 TYR B 240 ARG 0.004 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 118 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.558 Fit side-chains REVERT: A 124 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: A 244 ASP cc_start: 0.7948 (t0) cc_final: 0.7709 (t0) REVERT: A 283 MET cc_start: 0.8597 (tpp) cc_final: 0.8335 (tpp) REVERT: B 132 MET cc_start: 0.8413 (ptm) cc_final: 0.8191 (ptt) REVERT: B 244 ASP cc_start: 0.7707 (t0) cc_final: 0.7440 (m-30) REVERT: B 269 MET cc_start: 0.8959 (ttm) cc_final: 0.8689 (ttm) REVERT: B 325 MET cc_start: 0.9329 (mmm) cc_final: 0.9112 (mmt) REVERT: B 355 MET cc_start: 0.8547 (mmm) cc_final: 0.8284 (mtp) REVERT: C 349 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8697 (mp) REVERT: D 82 MET cc_start: 0.8759 (mmm) cc_final: 0.8349 (tpt) REVERT: E 283 MET cc_start: 0.8825 (tpp) cc_final: 0.8112 (mpp) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.2174 time to fit residues: 39.3697 Evaluate side-chains 116 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3602 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= 0.179 Angle : 0.592 6.751 20705 Z= 0.272 Chirality : 0.046 0.163 2305 Planarity : 0.003 0.030 2630 Dihedral : 8.377 89.856 2210 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.33 % Allowed : 11.87 % Favored : 86.79 % 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: -1.93 (0.19), residues: 1830 helix: -0.83 (0.23), residues: 540 sheet: -1.53 (0.27), residues: 365 loop : -1.36 (0.20), residues: 925 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 0.007 0.001 PHE C 200 TYR 0.010 0.001 TYR C 279 ARG 0.005 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 117 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.778 Fit side-chains REVERT: A 124 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8429 (m-10) REVERT: A 244 ASP cc_start: 0.7925 (t0) cc_final: 0.7661 (t0) REVERT: A 283 MET cc_start: 0.8553 (tpp) cc_final: 0.8294 (tpp) REVERT: B 132 MET cc_start: 0.8359 (ptm) cc_final: 0.8145 (ptt) REVERT: B 244 ASP cc_start: 0.7713 (t0) cc_final: 0.7438 (m-30) REVERT: B 269 MET cc_start: 0.8949 (ttm) cc_final: 0.8681 (ttm) REVERT: B 325 MET cc_start: 0.9355 (mmm) cc_final: 0.9140 (mmt) REVERT: B 355 MET cc_start: 0.8558 (mmm) cc_final: 0.8273 (mtp) REVERT: C 349 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8717 (mp) REVERT: D 82 MET cc_start: 0.8739 (mmm) cc_final: 0.8333 (tpt) REVERT: E 283 MET cc_start: 0.8801 (tpp) cc_final: 0.8077 (mpp) outliers start: 21 outliers final: 18 residues processed: 113 average time/residue: 0.2426 time to fit residues: 44.6718 Evaluate side-chains 116 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.0070 chunk 44 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- 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 = 0.2833 r_free = 0.2833 target = 0.060207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.050357 restraints weight = 46561.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.051955 restraints weight = 24607.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.053030 restraints weight = 15801.118| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15245 Z= 0.250 Angle : 0.630 6.745 20705 Z= 0.293 Chirality : 0.048 0.161 2305 Planarity : 0.004 0.033 2630 Dihedral : 8.484 92.952 2210 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.52 % Allowed : 11.94 % Favored : 86.54 % 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: -1.13 (0.22), residues: 580 sheet: -1.55 (0.27), residues: 365 loop : -1.46 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 340 HIS 0.002 0.001 HIS B 371 PHE 0.018 0.001 PHE E 375 TYR 0.010 0.001 TYR D 279 ARG 0.003 0.000 ARG B 183 =============================================================================== Job complete usr+sys time: 2161.88 seconds wall clock time: 40 minutes 50.96 seconds (2450.96 seconds total)