Starting phenix.real_space_refine on Tue Apr 7 12:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.map" model { file = "/net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9coc_45775/04_2026/9coc_45775.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 4 5.21 5 S 184 5.16 5 C 17068 2.51 5 N 4608 2.21 5 O 5266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27150 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3332 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3334 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3332 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3334 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3398 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3394 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3398 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3384 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.94, per 1000 atoms: 0.22 Number of scatterers: 27150 At special positions: 0 Unit cell: (115.785, 113.295, 200.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 184 16.00 P 20 15.00 Mg 4 11.99 O 5266 8.00 N 4608 7.00 C 17068 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6388 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 20 sheets defined 55.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.311A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.936A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 127 removed outlier: 4.751A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.144A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.646A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.544A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.513A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 392 removed outlier: 3.941A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.097A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.952A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 41 through 46 removed outlier: 4.017A pdb=" N ARG E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.636A pdb=" N PHE E 85 " --> pdb=" O GLY E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 108 through 126 removed outlier: 4.587A pdb=" N ASP E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 159 removed outlier: 3.962A pdb=" N THR E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 removed outlier: 3.837A pdb=" N GLN E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 214 Processing helix chain 'E' and resid 221 through 237 Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.097A pdb=" N GLN E 280 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG E 282 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.548A pdb=" N PHE E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 299 Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 322 through 337 removed outlier: 3.562A pdb=" N GLN E 334 " --> pdb=" O MET E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 341 Processing helix chain 'E' and resid 374 through 391 removed outlier: 3.675A pdb=" N PHE E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 removed outlier: 4.116A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 401 " --> pdb=" O TRP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 428 removed outlier: 3.813A pdb=" N PHE E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.537A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.205A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.657A pdb=" N PHE F 85 " --> pdb=" O GLY F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 106 through 127 removed outlier: 4.112A pdb=" N GLU F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.750A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.572A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 277 through 281 removed outlier: 3.629A pdb=" N GLN F 280 " --> pdb=" O GLY F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 295 Processing helix chain 'F' and resid 296 through 299 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.648A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 392 removed outlier: 4.133A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.178A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.896A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.089A pdb=" N ARG K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 70 through 79 Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.600A pdb=" N PHE K 85 " --> pdb=" O GLY K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 108 through 126 removed outlier: 4.551A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP K 118 " --> pdb=" O ASP K 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 159 Processing helix chain 'K' and resid 180 through 196 removed outlier: 3.893A pdb=" N GLN K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU K 194 " --> pdb=" O HIS K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 221 through 237 removed outlier: 3.652A pdb=" N THR K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 Processing helix chain 'K' and resid 249 through 258 Processing helix chain 'K' and resid 277 through 281 removed outlier: 3.632A pdb=" N GLN K 280 " --> pdb=" O GLY K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 295 Processing helix chain 'K' and resid 296 through 299 removed outlier: 3.559A pdb=" N MET K 299 " --> pdb=" O ALA K 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 296 through 299' Processing helix chain 'K' and resid 304 through 308 removed outlier: 3.560A pdb=" N HIS K 307 " --> pdb=" O ASP K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 337 Processing helix chain 'K' and resid 338 through 341 Processing helix chain 'K' and resid 373 through 391 removed outlier: 3.948A pdb=" N LEU K 377 " --> pdb=" O ALA K 373 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 401 removed outlier: 4.426A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 428 removed outlier: 3.694A pdb=" N PHE K 408 " --> pdb=" O ASP K 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.717A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 removed outlier: 4.286A pdb=" N PHE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.334A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.067A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 205 through 218 removed outlier: 3.504A pdb=" N ASP A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.506A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.773A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.695A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.999A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.089A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.926A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.755A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.795A pdb=" N ALA D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 removed outlier: 3.753A pdb=" N THR D 51 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.518A pdb=" N GLU D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 85 removed outlier: 4.320A pdb=" N GLN D 85 " --> pdb=" O THR D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 111 through 128 removed outlier: 4.495A pdb=" N ASP D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 removed outlier: 4.699A pdb=" N THR D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.690A pdb=" N LEU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 4.407A pdb=" N GLN D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 removed outlier: 3.861A pdb=" N TYR D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 removed outlier: 3.740A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 338 Processing helix chain 'D' and resid 383 through 400 removed outlier: 4.010A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.061A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 4.096A pdb=" N PHE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.770A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 removed outlier: 4.186A pdb=" N PHE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.645A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 108 through 129 removed outlier: 3.719A pdb=" N GLU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.081A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.556A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.806A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.999A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.805A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.124A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.003A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 437 removed outlier: 3.787A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 44 through 51 removed outlier: 3.716A pdb=" N THR I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 removed outlier: 3.647A pdb=" N GLU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 85 removed outlier: 4.324A pdb=" N GLN I 85 " --> pdb=" O THR I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 82 through 85' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 110 through 113 Processing helix chain 'I' and resid 114 through 128 removed outlier: 3.879A pdb=" N GLN I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 161 Processing helix chain 'I' and resid 182 through 195 Processing helix chain 'I' and resid 205 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.570A pdb=" N LEU I 227 " --> pdb=" O THR I 223 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 260 removed outlier: 4.435A pdb=" N GLN I 256 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR I 257 " --> pdb=" O THR I 253 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN I 258 " --> pdb=" O GLU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 282 removed outlier: 4.179A pdb=" N TYR I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 removed outlier: 3.763A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 338 removed outlier: 3.639A pdb=" N VAL I 328 " --> pdb=" O VAL I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 400 removed outlier: 3.974A pdb=" N ALA I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET I 398 " --> pdb=" O LYS I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 411 removed outlier: 4.047A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 436 removed outlier: 3.733A pdb=" N SER I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.752A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.685A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 90 through 92 removed outlier: 7.995A pdb=" N VAL E 91 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU E 65 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE E 64 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS E 6 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL E 66 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN E 8 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 3 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLN E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 5 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR E 136 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E 7 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N SER E 138 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ALA E 9 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ASN E 165 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE E 133 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE E 167 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU E 135 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL E 169 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS E 137 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET E 164 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR E 200 " --> pdb=" O MET E 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR E 166 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE E 202 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER E 168 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR E 199 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS E 201 " --> pdb=" O PRO E 268 " (cutoff:3.500A) removed outlier: 10.464A pdb=" N PHE E 270 " --> pdb=" O CYS E 201 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE E 265 " --> pdb=" O SER E 371 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N SER E 371 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.580A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASP F 203 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N PHE F 270 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.724A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 90 through 92 removed outlier: 8.161A pdb=" N VAL K 91 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU K 65 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE K 64 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS K 6 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL K 66 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLN K 8 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU K 3 " --> pdb=" O LEU K 130 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY K 132 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER K 138 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN K 131 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN K 165 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE K 133 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE K 167 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU K 135 " --> pdb=" O PHE K 167 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 169 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N HIS K 137 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET K 164 " --> pdb=" O GLU K 198 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TYR K 200 " --> pdb=" O MET K 164 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR K 166 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE K 202 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER K 168 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR K 199 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N CYS K 201 " --> pdb=" O PRO K 268 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N PHE K 270 " --> pdb=" O CYS K 201 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE K 265 " --> pdb=" O SER K 371 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER K 371 " --> pdb=" O PHE K 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.999A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.798A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.016A pdb=" N ILE D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE D 67 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL D 66 " --> pdb=" O CYS D 4 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL D 137 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D 7 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N SER D 165 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN D 133 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE D 135 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS D 200 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'D' and resid 269 through 273 Processing sheet with id=AB6, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.809A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS C 200 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB8, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.837A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.773A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL I 137 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE I 7 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER I 165 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS I 166 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N PHE I 202 " --> pdb=" O LYS I 166 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU I 168 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL I 204 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER I 170 " --> pdb=" O VAL I 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'I' and resid 269 through 273 1336 hydrogen bonds defined for protein. 3879 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: 5.18 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6347 1.33 - 1.46: 6585 1.46 - 1.58: 14515 1.58 - 1.70: 35 1.70 - 1.83: 288 Bond restraints: 27770 Sorted by residual: bond pdb=" N VAL C 204 " pdb=" CA VAL C 204 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.72e+00 bond pdb=" N GLU I 284 " pdb=" CA GLU I 284 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.23e-02 6.61e+03 9.49e+00 bond pdb=" N VAL I 371 " pdb=" CA VAL I 371 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.33e+00 bond pdb=" N THR E 178 " pdb=" CA THR E 178 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.21e-02 6.83e+03 9.28e+00 bond pdb=" C ASP A 306 " pdb=" N PRO A 307 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.19e-02 7.06e+03 9.20e+00 ... (remaining 27765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 36828 2.72 - 5.44: 789 5.44 - 8.16: 128 8.16 - 10.88: 12 10.88 - 13.61: 7 Bond angle restraints: 37764 Sorted by residual: angle pdb=" N GLU K 405 " pdb=" CA GLU K 405 " pdb=" C GLU K 405 " ideal model delta sigma weight residual 113.01 106.42 6.59 1.20e+00 6.94e-01 3.02e+01 angle pdb=" CB LYS B 336 " pdb=" CG LYS B 336 " pdb=" CD LYS B 336 " ideal model delta sigma weight residual 111.30 123.08 -11.78 2.30e+00 1.89e-01 2.62e+01 angle pdb=" CB LYS B 216 " pdb=" CG LYS B 216 " pdb=" CD LYS B 216 " ideal model delta sigma weight residual 111.30 122.80 -11.50 2.30e+00 1.89e-01 2.50e+01 angle pdb=" CB ARG I 339 " pdb=" CG ARG I 339 " pdb=" CD ARG I 339 " ideal model delta sigma weight residual 111.30 122.73 -11.43 2.30e+00 1.89e-01 2.47e+01 angle pdb=" CG ARG F 359 " pdb=" CD ARG F 359 " pdb=" NE ARG F 359 " ideal model delta sigma weight residual 112.00 122.23 -10.23 2.20e+00 2.07e-01 2.16e+01 ... (remaining 37759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 16028 35.81 - 71.62: 360 71.62 - 107.42: 37 107.42 - 143.23: 10 143.23 - 179.04: 5 Dihedral angle restraints: 16440 sinusoidal: 6466 harmonic: 9974 Sorted by residual: dihedral pdb=" C5' GTP I 501 " pdb=" O5' GTP I 501 " pdb=" PA GTP I 501 " pdb=" O3A GTP I 501 " ideal model delta sinusoidal sigma weight residual 69.27 -109.77 179.04 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.43 -166.30 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.80 -165.93 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 16437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3047 0.052 - 0.104: 851 0.104 - 0.156: 226 0.156 - 0.208: 28 0.208 - 0.260: 2 Chirality restraints: 4154 Sorted by residual: chirality pdb=" CA ILE I 219 " pdb=" N ILE I 219 " pdb=" C ILE I 219 " pdb=" CB ILE I 219 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE C 219 " pdb=" N ILE C 219 " pdb=" C ILE C 219 " pdb=" CB ILE C 219 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE K 155 " pdb=" CA ILE K 155 " pdb=" CG1 ILE K 155 " pdb=" CG2 ILE K 155 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 4151 not shown) Planarity restraints: 4924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 359 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ARG F 359 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG F 359 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY F 360 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 120 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" CG ASP D 120 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASP D 120 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP D 120 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 391 " 0.255 9.50e-02 1.11e+02 1.14e-01 8.06e+00 pdb=" NE ARG E 391 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 391 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 391 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 391 " 0.008 2.00e-02 2.50e+03 ... (remaining 4921 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 120 2.55 - 3.14: 21135 3.14 - 3.73: 43856 3.73 - 4.31: 62813 4.31 - 4.90: 106095 Nonbonded interactions: 234019 Sorted by model distance: nonbonded pdb=" O1G GTP I 501 " pdb="MG MG I 502 " model vdw 1.964 2.170 nonbonded pdb=" O2B GTP C 501 " pdb="MG MG C 502 " model vdw 1.978 2.170 nonbonded pdb=" O2B GTP I 501 " pdb="MG MG I 502 " model vdw 1.980 2.170 nonbonded pdb=" OE2 GLU C 71 " pdb="MG MG C 502 " model vdw 1.980 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 1.982 2.170 ... (remaining 234014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 439 or resid 501 through 502)) selection = (chain 'D' and (resid 1 through 439 or resid 501 through 502)) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 1 through 335 or (resid 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 501)) selection = (chain 'E' and (resid 1 through 281 or (resid 282 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 501)) selection = (chain 'F' and (resid 1 through 335 or (resid 336 and (name N or name CA or name \ C or name O or name CB )) or resid 337 through 501)) selection = (chain 'K' and (resid 1 through 281 or (resid 282 through 283 and (name N or nam \ e CA or name C or name O or name CB )) or resid 284 through 501)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 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: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.950 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.006 0.069 27770 Z= 0.279 Angle : 0.983 13.606 37764 Z= 0.532 Chirality : 0.052 0.260 4154 Planarity : 0.007 0.114 4924 Dihedral : 16.016 179.039 10052 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.45 % Allowed : 8.34 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3438 helix: 0.54 (0.12), residues: 1527 sheet: -0.20 (0.22), residues: 544 loop : -0.59 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 308 TYR 0.027 0.002 TYR D 224 PHE 0.022 0.002 PHE K 92 TRP 0.019 0.002 TRP A 21 HIS 0.013 0.002 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00612 (27770) covalent geometry : angle 0.98350 (37764) hydrogen bonds : bond 0.13398 ( 1336) hydrogen bonds : angle 6.12062 ( 3879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 559 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.7798 (mt0) cc_final: 0.7177 (mm110) REVERT: B 122 LYS cc_start: 0.6973 (ttpp) cc_final: 0.6743 (ttmt) REVERT: B 153 SER cc_start: 0.7700 (t) cc_final: 0.7378 (p) REVERT: B 154 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8118 (mttp) REVERT: B 161 ASP cc_start: 0.7585 (t0) cc_final: 0.6969 (t0) REVERT: B 164 MET cc_start: 0.8396 (tpp) cc_final: 0.8001 (tpp) REVERT: B 209 ASP cc_start: 0.7549 (m-30) cc_final: 0.7285 (t0) REVERT: B 267 MET cc_start: 0.7821 (mtp) cc_final: 0.7226 (ptp) REVERT: B 332 ASN cc_start: 0.7538 (t0) cc_final: 0.7170 (m110) REVERT: B 362 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7705 (ttpt) REVERT: B 379 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7992 (mtpp) REVERT: E 37 HIS cc_start: 0.8350 (m-70) cc_final: 0.8009 (m-70) REVERT: E 86 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7353 (ttp-170) REVERT: E 161 ASP cc_start: 0.7500 (t70) cc_final: 0.6770 (t0) REVERT: E 194 GLU cc_start: 0.8265 (pt0) cc_final: 0.7684 (pm20) REVERT: E 205 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: E 280 GLN cc_start: 0.8198 (mt0) cc_final: 0.7828 (mp10) REVERT: E 328 GLU cc_start: 0.6506 (tm-30) cc_final: 0.6155 (pt0) REVERT: E 362 LYS cc_start: 0.8260 (mttt) cc_final: 0.7930 (ptmm) REVERT: E 403 MET cc_start: 0.8336 (ptm) cc_final: 0.7563 (ptp) REVERT: F 53 GLU cc_start: 0.8449 (tt0) cc_final: 0.7974 (tp30) REVERT: F 88 ASP cc_start: 0.8481 (m-30) cc_final: 0.8035 (m-30) REVERT: F 95 SER cc_start: 0.8522 (m) cc_final: 0.8044 (p) REVERT: F 121 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7559 (ttp-110) REVERT: F 212 PHE cc_start: 0.6043 (m-10) cc_final: 0.5823 (t80) REVERT: F 213 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7525 (ttm110) REVERT: F 232 THR cc_start: 0.7776 (m) cc_final: 0.7543 (p) REVERT: F 300 MET cc_start: 0.8455 (mtt) cc_final: 0.8035 (mtp) REVERT: F 330 MET cc_start: 0.7793 (mmm) cc_final: 0.7537 (mmp) REVERT: F 388 MET cc_start: 0.8772 (mtm) cc_final: 0.8439 (mtm) REVERT: F 399 THR cc_start: 0.7718 (m) cc_final: 0.7341 (p) REVERT: F 406 MET cc_start: 0.7351 (tpp) cc_final: 0.6890 (tpp) REVERT: F 413 SER cc_start: 0.8300 (t) cc_final: 0.7948 (p) REVERT: K 55 THR cc_start: 0.8007 (m) cc_final: 0.7633 (p) REVERT: K 83 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7618 (tt0) REVERT: K 88 ASP cc_start: 0.8478 (m-30) cc_final: 0.8218 (m-30) REVERT: K 103 LYS cc_start: 0.8054 (tttt) cc_final: 0.7769 (tttm) REVERT: K 114 ASP cc_start: 0.8722 (m-30) cc_final: 0.8265 (m-30) REVERT: K 121 ARG cc_start: 0.7061 (ttm110) cc_final: 0.6837 (mtm-85) REVERT: K 267 MET cc_start: 0.8152 (mtp) cc_final: 0.7801 (mtm) REVERT: K 288 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6903 (tm-30) REVERT: K 321 MET cc_start: 0.8971 (ptp) cc_final: 0.8743 (ptp) REVERT: K 332 ASN cc_start: 0.8318 (m-40) cc_final: 0.7993 (m-40) REVERT: K 362 LYS cc_start: 0.8459 (ptmt) cc_final: 0.7916 (mppt) REVERT: K 415 MET cc_start: 0.6843 (tpp) cc_final: 0.6557 (mmt) REVERT: A 1 MET cc_start: 0.6591 (tpp) cc_final: 0.5843 (tmm) REVERT: A 24 TYR cc_start: 0.7101 (m-10) cc_final: 0.6122 (m-80) REVERT: A 50 ASN cc_start: 0.7858 (t0) cc_final: 0.7187 (t0) REVERT: A 123 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6744 (ttp-110) REVERT: A 284 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7084 (mm-30) REVERT: A 342 GLN cc_start: 0.7994 (mt0) cc_final: 0.7163 (mm110) REVERT: A 361 THR cc_start: 0.8293 (m) cc_final: 0.8015 (p) REVERT: A 370 LYS cc_start: 0.8462 (tppp) cc_final: 0.7945 (tptp) REVERT: A 430 LYS cc_start: 0.8325 (tttt) cc_final: 0.7869 (tppp) REVERT: D 52 PHE cc_start: 0.8000 (m-80) cc_final: 0.7767 (m-10) REVERT: D 90 GLU cc_start: 0.7413 (mp0) cc_final: 0.6736 (tp30) REVERT: D 97 GLU cc_start: 0.6621 (tt0) cc_final: 0.5865 (pt0) REVERT: D 98 ASP cc_start: 0.6897 (t0) cc_final: 0.6659 (t0) REVERT: D 120 ASP cc_start: 0.7656 (m-30) cc_final: 0.7347 (m-30) REVERT: D 168 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 251 ASP cc_start: 0.7446 (m-30) cc_final: 0.6986 (p0) REVERT: D 254 GLU cc_start: 0.3346 (mm-30) cc_final: 0.1605 (mm-30) REVERT: D 284 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6938 (mm-30) REVERT: D 287 SER cc_start: 0.7357 (t) cc_final: 0.7044 (m) REVERT: D 290 GLU cc_start: 0.7536 (mp0) cc_final: 0.7227 (mt-10) REVERT: D 434 GLU cc_start: 0.7332 (tt0) cc_final: 0.7008 (tm-30) REVERT: C 50 ASN cc_start: 0.7737 (t0) cc_final: 0.7302 (t0) REVERT: C 113 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7623 (mm-30) REVERT: C 128 GLN cc_start: 0.7364 (tt0) cc_final: 0.6814 (tm-30) REVERT: C 282 TYR cc_start: 0.7622 (m-80) cc_final: 0.7400 (m-10) REVERT: C 302 MET cc_start: 0.8459 (mtt) cc_final: 0.8198 (mtm) REVERT: C 337 THR cc_start: 0.7414 (m) cc_final: 0.7059 (p) REVERT: C 415 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7228 (tt0) REVERT: I 55 GLU cc_start: 0.7680 (tt0) cc_final: 0.7452 (tp30) REVERT: I 90 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7403 (tm-30) REVERT: I 211 ASP cc_start: 0.7760 (m-30) cc_final: 0.7354 (m-30) REVERT: I 251 ASP cc_start: 0.7474 (m-30) cc_final: 0.7085 (m-30) REVERT: I 279 GLU cc_start: 0.7227 (mp0) cc_final: 0.6733 (mp0) REVERT: I 283 HIS cc_start: 0.7117 (m90) cc_final: 0.6325 (m90) REVERT: I 326 LYS cc_start: 0.8063 (tttp) cc_final: 0.7519 (mptt) REVERT: I 388 TRP cc_start: 0.7259 (m-90) cc_final: 0.7013 (m100) REVERT: I 425 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7107 (mmm) REVERT: I 430 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7918 (mmtm) outliers start: 13 outliers final: 1 residues processed: 563 average time/residue: 0.8103 time to fit residues: 515.0462 Evaluate side-chains 319 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain I residue 425 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0470 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 37 HIS B 83 GLN B 99 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 307 HIS E 165 ASN E 204 ASN E 279 GLN E 291 GLN E 307 HIS E 348 ASN F 137 HIS F 204 ASN K 6 HIS K 100 ASN K 137 HIS K 204 ASN K 347 ASN K 396 HIS A 28 HIS A 206 ASN A 266 HIS D 15 GLN D 28 HIS D 102 ASN D 309 HIS C 139 HIS C 206 ASN C 309 HIS I 28 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084661 restraints weight = 41703.583| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.68 r_work: 0.3138 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27770 Z= 0.138 Angle : 0.570 7.601 37764 Z= 0.294 Chirality : 0.044 0.149 4154 Planarity : 0.004 0.042 4924 Dihedral : 11.121 173.994 3852 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.15 % Allowed : 11.66 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3438 helix: 1.21 (0.13), residues: 1532 sheet: 0.15 (0.22), residues: 550 loop : -0.27 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 162 TYR 0.012 0.001 TYR C 24 PHE 0.013 0.001 PHE B 260 TRP 0.016 0.002 TRP I 21 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00309 (27770) covalent geometry : angle 0.57038 (37764) hydrogen bonds : bond 0.04465 ( 1336) hydrogen bonds : angle 4.76088 ( 3879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8661 (mt0) cc_final: 0.8346 (mm110) REVERT: B 161 ASP cc_start: 0.7821 (t0) cc_final: 0.7335 (t0) REVERT: B 165 ASN cc_start: 0.8412 (m-40) cc_final: 0.8202 (m-40) REVERT: B 332 ASN cc_start: 0.8342 (t0) cc_final: 0.8024 (m-40) REVERT: B 362 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8331 (ttpt) REVERT: B 377 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 53 GLU cc_start: 0.8162 (tt0) cc_final: 0.7662 (tp30) REVERT: E 125 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: E 291 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8274 (mp10) REVERT: E 406 MET cc_start: 0.6602 (tpp) cc_final: 0.6351 (tpp) REVERT: F 95 SER cc_start: 0.8754 (m) cc_final: 0.8545 (p) REVERT: F 157 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: F 213 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7778 (mtm110) REVERT: F 281 TYR cc_start: 0.7758 (m-10) cc_final: 0.7553 (m-10) REVERT: F 388 MET cc_start: 0.9218 (mtm) cc_final: 0.8940 (mtm) REVERT: F 399 THR cc_start: 0.8559 (m) cc_final: 0.8287 (p) REVERT: K 103 LYS cc_start: 0.8960 (tttt) cc_final: 0.8735 (tttm) REVERT: K 114 ASP cc_start: 0.8717 (m-30) cc_final: 0.8422 (m-30) REVERT: K 121 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7833 (mtm110) REVERT: K 129 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7959 (t) REVERT: K 131 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: K 415 MET cc_start: 0.7643 (tpp) cc_final: 0.7428 (tpp) REVERT: A 24 TYR cc_start: 0.8363 (m-10) cc_final: 0.7425 (m-80) REVERT: A 50 ASN cc_start: 0.8305 (t0) cc_final: 0.7884 (t0) REVERT: A 136 LEU cc_start: 0.9000 (mt) cc_final: 0.8796 (mt) REVERT: A 167 LEU cc_start: 0.8791 (mt) cc_final: 0.8590 (mp) REVERT: A 322 ASP cc_start: 0.9154 (t70) cc_final: 0.8907 (t0) REVERT: D 254 GLU cc_start: 0.4908 (mm-30) cc_final: 0.3224 (mm-30) REVERT: D 290 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: C 50 ASN cc_start: 0.8699 (t0) cc_final: 0.8364 (t0) REVERT: C 128 GLN cc_start: 0.7864 (tt0) cc_final: 0.7391 (tm-30) REVERT: C 284 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7580 (tp30) REVERT: C 337 THR cc_start: 0.8337 (m) cc_final: 0.8114 (p) REVERT: C 386 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: C 425 MET cc_start: 0.8700 (mmm) cc_final: 0.8489 (mmm) REVERT: I 85 GLN cc_start: 0.8790 (mm110) cc_final: 0.8502 (mt0) REVERT: I 90 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8254 (tm-30) REVERT: I 211 ASP cc_start: 0.8559 (m-30) cc_final: 0.8291 (m-30) REVERT: I 279 GLU cc_start: 0.7712 (mp0) cc_final: 0.7253 (mp0) REVERT: I 283 HIS cc_start: 0.7807 (m90) cc_final: 0.7301 (m90) REVERT: I 326 LYS cc_start: 0.8561 (tttp) cc_final: 0.8187 (mptt) REVERT: I 425 MET cc_start: 0.8838 (tpp) cc_final: 0.7729 (mpm) REVERT: I 430 LYS cc_start: 0.8563 (mmtm) cc_final: 0.8337 (mmtm) REVERT: I 437 VAL cc_start: 0.8806 (t) cc_final: 0.8550 (m) outliers start: 62 outliers final: 14 residues processed: 372 average time/residue: 0.7463 time to fit residues: 317.8276 Evaluate side-chains 294 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 177 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 165 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 263 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 37 HIS B 131 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 279 GLN B 298 ASN B 348 ASN E 37 HIS E 165 ASN F 307 HIS F 335 ASN K 131 GLN D 91 GLN D 226 ASN D 372 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081561 restraints weight = 42126.534| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.84 r_work: 0.3077 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27770 Z= 0.149 Angle : 0.557 7.572 37764 Z= 0.285 Chirality : 0.044 0.150 4154 Planarity : 0.004 0.039 4924 Dihedral : 10.811 172.468 3844 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.84 % Allowed : 12.98 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3438 helix: 1.30 (0.13), residues: 1536 sheet: 0.19 (0.22), residues: 527 loop : -0.24 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 213 TYR 0.011 0.001 TYR F 59 PHE 0.015 0.001 PHE B 92 TRP 0.015 0.002 TRP I 21 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00340 (27770) covalent geometry : angle 0.55663 (37764) hydrogen bonds : bond 0.04385 ( 1336) hydrogen bonds : angle 4.62207 ( 3879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 298 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLN cc_start: 0.8670 (mt0) cc_final: 0.8292 (mm-40) REVERT: B 64 ILE cc_start: 0.9228 (mp) cc_final: 0.9019 (mm) REVERT: B 161 ASP cc_start: 0.7855 (t0) cc_final: 0.7364 (t0) REVERT: B 165 ASN cc_start: 0.8430 (m-40) cc_final: 0.8157 (m-40) REVERT: B 241 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8084 (ttp80) REVERT: B 332 ASN cc_start: 0.8360 (t0) cc_final: 0.8158 (m-40) REVERT: B 362 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8327 (ttpt) REVERT: E 53 GLU cc_start: 0.8140 (tt0) cc_final: 0.7637 (tp30) REVERT: E 125 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: E 257 MET cc_start: 0.8428 (mmm) cc_final: 0.8160 (mtp) REVERT: E 406 MET cc_start: 0.6959 (tpp) cc_final: 0.6744 (tpp) REVERT: E 407 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: E 424 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: F 95 SER cc_start: 0.8755 (m) cc_final: 0.8544 (p) REVERT: F 157 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: F 213 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7744 (mtm110) REVERT: F 388 MET cc_start: 0.9221 (mtm) cc_final: 0.8998 (mtm) REVERT: F 399 THR cc_start: 0.8644 (m) cc_final: 0.8362 (p) REVERT: K 114 ASP cc_start: 0.8760 (m-30) cc_final: 0.8506 (m-30) REVERT: K 129 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8090 (t) REVERT: K 279 GLN cc_start: 0.7966 (mt0) cc_final: 0.7615 (mt0) REVERT: K 280 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6559 (mm-40) REVERT: K 282 ARG cc_start: 0.8166 (ppt90) cc_final: 0.7359 (ttm-80) REVERT: K 299 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8368 (mpm) REVERT: K 323 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8014 (mmm) REVERT: A 24 TYR cc_start: 0.8504 (m-10) cc_final: 0.7518 (m-80) REVERT: A 50 ASN cc_start: 0.8372 (t0) cc_final: 0.7933 (t0) REVERT: A 167 LEU cc_start: 0.8722 (mt) cc_final: 0.8521 (mp) REVERT: A 302 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8045 (mpt) REVERT: A 339 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7556 (tpm170) REVERT: D 290 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: C 50 ASN cc_start: 0.8710 (t0) cc_final: 0.8364 (t0) REVERT: C 90 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 128 GLN cc_start: 0.7822 (tt0) cc_final: 0.7339 (tm-30) REVERT: C 215 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8457 (mtm110) REVERT: C 337 THR cc_start: 0.8444 (m) cc_final: 0.8219 (p) REVERT: C 377 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8606 (ttm) REVERT: C 386 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: I 24 TYR cc_start: 0.8728 (m-10) cc_final: 0.8517 (m-10) REVERT: I 85 GLN cc_start: 0.8838 (mm110) cc_final: 0.8525 (mt0) REVERT: I 90 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8389 (tm-30) REVERT: I 141 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: I 170 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8720 (m) REVERT: I 211 ASP cc_start: 0.8645 (m-30) cc_final: 0.8394 (m-30) REVERT: I 279 GLU cc_start: 0.7814 (mp0) cc_final: 0.7518 (mp0) REVERT: I 326 LYS cc_start: 0.8619 (tttp) cc_final: 0.8178 (mptt) REVERT: I 377 MET cc_start: 0.9047 (tmm) cc_final: 0.8714 (tmm) REVERT: I 425 MET cc_start: 0.8891 (tpp) cc_final: 0.7703 (mpm) REVERT: I 430 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8336 (mmtm) REVERT: I 437 VAL cc_start: 0.8858 (t) cc_final: 0.8593 (m) outliers start: 82 outliers final: 29 residues processed: 351 average time/residue: 0.7541 time to fit residues: 302.8658 Evaluate side-chains 298 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 424 GLN Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain K residue 55 THR Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 381 ILE Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 112 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 330 optimal weight: 0.0070 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 236 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 131 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN E 165 ASN K 131 GLN K 423 GLN I 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082404 restraints weight = 41975.471| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.84 r_work: 0.3091 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27770 Z= 0.122 Angle : 0.528 7.669 37764 Z= 0.269 Chirality : 0.043 0.146 4154 Planarity : 0.004 0.036 4924 Dihedral : 10.535 169.304 3844 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.77 % Allowed : 14.08 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3438 helix: 1.40 (0.13), residues: 1539 sheet: 0.25 (0.22), residues: 527 loop : -0.23 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 213 TYR 0.010 0.001 TYR A 185 PHE 0.013 0.001 PHE I 49 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00272 (27770) covalent geometry : angle 0.52835 (37764) hydrogen bonds : bond 0.04010 ( 1336) hydrogen bonds : angle 4.52123 ( 3879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 1.052 Fit side-chains REVERT: B 15 GLN cc_start: 0.8634 (mt0) cc_final: 0.8323 (mm110) REVERT: B 161 ASP cc_start: 0.7835 (t0) cc_final: 0.7361 (t0) REVERT: B 165 ASN cc_start: 0.8387 (m-40) cc_final: 0.8104 (m-40) REVERT: B 241 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8218 (ttp80) REVERT: B 362 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8145 (ttpp) REVERT: E 53 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: E 111 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: E 125 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: E 257 MET cc_start: 0.8354 (mmm) cc_final: 0.7961 (mtp) REVERT: E 280 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: F 95 SER cc_start: 0.8688 (m) cc_final: 0.8482 (p) REVERT: F 233 MET cc_start: 0.8973 (mtp) cc_final: 0.8701 (ttt) REVERT: F 399 THR cc_start: 0.8621 (m) cc_final: 0.8318 (p) REVERT: F 406 MET cc_start: 0.7962 (tpp) cc_final: 0.7450 (tpp) REVERT: K 114 ASP cc_start: 0.8744 (m-30) cc_final: 0.8488 (m-30) REVERT: K 129 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8114 (t) REVERT: K 279 GLN cc_start: 0.7991 (mt0) cc_final: 0.7748 (mt0) REVERT: K 280 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6613 (mm-40) REVERT: K 282 ARG cc_start: 0.8011 (ppt90) cc_final: 0.7436 (ptp-170) REVERT: K 299 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8541 (mpp) REVERT: K 323 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: K 362 LYS cc_start: 0.8930 (ptmt) cc_final: 0.8717 (mppt) REVERT: K 415 MET cc_start: 0.8170 (tpp) cc_final: 0.7962 (mtp) REVERT: A 24 TYR cc_start: 0.8480 (m-10) cc_final: 0.7539 (m-80) REVERT: A 50 ASN cc_start: 0.8339 (t0) cc_final: 0.7920 (t0) REVERT: A 84 ARG cc_start: 0.8286 (ptp90) cc_final: 0.8022 (ptp90) REVERT: A 167 LEU cc_start: 0.8779 (mt) cc_final: 0.8550 (mp) REVERT: A 302 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.7975 (mpt) REVERT: C 24 TYR cc_start: 0.8946 (m-10) cc_final: 0.8194 (m-80) REVERT: C 50 ASN cc_start: 0.8703 (t0) cc_final: 0.8362 (t0) REVERT: C 90 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7322 (tm-30) REVERT: C 128 GLN cc_start: 0.7756 (tt0) cc_final: 0.7293 (tm-30) REVERT: C 215 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8468 (mtm110) REVERT: C 386 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: I 24 TYR cc_start: 0.8778 (m-10) cc_final: 0.8536 (m-10) REVERT: I 97 GLU cc_start: 0.7829 (tt0) cc_final: 0.7534 (tp30) REVERT: I 141 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8117 (m-80) REVERT: I 170 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (m) REVERT: I 211 ASP cc_start: 0.8638 (m-30) cc_final: 0.8407 (m-30) REVERT: I 279 GLU cc_start: 0.7821 (mp0) cc_final: 0.7538 (mp0) REVERT: I 326 LYS cc_start: 0.8599 (tttp) cc_final: 0.8136 (mptt) REVERT: I 425 MET cc_start: 0.8902 (tpp) cc_final: 0.8633 (tpp) REVERT: I 437 VAL cc_start: 0.8873 (t) cc_final: 0.8603 (m) outliers start: 80 outliers final: 24 residues processed: 324 average time/residue: 0.7984 time to fit residues: 294.5435 Evaluate side-chains 286 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 240 optimal weight: 0.7980 chunk 185 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 296 optimal weight: 0.6980 chunk 239 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 131 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 279 GLN E 165 ASN F 298 ASN K 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081015 restraints weight = 42043.022| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.91 r_work: 0.3067 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27770 Z= 0.137 Angle : 0.532 8.454 37764 Z= 0.271 Chirality : 0.043 0.151 4154 Planarity : 0.004 0.039 4924 Dihedral : 10.482 168.483 3844 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.63 % Allowed : 14.95 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3438 helix: 1.31 (0.13), residues: 1566 sheet: 0.14 (0.23), residues: 502 loop : -0.30 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 213 TYR 0.011 0.001 TYR C 161 PHE 0.016 0.001 PHE I 49 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00314 (27770) covalent geometry : angle 0.53244 (37764) hydrogen bonds : bond 0.04092 ( 1336) hydrogen bonds : angle 4.48631 ( 3879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 1.063 Fit side-chains REVERT: B 15 GLN cc_start: 0.8693 (mt0) cc_final: 0.8259 (mm-40) REVERT: B 241 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (ttp80) REVERT: B 332 ASN cc_start: 0.8050 (m-40) cc_final: 0.7735 (m-40) REVERT: B 362 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8192 (ttpp) REVERT: B 415 MET cc_start: 0.8688 (mmm) cc_final: 0.8404 (mtp) REVERT: E 53 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: E 111 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: E 125 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: E 257 MET cc_start: 0.8402 (mmm) cc_final: 0.7954 (mtp) REVERT: F 95 SER cc_start: 0.8727 (m) cc_final: 0.8513 (p) REVERT: F 125 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8102 (mm-30) REVERT: F 213 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7364 (mtm110) REVERT: F 233 MET cc_start: 0.8940 (mtp) cc_final: 0.8723 (ttt) REVERT: F 399 THR cc_start: 0.8600 (m) cc_final: 0.8253 (p) REVERT: F 406 MET cc_start: 0.7873 (tpp) cc_final: 0.7352 (tpp) REVERT: K 114 ASP cc_start: 0.8774 (m-30) cc_final: 0.8495 (m-30) REVERT: K 129 CYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8181 (t) REVERT: K 279 GLN cc_start: 0.8014 (mt0) cc_final: 0.7726 (mt0) REVERT: K 280 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6573 (mm-40) REVERT: K 282 ARG cc_start: 0.8004 (ppt90) cc_final: 0.7398 (ptp-170) REVERT: K 299 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8329 (mpp) REVERT: K 323 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: K 362 LYS cc_start: 0.8928 (ptmt) cc_final: 0.8642 (mppt) REVERT: K 415 MET cc_start: 0.8170 (tpp) cc_final: 0.7761 (ttp) REVERT: A 24 TYR cc_start: 0.8483 (m-10) cc_final: 0.7459 (m-80) REVERT: A 50 ASN cc_start: 0.8348 (t0) cc_final: 0.7894 (t0) REVERT: A 167 LEU cc_start: 0.8785 (mt) cc_final: 0.8561 (mp) REVERT: A 302 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7909 (mpt) REVERT: D 254 GLU cc_start: 0.4852 (mm-30) cc_final: 0.3211 (mm-30) REVERT: C 24 TYR cc_start: 0.9001 (m-10) cc_final: 0.8245 (m-80) REVERT: C 50 ASN cc_start: 0.8720 (t0) cc_final: 0.8333 (t0) REVERT: C 90 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 128 GLN cc_start: 0.7744 (tt0) cc_final: 0.7257 (tm-30) REVERT: C 215 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8476 (mtm110) REVERT: C 377 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8572 (ttm) REVERT: C 386 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: I 24 TYR cc_start: 0.8861 (m-10) cc_final: 0.8567 (m-10) REVERT: I 141 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: I 170 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8710 (m) REVERT: I 211 ASP cc_start: 0.8608 (m-30) cc_final: 0.8353 (m-30) REVERT: I 279 GLU cc_start: 0.7870 (mp0) cc_final: 0.7578 (mp0) REVERT: I 377 MET cc_start: 0.9042 (tmm) cc_final: 0.8760 (tmm) REVERT: I 437 VAL cc_start: 0.8842 (t) cc_final: 0.8563 (m) outliers start: 76 outliers final: 32 residues processed: 322 average time/residue: 0.7783 time to fit residues: 286.2235 Evaluate side-chains 294 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 395 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 139 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 228 optimal weight: 0.0870 chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 203 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN B 37 HIS B 131 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN E 165 ASN K 131 GLN D 216 ASN I 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082671 restraints weight = 41889.306| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.86 r_work: 0.3096 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27770 Z= 0.113 Angle : 0.513 8.188 37764 Z= 0.260 Chirality : 0.043 0.145 4154 Planarity : 0.004 0.043 4924 Dihedral : 10.274 168.389 3844 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.46 % Allowed : 15.33 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3438 helix: 1.44 (0.13), residues: 1548 sheet: 0.07 (0.23), residues: 504 loop : -0.25 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 390 TYR 0.009 0.001 TYR A 161 PHE 0.011 0.001 PHE F 367 TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00250 (27770) covalent geometry : angle 0.51305 (37764) hydrogen bonds : bond 0.03814 ( 1336) hydrogen bonds : angle 4.42692 ( 3879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 1.061 Fit side-chains REVERT: B 15 GLN cc_start: 0.8641 (mt0) cc_final: 0.8331 (mm110) REVERT: B 241 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8142 (ttp80) REVERT: B 332 ASN cc_start: 0.8058 (m-40) cc_final: 0.7703 (m-40) REVERT: B 362 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8250 (ttpp) REVERT: E 53 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: E 111 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 125 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: E 257 MET cc_start: 0.8272 (mmm) cc_final: 0.7873 (mtp) REVERT: F 399 THR cc_start: 0.8570 (m) cc_final: 0.8253 (p) REVERT: K 114 ASP cc_start: 0.8710 (m-30) cc_final: 0.8453 (m-30) REVERT: K 125 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: K 279 GLN cc_start: 0.7913 (mt0) cc_final: 0.7643 (mt0) REVERT: K 280 GLN cc_start: 0.6951 (mm-40) cc_final: 0.6611 (mm-40) REVERT: K 282 ARG cc_start: 0.8025 (ppt90) cc_final: 0.7511 (ptp-170) REVERT: K 299 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: K 323 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7996 (mmm) REVERT: K 362 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8568 (mppt) REVERT: K 415 MET cc_start: 0.8203 (tpp) cc_final: 0.7780 (ttp) REVERT: A 24 TYR cc_start: 0.8457 (m-10) cc_final: 0.7471 (m-80) REVERT: A 50 ASN cc_start: 0.8292 (t0) cc_final: 0.7888 (t0) REVERT: A 120 ASP cc_start: 0.8397 (t0) cc_final: 0.8089 (t0) REVERT: A 167 LEU cc_start: 0.8777 (mt) cc_final: 0.8559 (mp) REVERT: A 302 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.7824 (mpt) REVERT: A 339 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7762 (tpm170) REVERT: A 390 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7727 (ptp90) REVERT: D 52 PHE cc_start: 0.8707 (m-80) cc_final: 0.8465 (m-80) REVERT: D 254 GLU cc_start: 0.4764 (mm-30) cc_final: 0.3314 (mm-30) REVERT: D 304 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8531 (mmmm) REVERT: C 24 TYR cc_start: 0.8971 (m-10) cc_final: 0.8218 (m-80) REVERT: C 50 ASN cc_start: 0.8728 (t0) cc_final: 0.8385 (t0) REVERT: C 128 GLN cc_start: 0.7777 (tt0) cc_final: 0.7305 (tm-30) REVERT: C 215 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8549 (mtm110) REVERT: C 377 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8518 (ttm) REVERT: C 386 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: C 430 LYS cc_start: 0.8457 (mppt) cc_final: 0.8213 (mmtt) REVERT: I 24 TYR cc_start: 0.8917 (m-10) cc_final: 0.8625 (m-10) REVERT: I 141 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: I 170 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8669 (m) REVERT: I 211 ASP cc_start: 0.8615 (m-30) cc_final: 0.8379 (m-30) REVERT: I 279 GLU cc_start: 0.7868 (mp0) cc_final: 0.7628 (mp0) REVERT: I 377 MET cc_start: 0.9027 (tmm) cc_final: 0.8760 (tmm) outliers start: 71 outliers final: 30 residues processed: 326 average time/residue: 0.7727 time to fit residues: 288.3799 Evaluate side-chains 284 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain I residue 141 PHE Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 231 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 37 HIS B 131 GLN E 165 ASN F 6 HIS F 8 GLN K 15 GLN K 131 GLN D 139 HIS D 206 ASN D 300 ASN I 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081766 restraints weight = 41848.629| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.90 r_work: 0.3081 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27770 Z= 0.125 Angle : 0.528 10.838 37764 Z= 0.266 Chirality : 0.043 0.145 4154 Planarity : 0.004 0.041 4924 Dihedral : 10.224 167.508 3844 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.56 % Allowed : 15.54 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3438 helix: 1.46 (0.13), residues: 1548 sheet: 0.01 (0.23), residues: 513 loop : -0.22 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 390 TYR 0.010 0.001 TYR C 161 PHE 0.033 0.001 PHE I 49 TRP 0.013 0.001 TRP A 21 HIS 0.005 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00284 (27770) covalent geometry : angle 0.52790 (37764) hydrogen bonds : bond 0.03914 ( 1336) hydrogen bonds : angle 4.41756 ( 3879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 260 time to evaluate : 0.970 Fit side-chains REVERT: B 15 GLN cc_start: 0.8663 (mt0) cc_final: 0.8237 (mm-40) REVERT: B 241 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8043 (ttp80) REVERT: B 332 ASN cc_start: 0.8070 (m-40) cc_final: 0.7718 (m-40) REVERT: B 362 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8402 (ttmt) REVERT: E 53 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: E 111 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: E 257 MET cc_start: 0.8299 (mmm) cc_final: 0.7893 (mtp) REVERT: F 399 THR cc_start: 0.8573 (m) cc_final: 0.8217 (p) REVERT: F 406 MET cc_start: 0.7971 (tpp) cc_final: 0.7520 (tpp) REVERT: K 114 ASP cc_start: 0.8783 (m-30) cc_final: 0.8509 (m-30) REVERT: K 279 GLN cc_start: 0.7899 (mt0) cc_final: 0.7611 (mt0) REVERT: K 280 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6601 (mm-40) REVERT: K 282 ARG cc_start: 0.8048 (ppt90) cc_final: 0.7499 (ptp-170) REVERT: K 299 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8447 (mpp) REVERT: K 323 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8004 (mmm) REVERT: K 362 LYS cc_start: 0.8866 (ptmt) cc_final: 0.8495 (mppt) REVERT: K 415 MET cc_start: 0.8190 (tpp) cc_final: 0.7776 (ttp) REVERT: A 24 TYR cc_start: 0.8490 (m-10) cc_final: 0.7476 (m-80) REVERT: A 50 ASN cc_start: 0.8326 (t0) cc_final: 0.7873 (t0) REVERT: A 120 ASP cc_start: 0.8397 (t0) cc_final: 0.8117 (t0) REVERT: A 167 LEU cc_start: 0.8831 (mt) cc_final: 0.8548 (mp) REVERT: A 302 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.7852 (mpt) REVERT: A 339 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7709 (tpm170) REVERT: A 390 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7744 (ptp90) REVERT: D 123 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7603 (ttp-110) REVERT: D 254 GLU cc_start: 0.4612 (mm-30) cc_final: 0.3344 (mm-30) REVERT: D 304 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8477 (mmmm) REVERT: C 24 TYR cc_start: 0.8982 (m-10) cc_final: 0.8212 (m-80) REVERT: C 50 ASN cc_start: 0.8718 (t0) cc_final: 0.8344 (t0) REVERT: C 128 GLN cc_start: 0.7718 (tt0) cc_final: 0.7195 (tm-30) REVERT: C 215 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8479 (mtm110) REVERT: C 377 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8565 (ttm) REVERT: C 386 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: I 24 TYR cc_start: 0.8966 (m-10) cc_final: 0.8544 (m-10) REVERT: I 195 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8780 (tt) REVERT: I 211 ASP cc_start: 0.8610 (m-30) cc_final: 0.8356 (m-30) REVERT: I 279 GLU cc_start: 0.7927 (mp0) cc_final: 0.7696 (mp0) REVERT: I 377 MET cc_start: 0.9036 (tmm) cc_final: 0.8765 (tmm) outliers start: 74 outliers final: 39 residues processed: 307 average time/residue: 0.7753 time to fit residues: 271.8343 Evaluate side-chains 293 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 330 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 338 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN K 100 ASN I 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082020 restraints weight = 42179.435| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.86 r_work: 0.3084 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27770 Z= 0.130 Angle : 0.528 10.253 37764 Z= 0.267 Chirality : 0.043 0.149 4154 Planarity : 0.004 0.039 4924 Dihedral : 10.197 167.441 3844 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.15 % Allowed : 16.23 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3438 helix: 1.44 (0.13), residues: 1548 sheet: 0.01 (0.23), residues: 513 loop : -0.21 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 390 TYR 0.011 0.001 TYR F 59 PHE 0.012 0.001 PHE B 90 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00296 (27770) covalent geometry : angle 0.52817 (37764) hydrogen bonds : bond 0.03949 ( 1336) hydrogen bonds : angle 4.43262 ( 3879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 1.054 Fit side-chains REVERT: B 15 GLN cc_start: 0.8651 (mt0) cc_final: 0.8263 (mm-40) REVERT: B 241 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8093 (ttp80) REVERT: B 332 ASN cc_start: 0.8093 (m-40) cc_final: 0.7877 (m110) REVERT: B 362 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8493 (ttmt) REVERT: E 53 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: E 111 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: E 125 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: E 257 MET cc_start: 0.8328 (mmm) cc_final: 0.7902 (mtp) REVERT: F 399 THR cc_start: 0.8649 (m) cc_final: 0.8312 (p) REVERT: F 406 MET cc_start: 0.7985 (tpp) cc_final: 0.7569 (tpp) REVERT: K 41 ASP cc_start: 0.7718 (m-30) cc_final: 0.7493 (t0) REVERT: K 279 GLN cc_start: 0.7933 (mt0) cc_final: 0.7656 (mt0) REVERT: K 280 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6601 (mm-40) REVERT: K 282 ARG cc_start: 0.8140 (ppt90) cc_final: 0.7591 (ptp-170) REVERT: K 299 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8479 (mpp) REVERT: K 323 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: K 362 LYS cc_start: 0.8884 (ptmt) cc_final: 0.8552 (mppt) REVERT: K 415 MET cc_start: 0.8221 (tpp) cc_final: 0.7831 (ttp) REVERT: A 24 TYR cc_start: 0.8508 (m-10) cc_final: 0.7508 (m-80) REVERT: A 50 ASN cc_start: 0.8444 (t0) cc_final: 0.8031 (t0) REVERT: A 120 ASP cc_start: 0.8432 (t0) cc_final: 0.8127 (t0) REVERT: A 302 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7806 (mpt) REVERT: A 390 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7762 (ptp90) REVERT: A 413 MET cc_start: 0.8519 (ttm) cc_final: 0.8306 (ttp) REVERT: D 52 PHE cc_start: 0.8744 (m-80) cc_final: 0.8433 (m-80) REVERT: D 254 GLU cc_start: 0.4829 (mm-30) cc_final: 0.3524 (mm-30) REVERT: D 304 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8508 (mmmm) REVERT: C 24 TYR cc_start: 0.8965 (m-10) cc_final: 0.8220 (m-80) REVERT: C 50 ASN cc_start: 0.8728 (t0) cc_final: 0.8393 (t0) REVERT: C 128 GLN cc_start: 0.7784 (tt0) cc_final: 0.7264 (tm-30) REVERT: C 215 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8529 (mtm110) REVERT: C 284 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 377 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8566 (ttm) REVERT: C 386 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: I 24 TYR cc_start: 0.8970 (m-10) cc_final: 0.8571 (m-10) REVERT: I 279 GLU cc_start: 0.7936 (mp0) cc_final: 0.7713 (mp0) REVERT: I 377 MET cc_start: 0.9039 (tmm) cc_final: 0.8781 (tmm) outliers start: 62 outliers final: 40 residues processed: 295 average time/residue: 0.7776 time to fit residues: 261.8949 Evaluate side-chains 290 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 254 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 chunk 278 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 183 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN F 6 HIS ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081744 restraints weight = 41985.443| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.90 r_work: 0.3085 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27770 Z= 0.126 Angle : 0.537 12.268 37764 Z= 0.270 Chirality : 0.043 0.146 4154 Planarity : 0.004 0.039 4924 Dihedral : 10.148 167.099 3844 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.87 % Allowed : 16.57 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3438 helix: 1.44 (0.13), residues: 1548 sheet: 0.01 (0.23), residues: 513 loop : -0.19 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 339 TYR 0.010 0.001 TYR C 161 PHE 0.033 0.001 PHE I 49 TRP 0.014 0.001 TRP K 101 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00288 (27770) covalent geometry : angle 0.53690 (37764) hydrogen bonds : bond 0.03909 ( 1336) hydrogen bonds : angle 4.41739 ( 3879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 1.014 Fit side-chains REVERT: B 15 GLN cc_start: 0.8659 (mt0) cc_final: 0.8234 (mm-40) REVERT: B 241 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8066 (ttp80) REVERT: B 332 ASN cc_start: 0.8187 (m-40) cc_final: 0.7978 (m-40) REVERT: B 362 LYS cc_start: 0.8765 (ttpp) cc_final: 0.8424 (ttmt) REVERT: E 53 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7703 (tp30) REVERT: E 111 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: E 125 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: E 257 MET cc_start: 0.8366 (mmm) cc_final: 0.8000 (mtp) REVERT: F 399 THR cc_start: 0.8596 (m) cc_final: 0.8243 (p) REVERT: F 406 MET cc_start: 0.7992 (tpp) cc_final: 0.7498 (tpp) REVERT: K 41 ASP cc_start: 0.7738 (m-30) cc_final: 0.7417 (t0) REVERT: K 279 GLN cc_start: 0.7931 (mt0) cc_final: 0.7655 (mt0) REVERT: K 280 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6584 (mm-40) REVERT: K 281 TYR cc_start: 0.7536 (m-80) cc_final: 0.7181 (m-80) REVERT: K 282 ARG cc_start: 0.7932 (ppt90) cc_final: 0.7508 (ptp-170) REVERT: K 299 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8426 (mpp) REVERT: K 323 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8018 (mmm) REVERT: K 362 LYS cc_start: 0.8882 (ptmt) cc_final: 0.8478 (mppt) REVERT: K 415 MET cc_start: 0.8198 (tpp) cc_final: 0.7796 (ttp) REVERT: A 24 TYR cc_start: 0.8502 (m-10) cc_final: 0.7481 (m-80) REVERT: A 50 ASN cc_start: 0.8440 (t0) cc_final: 0.7987 (t0) REVERT: A 120 ASP cc_start: 0.8416 (t0) cc_final: 0.8115 (t0) REVERT: A 302 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7790 (mpt) REVERT: A 390 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7748 (ptp90) REVERT: D 123 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7610 (ttp-110) REVERT: D 254 GLU cc_start: 0.4703 (mm-30) cc_final: 0.3255 (mm-30) REVERT: D 304 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8458 (mmmm) REVERT: C 24 TYR cc_start: 0.8980 (m-10) cc_final: 0.8210 (m-80) REVERT: C 50 ASN cc_start: 0.8734 (t0) cc_final: 0.8371 (t0) REVERT: C 128 GLN cc_start: 0.7706 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 215 ARG cc_start: 0.8872 (mtm-85) cc_final: 0.8493 (mtm110) REVERT: C 284 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 377 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8573 (ttm) REVERT: C 386 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8189 (mm-30) REVERT: I 24 TYR cc_start: 0.8987 (m-10) cc_final: 0.8557 (m-10) REVERT: I 195 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8791 (tt) REVERT: I 279 GLU cc_start: 0.7947 (mp0) cc_final: 0.7727 (mp0) REVERT: I 377 MET cc_start: 0.9030 (tmm) cc_final: 0.8765 (tmm) outliers start: 54 outliers final: 35 residues processed: 285 average time/residue: 0.7929 time to fit residues: 257.5550 Evaluate side-chains 286 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 158 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078049 restraints weight = 42347.993| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.87 r_work: 0.3015 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27770 Z= 0.211 Angle : 0.611 11.733 37764 Z= 0.311 Chirality : 0.046 0.156 4154 Planarity : 0.004 0.040 4924 Dihedral : 10.635 166.617 3844 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.66 % Allowed : 16.85 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3438 helix: 1.31 (0.13), residues: 1517 sheet: -0.07 (0.23), residues: 513 loop : -0.16 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 213 TYR 0.017 0.002 TYR D 24 PHE 0.017 0.002 PHE B 90 TRP 0.013 0.002 TRP D 388 HIS 0.006 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00498 (27770) covalent geometry : angle 0.61136 (37764) hydrogen bonds : bond 0.04707 ( 1336) hydrogen bonds : angle 4.63372 ( 3879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 1.059 Fit side-chains REVERT: B 15 GLN cc_start: 0.8742 (mt0) cc_final: 0.8330 (mm-40) REVERT: B 241 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: B 332 ASN cc_start: 0.8080 (m-40) cc_final: 0.7646 (m-40) REVERT: B 362 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8338 (ttpp) REVERT: E 53 GLU cc_start: 0.8248 (tt0) cc_final: 0.7714 (tp30) REVERT: E 74 ASP cc_start: 0.8223 (p0) cc_final: 0.7921 (m-30) REVERT: E 111 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: E 257 MET cc_start: 0.8453 (mmm) cc_final: 0.8006 (mtp) REVERT: F 399 THR cc_start: 0.8753 (m) cc_final: 0.8450 (p) REVERT: F 406 MET cc_start: 0.8040 (tpp) cc_final: 0.7596 (tpp) REVERT: K 41 ASP cc_start: 0.7833 (m-30) cc_final: 0.7588 (t0) REVERT: K 280 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6653 (mm-40) REVERT: K 281 TYR cc_start: 0.7664 (m-80) cc_final: 0.7348 (m-80) REVERT: K 282 ARG cc_start: 0.8130 (ppt90) cc_final: 0.7647 (ptp-170) REVERT: K 299 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8441 (mpm) REVERT: K 362 LYS cc_start: 0.9086 (ptmt) cc_final: 0.8610 (mppt) REVERT: K 415 MET cc_start: 0.8294 (tpp) cc_final: 0.7942 (ttp) REVERT: A 24 TYR cc_start: 0.8600 (m-10) cc_final: 0.7539 (m-80) REVERT: A 120 ASP cc_start: 0.8447 (t0) cc_final: 0.8120 (t0) REVERT: A 390 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7788 (ptp90) REVERT: D 24 TYR cc_start: 0.8484 (m-10) cc_final: 0.8130 (m-10) REVERT: D 52 PHE cc_start: 0.8864 (m-80) cc_final: 0.8414 (m-80) REVERT: C 24 TYR cc_start: 0.9063 (m-10) cc_final: 0.8311 (m-80) REVERT: C 50 ASN cc_start: 0.8765 (t0) cc_final: 0.8457 (t0) REVERT: C 128 GLN cc_start: 0.7812 (tt0) cc_final: 0.7266 (tm-30) REVERT: C 215 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8475 (mtm110) REVERT: C 284 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7761 (mt-10) REVERT: C 386 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8167 (mm-30) REVERT: I 24 TYR cc_start: 0.9086 (m-10) cc_final: 0.8633 (m-10) REVERT: I 141 PHE cc_start: 0.8893 (m-10) cc_final: 0.8530 (m-80) REVERT: I 279 GLU cc_start: 0.8006 (mp0) cc_final: 0.7732 (mp0) REVERT: I 377 MET cc_start: 0.9063 (tmm) cc_final: 0.8807 (tmm) outliers start: 48 outliers final: 38 residues processed: 280 average time/residue: 0.8095 time to fit residues: 258.0025 Evaluate side-chains 282 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 ARG Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 103 LYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 100 ASN Chi-restraints excluded: chain K residue 125 GLU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 83 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 335 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN B 279 GLN E 6 HIS ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080248 restraints weight = 41863.156| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.88 r_work: 0.3060 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27770 Z= 0.138 Angle : 0.561 11.693 37764 Z= 0.284 Chirality : 0.043 0.147 4154 Planarity : 0.004 0.041 4924 Dihedral : 10.419 168.985 3844 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.59 % Allowed : 17.09 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3438 helix: 1.31 (0.13), residues: 1544 sheet: -0.07 (0.23), residues: 502 loop : -0.18 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 339 TYR 0.012 0.001 TYR D 24 PHE 0.026 0.001 PHE I 49 TRP 0.020 0.002 TRP D 388 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00317 (27770) covalent geometry : angle 0.56083 (37764) hydrogen bonds : bond 0.04124 ( 1336) hydrogen bonds : angle 4.54112 ( 3879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8585.15 seconds wall clock time: 147 minutes 28.47 seconds (8848.47 seconds total)