Starting phenix.real_space_refine on Tue Aug 26 18:04:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yk5_33887/08_2025/7yk5_33887.map" } resolution = 2.0 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 248 5.16 5 C 25288 2.51 5 N 6844 2.21 5 O 7552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39948 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3746 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 465} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'HYP:plan-1': 2, 'CSO:plan-1': 1, 'LYO:plan-1': 2, 'HLU:plan-1': 1, 'KCX:plan-1': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "J" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "K" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "L" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "M" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "O" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "P" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "h" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "g" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "f" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "e" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "d" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "c" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "b" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "a" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 68 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'CAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.88, per 1000 atoms: 0.22 Number of scatterers: 39948 At special positions: 0 Unit cell: (136.422, 136.422, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 248 16.00 P 16 15.00 O 7552 8.00 N 6844 7.00 C 25288 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9248 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 40 sheets defined 43.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.559A pdb=" N ASP A 76 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.654A pdb=" N TYR A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 185 through 200 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.560A pdb=" N ARG A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 276 through 290 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.914A pdb=" N ARG A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.763A pdb=" N ILE A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.502A pdb=" N GLY A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 455 Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 73 through 79 removed outlier: 3.565A pdb=" N ASP B 76 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.655A pdb=" N TYR B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 217 through 237 removed outlier: 3.559A pdb=" N ARG B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.916A pdb=" N ARG B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.763A pdb=" N ILE B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.519A pdb=" N GLY B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'C' and resid 73 through 79 removed outlier: 3.559A pdb=" N ASP C 76 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 removed outlier: 3.655A pdb=" N TYR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 217 through 237 removed outlier: 3.560A pdb=" N ARG C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.915A pdb=" N ARG C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.763A pdb=" N ILE C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 389 through 398 removed outlier: 3.502A pdb=" N GLY C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'C' and resid 444 through 455 Processing helix chain 'C' and resid 457 through 467 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 22 through 26 Processing helix chain 'D' and resid 53 through 65 Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.563A pdb=" N ASP D 76 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 3.655A pdb=" N TYR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 217 through 237 removed outlier: 3.560A pdb=" N ARG D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 276 through 290 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.916A pdb=" N ARG D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 removed outlier: 3.764A pdb=" N ILE D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 360 through 364 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.501A pdb=" N GLY D 398 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 411 Processing helix chain 'D' and resid 415 through 436 Processing helix chain 'D' and resid 444 through 455 Processing helix chain 'D' and resid 457 through 467 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'E' and resid 73 through 79 removed outlier: 3.559A pdb=" N ASP E 76 " --> pdb=" O VAL E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.656A pdb=" N TYR E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 185 through 200 Processing helix chain 'E' and resid 217 through 237 removed outlier: 3.559A pdb=" N ARG E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 276 through 290 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.915A pdb=" N ARG E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 325 removed outlier: 3.764A pdb=" N ILE E 317 " --> pdb=" O ASN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 Processing helix chain 'E' and resid 360 through 364 Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 398 removed outlier: 3.502A pdb=" N GLY E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'E' and resid 444 through 455 Processing helix chain 'E' and resid 457 through 467 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'F' and resid 73 through 79 removed outlier: 3.565A pdb=" N ASP F 76 " --> pdb=" O VAL F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 85 removed outlier: 3.633A pdb=" N TYR F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 112 Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 145 through 150 Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 185 through 200 Processing helix chain 'F' and resid 217 through 237 removed outlier: 3.560A pdb=" N ARG F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 276 through 290 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.916A pdb=" N ARG F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 removed outlier: 3.764A pdb=" N ILE F 317 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 360 through 364 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.503A pdb=" N GLY F 398 " --> pdb=" O VAL F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 411 Processing helix chain 'F' and resid 415 through 436 Processing helix chain 'F' and resid 444 through 455 Processing helix chain 'F' and resid 457 through 467 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'G' and resid 73 through 79 removed outlier: 3.559A pdb=" N ASP G 76 " --> pdb=" O VAL G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 removed outlier: 3.654A pdb=" N TYR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 112 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'G' and resid 158 through 167 Processing helix chain 'G' and resid 185 through 200 Processing helix chain 'G' and resid 217 through 237 removed outlier: 3.561A pdb=" N ARG G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 276 through 290 Processing helix chain 'G' and resid 301 through 306 removed outlier: 3.915A pdb=" N ARG G 306 " --> pdb=" O SER G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.764A pdb=" N ILE G 317 " --> pdb=" O ASN G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 360 through 364 Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 389 through 398 removed outlier: 3.502A pdb=" N GLY G 398 " --> pdb=" O VAL G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 415 through 436 Processing helix chain 'G' and resid 444 through 455 Processing helix chain 'G' and resid 457 through 467 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 22 through 26 Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'H' and resid 73 through 79 removed outlier: 3.565A pdb=" N ASP H 76 " --> pdb=" O VAL H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 removed outlier: 3.654A pdb=" N TYR H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 112 Processing helix chain 'H' and resid 116 through 125 Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'H' and resid 158 through 167 Processing helix chain 'H' and resid 185 through 200 Processing helix chain 'H' and resid 217 through 237 removed outlier: 3.561A pdb=" N ARG H 221 " --> pdb=" O ARG H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 264 Processing helix chain 'H' and resid 276 through 290 Processing helix chain 'H' and resid 301 through 306 removed outlier: 3.915A pdb=" N ARG H 306 " --> pdb=" O SER H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 325 removed outlier: 3.764A pdb=" N ILE H 317 " --> pdb=" O ASN H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 354 Processing helix chain 'H' and resid 360 through 364 Processing helix chain 'H' and resid 386 through 388 No H-bonds generated for 'chain 'H' and resid 386 through 388' Processing helix chain 'H' and resid 389 through 398 removed outlier: 3.508A pdb=" N GLY H 398 " --> pdb=" O VAL H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 411 Processing helix chain 'H' and resid 415 through 436 Processing helix chain 'H' and resid 444 through 455 Processing helix chain 'H' and resid 457 through 467 Processing helix chain 'I' and resid 15 through 29 removed outlier: 3.589A pdb=" N LYS I 29 " --> pdb=" O TYR I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 removed outlier: 4.062A pdb=" N VAL I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 15 through 29 removed outlier: 3.588A pdb=" N LYS J 29 " --> pdb=" O TYR J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 75 removed outlier: 4.053A pdb=" N VAL J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'K' and resid 15 through 29 removed outlier: 3.588A pdb=" N LYS K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 75 removed outlier: 4.067A pdb=" N VAL K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'L' and resid 15 through 29 removed outlier: 3.587A pdb=" N LYS L 29 " --> pdb=" O TYR L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 75 removed outlier: 4.053A pdb=" N VAL L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'M' and resid 15 through 29 removed outlier: 3.586A pdb=" N LYS M 29 " --> pdb=" O TYR M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 75 removed outlier: 4.075A pdb=" N VAL M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 133 Processing helix chain 'N' and resid 15 through 29 removed outlier: 3.583A pdb=" N LYS N 29 " --> pdb=" O TYR N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 75 removed outlier: 4.056A pdb=" N VAL N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 133 Processing helix chain 'O' and resid 15 through 29 removed outlier: 3.587A pdb=" N LYS O 29 " --> pdb=" O TYR O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 75 removed outlier: 4.065A pdb=" N VAL O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 133 Processing helix chain 'P' and resid 15 through 29 removed outlier: 3.589A pdb=" N LYS P 29 " --> pdb=" O TYR P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 75 removed outlier: 4.072A pdb=" N VAL P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 133 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 93 removed outlier: 5.832A pdb=" N ALA A 88 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 106 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 90 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 41 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A 142 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 43 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 136 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU A 174 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N KCX A 205 " --> pdb=" O HLU A 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 176 " --> pdb=" O KCX A 205 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU A 204 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ASN A 245 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER A 242 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET A 270 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A 244 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP A 272 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 269 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 297 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 271 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A 330 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 329 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 173 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.841A pdb=" N ALA B 88 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA B 106 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG B 90 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 41 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET B 142 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 43 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 136 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU B 174 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N KCX B 205 " --> pdb=" O HLU B 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA B 176 " --> pdb=" O KCX B 205 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 204 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN B 245 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER B 242 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET B 270 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU B 244 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP B 272 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 269 " --> pdb=" O HIS B 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS B 297 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 271 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS B 330 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 329 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 173 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 93 removed outlier: 5.841A pdb=" N ALA C 88 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA C 106 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 90 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 41 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET C 142 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 43 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 136 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLY C 311 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 137 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU C 174 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N KCX C 205 " --> pdb=" O HLU C 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 176 " --> pdb=" O KCX C 205 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU C 204 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN C 245 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER C 242 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET C 270 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 244 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP C 272 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 269 " --> pdb=" O HIS C 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS C 297 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 271 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS C 330 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 329 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 173 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 93 removed outlier: 5.841A pdb=" N ALA D 88 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA D 106 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 90 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 41 " --> pdb=" O MET D 142 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET D 142 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D 43 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 136 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU D 174 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N KCX D 205 " --> pdb=" O HLU D 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA D 176 " --> pdb=" O KCX D 205 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 204 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN D 245 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER D 242 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET D 270 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 244 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP D 272 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 269 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS D 297 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 271 " --> pdb=" O HIS D 297 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS D 330 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 329 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 173 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 93 removed outlier: 5.841A pdb=" N ALA E 88 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA E 106 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 90 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU E 41 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET E 142 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 43 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 136 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.700A pdb=" N HLU E 174 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N KCX E 205 " --> pdb=" O HLU E 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA E 176 " --> pdb=" O KCX E 205 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU E 204 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN E 245 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER E 242 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET E 270 " --> pdb=" O SER E 242 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU E 244 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP E 272 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL E 269 " --> pdb=" O HIS E 295 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS E 297 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 271 " --> pdb=" O HIS E 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS E 330 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE E 329 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU E 173 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 356 through 357 Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 93 removed outlier: 5.841A pdb=" N ALA F 88 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA F 106 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 90 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU F 41 " --> pdb=" O MET F 142 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET F 142 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU F 43 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 136 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLY F 311 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU F 137 " --> pdb=" O GLY F 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU F 174 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N KCX F 205 " --> pdb=" O HLU F 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA F 176 " --> pdb=" O KCX F 205 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU F 204 " --> pdb=" O TYR F 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN F 245 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER F 242 " --> pdb=" O VAL F 268 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET F 270 " --> pdb=" O SER F 242 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU F 244 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP F 272 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 269 " --> pdb=" O HIS F 295 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS F 297 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE F 271 " --> pdb=" O HIS F 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS F 330 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 329 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU F 173 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 356 through 357 Processing sheet with id=AC1, first strand: chain 'G' and resid 87 through 93 removed outlier: 5.834A pdb=" N ALA G 88 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA G 106 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG G 90 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU G 41 " --> pdb=" O MET G 142 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET G 142 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU G 43 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 136 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.720A pdb=" N HLU G 174 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N KCX G 205 " --> pdb=" O HLU G 174 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA G 176 " --> pdb=" O KCX G 205 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU G 204 " --> pdb=" O TYR G 243 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASN G 245 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER G 242 " --> pdb=" O VAL G 268 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET G 270 " --> pdb=" O SER G 242 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU G 244 " --> pdb=" O MET G 270 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP G 272 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 269 " --> pdb=" O HIS G 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS G 297 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE G 271 " --> pdb=" O HIS G 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS G 330 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE G 329 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 173 " --> pdb=" O LEU G 403 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 356 through 357 Processing sheet with id=AC4, first strand: chain 'H' and resid 87 through 93 removed outlier: 5.839A pdb=" N ALA H 88 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA H 106 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 90 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU H 41 " --> pdb=" O MET H 142 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET H 142 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU H 43 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 136 " --> pdb=" O THR H 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 173 through 177 removed outlier: 6.701A pdb=" N HLU H 174 " --> pdb=" O PHE H 203 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N KCX H 205 " --> pdb=" O HLU H 174 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA H 176 " --> pdb=" O KCX H 205 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU H 204 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN H 245 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER H 242 " --> pdb=" O VAL H 268 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET H 270 " --> pdb=" O SER H 242 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU H 244 " --> pdb=" O MET H 270 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP H 272 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 269 " --> pdb=" O HIS H 295 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS H 297 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE H 271 " --> pdb=" O HIS H 297 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS H 330 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 329 " --> pdb=" O VAL H 380 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU H 173 " --> pdb=" O LEU H 403 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 356 through 357 Processing sheet with id=AC7, first strand: chain 'I' and resid 49 through 50 removed outlier: 7.287A pdb=" N ILE I 80 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE I 99 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE I 82 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA I 84 " --> pdb=" O VAL I 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 109 through 115 Processing sheet with id=AC9, first strand: chain 'J' and resid 49 through 50 removed outlier: 7.286A pdb=" N ILE J 80 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE J 99 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE J 82 " --> pdb=" O SER J 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER J 97 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA J 84 " --> pdb=" O VAL J 95 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 109 through 115 Processing sheet with id=AD2, first strand: chain 'K' and resid 49 through 50 removed outlier: 7.294A pdb=" N ILE K 80 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE K 99 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE K 82 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER K 97 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA K 84 " --> pdb=" O VAL K 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 109 through 115 Processing sheet with id=AD4, first strand: chain 'L' and resid 49 through 50 removed outlier: 7.297A pdb=" N ILE L 80 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE L 99 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE L 82 " --> pdb=" O SER L 97 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER L 97 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA L 84 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 109 through 115 Processing sheet with id=AD6, first strand: chain 'M' and resid 49 through 50 removed outlier: 7.283A pdb=" N ILE M 80 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE M 99 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE M 82 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER M 97 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA M 84 " --> pdb=" O VAL M 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 109 through 115 Processing sheet with id=AD8, first strand: chain 'N' and resid 49 through 50 removed outlier: 7.287A pdb=" N ILE N 80 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE N 99 " --> pdb=" O ILE N 80 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE N 82 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER N 97 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA N 84 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 109 through 115 Processing sheet with id=AE1, first strand: chain 'O' and resid 49 through 50 removed outlier: 7.283A pdb=" N ILE O 80 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE O 99 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE O 82 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER O 97 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA O 84 " --> pdb=" O VAL O 95 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 109 through 115 Processing sheet with id=AE3, first strand: chain 'P' and resid 49 through 50 removed outlier: 7.285A pdb=" N ILE P 80 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE P 99 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE P 82 " --> pdb=" O SER P 97 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER P 97 " --> pdb=" O ILE P 82 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA P 84 " --> pdb=" O VAL P 95 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 109 through 115 1685 hydrogen bonds defined for protein. 4557 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: 7.97 Time building geometry restraints manager: 3.87 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: 7988 1.33 - 1.46: 10246 1.46 - 1.58: 22218 1.58 - 1.70: 24 1.70 - 1.83: 400 Bond restraints: 40876 Sorted by residual: bond pdb=" N GLN C 213 " pdb=" CA GLN C 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.65e+01 bond pdb=" N GLN A 213 " pdb=" CA GLN A 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.65e+01 bond pdb=" N GLN E 213 " pdb=" CA GLN E 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.61e+01 bond pdb=" N GLN H 213 " pdb=" CA GLN H 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.58e+01 bond pdb=" N GLN D 213 " pdb=" CA GLN D 213 " ideal model delta sigma weight residual 1.455 1.491 -0.036 7.00e-03 2.04e+04 2.58e+01 ... (remaining 40871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 46802 2.16 - 4.33: 8396 4.33 - 6.49: 246 6.49 - 8.65: 32 8.65 - 10.82: 8 Bond angle restraints: 55484 Sorted by residual: angle pdb=" CA GLY P 6 " pdb=" C GLY P 6 " pdb=" O GLY P 6 " ideal model delta sigma weight residual 122.45 117.96 4.49 7.20e-01 1.93e+00 3.89e+01 angle pdb=" CA GLY N 6 " pdb=" C GLY N 6 " pdb=" O GLY N 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY M 6 " pdb=" C GLY M 6 " pdb=" O GLY M 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY I 6 " pdb=" C GLY I 6 " pdb=" O GLY I 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 angle pdb=" CA GLY O 6 " pdb=" C GLY O 6 " pdb=" O GLY O 6 " ideal model delta sigma weight residual 122.45 117.98 4.47 7.20e-01 1.93e+00 3.85e+01 ... (remaining 55479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 22972 35.60 - 71.21: 835 71.21 - 106.81: 73 106.81 - 142.41: 8 142.41 - 178.02: 4 Dihedral angle restraints: 23892 sinusoidal: 9360 harmonic: 14532 Sorted by residual: dihedral pdb=" C3 CAP H 501 " pdb=" C CAP H 501 " pdb=" C2 CAP H 501 " pdb=" O6 CAP H 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.12 -178.02 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP F 501 " pdb=" C CAP F 501 " pdb=" C2 CAP F 501 " pdb=" O6 CAP F 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.14 -177.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C3 CAP B 501 " pdb=" C CAP B 501 " pdb=" C2 CAP B 501 " pdb=" O6 CAP B 501 " ideal model delta sinusoidal sigma weight residual 81.86 -100.14 -177.99 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 23889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3000 0.076 - 0.152: 2458 0.152 - 0.228: 510 0.228 - 0.305: 16 0.305 - 0.381: 8 Chirality restraints: 5992 Sorted by residual: chirality pdb=" CB HLU E 174 " pdb=" CA HLU E 174 " pdb=" CG HLU E 174 " pdb=" OH HLU E 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB HLU F 174 " pdb=" CA HLU F 174 " pdb=" CG HLU F 174 " pdb=" OH HLU F 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB HLU A 174 " pdb=" CA HLU A 174 " pdb=" CG HLU A 174 " pdb=" OH HLU A 174 " both_signs ideal model delta sigma weight residual False 2.36 1.98 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5989 not shown) Planarity restraints: 7120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 298 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.06e+00 pdb=" C ARG A 298 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG A 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 299 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 298 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ARG E 298 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG E 298 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA E 299 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 298 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C ARG D 298 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG D 298 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA D 299 " 0.008 2.00e-02 2.50e+03 ... (remaining 7117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1086 2.71 - 3.25: 38844 3.25 - 3.80: 63446 3.80 - 4.35: 89141 4.35 - 4.90: 136011 Nonbonded interactions: 328528 Sorted by model distance: nonbonded pdb=" O PRO i 75 " pdb=" CZ2 TRP l 73 " model vdw 2.157 3.340 nonbonded pdb=" O PRO k 75 " pdb=" CZ2 TRP j 73 " model vdw 2.165 3.340 nonbonded pdb=" CZ2 TRP i 73 " pdb=" O PRO j 75 " model vdw 2.233 3.340 nonbonded pdb=" CZ2 TRP k 73 " pdb=" O PRO l 75 " model vdw 2.253 3.340 nonbonded pdb=" NE ARG F 90 " pdb=" OD2 ASP F 92 " model vdw 2.255 3.120 ... (remaining 328523 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 1.410 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 34.530 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.160 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.077 40876 Z= 1.043 Angle : 1.490 10.817 55484 Z= 1.111 Chirality : 0.094 0.381 5992 Planarity : 0.003 0.014 7120 Dihedral : 17.332 178.016 14644 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 7.75 % Allowed : 8.11 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: -2.45 (0.09), residues: 4816 helix: -1.73 (0.09), residues: 1896 sheet: -0.04 (0.21), residues: 440 loop : -1.81 (0.10), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 90 TYR 0.017 0.002 TYR G 16 PHE 0.011 0.001 PHE C 367 TRP 0.012 0.001 TRP H 218 HIS 0.005 0.001 HIS H 146 Details of bonding type rmsd covalent geometry : bond 0.01364 (40876) covalent geometry : angle 1.49047 (55484) hydrogen bonds : bond 0.23740 ( 1685) hydrogen bonds : angle 6.85519 ( 4557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 316 poor density : 814 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.5436 (m) cc_final: 0.5131 (t) REVERT: A 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5189 (mtp) REVERT: A 37 ASN cc_start: 0.5643 (m-40) cc_final: 0.4764 (p0) REVERT: A 90 ARG cc_start: 0.4691 (OUTLIER) cc_final: 0.3832 (tmt90) REVERT: A 207 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.4817 (t70) REVERT: B 20 VAL cc_start: 0.5436 (m) cc_final: 0.5128 (t) REVERT: B 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5166 (mtp) REVERT: B 37 ASN cc_start: 0.5633 (m-40) cc_final: 0.4761 (p0) REVERT: B 207 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4793 (t70) REVERT: C 20 VAL cc_start: 0.5437 (m) cc_final: 0.5131 (t) REVERT: C 26 MET cc_start: 0.5435 (mtt) cc_final: 0.5161 (mtp) REVERT: C 37 ASN cc_start: 0.5605 (m-40) cc_final: 0.4736 (p0) REVERT: C 207 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.4784 (t70) REVERT: D 20 VAL cc_start: 0.5404 (m) cc_final: 0.5091 (t) REVERT: D 26 MET cc_start: 0.5465 (mtt) cc_final: 0.5186 (mtp) REVERT: D 37 ASN cc_start: 0.5658 (m-40) cc_final: 0.4773 (p0) REVERT: D 207 ASP cc_start: 0.5378 (OUTLIER) cc_final: 0.4796 (t70) REVERT: E 20 VAL cc_start: 0.5409 (m) cc_final: 0.5092 (t) REVERT: E 26 MET cc_start: 0.5431 (mtt) cc_final: 0.5162 (mtp) REVERT: E 37 ASN cc_start: 0.5628 (m-40) cc_final: 0.4769 (p0) REVERT: E 207 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.4748 (t70) REVERT: F 20 VAL cc_start: 0.5405 (m) cc_final: 0.5091 (t) REVERT: F 26 MET cc_start: 0.5468 (mtt) cc_final: 0.5187 (mtp) REVERT: F 37 ASN cc_start: 0.5709 (m-40) cc_final: 0.4822 (p0) REVERT: F 207 ASP cc_start: 0.5398 (OUTLIER) cc_final: 0.4821 (t70) REVERT: G 20 VAL cc_start: 0.5461 (m) cc_final: 0.5139 (t) REVERT: G 26 MET cc_start: 0.5459 (mtt) cc_final: 0.5180 (mtp) REVERT: G 37 ASN cc_start: 0.5627 (m-40) cc_final: 0.4705 (p0) REVERT: G 207 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.4789 (t70) REVERT: H 20 VAL cc_start: 0.5434 (m) cc_final: 0.5127 (t) REVERT: H 26 MET cc_start: 0.5460 (mtt) cc_final: 0.5192 (mtp) REVERT: H 37 ASN cc_start: 0.5586 (m-40) cc_final: 0.4722 (p0) REVERT: H 207 ASP cc_start: 0.5335 (OUTLIER) cc_final: 0.4752 (t70) REVERT: i 76 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5636 (ttt180) REVERT: k 76 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5567 (ttt180) REVERT: j 76 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.5604 (ttt180) REVERT: l 76 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5522 (ttt180) outliers start: 316 outliers final: 72 residues processed: 967 average time/residue: 0.7086 time to fit residues: 818.2771 Evaluate side-chains 638 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 553 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 444 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 444 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 444 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 444 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain k residue 76 ARG Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain l residue 76 ARG Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 89 MET Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 89 MET Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 89 MET Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 89 MET Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 452 ASN B 211 ASN B 448 GLN B 452 ASN C 211 ASN C 452 ASN D 211 ASN D 452 ASN E 211 ASN E 452 ASN F 211 ASN F 452 ASN G 211 ASN G 448 GLN G 452 ASN H 211 ASN H 452 ASN I 131 GLN J 131 GLN J 133 ASN K 131 GLN L 131 GLN L 133 ASN M 131 GLN N 131 GLN N 133 ASN O 131 GLN P 131 GLN P 133 ASN h 91 GLN g 91 GLN f 91 GLN e 91 GLN d 91 GLN c 91 GLN b 91 GLN a 91 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.140582 restraints weight = 23480.763| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.17 r_work: 0.3334 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 1.09 restraints_weight: 0.2500 r_work: 0.3171 rms_B_bonded: 2.14 restraints_weight: 0.1250 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 40876 Z= 0.146 Angle : 0.569 4.983 55484 Z= 0.311 Chirality : 0.044 0.175 5992 Planarity : 0.004 0.035 7120 Dihedral : 10.246 179.737 5953 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 10.91 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: -0.11 (0.11), residues: 4816 helix: 1.25 (0.12), residues: 1912 sheet: -0.46 (0.17), residues: 800 loop : -1.14 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 69 TYR 0.011 0.001 TYR D 396 PHE 0.011 0.001 PHE D 405 TRP 0.013 0.001 TRP B 218 HIS 0.006 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00252 (40876) covalent geometry : angle 0.56857 (55484) hydrogen bonds : bond 0.05669 ( 1685) hydrogen bonds : angle 4.44032 ( 4557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 586 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8157 (t70) REVERT: B 207 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8162 (t70) REVERT: C 207 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8157 (t70) REVERT: D 207 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8171 (t70) REVERT: E 207 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8140 (t70) REVERT: F 207 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8181 (t70) REVERT: G 207 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8161 (t70) REVERT: H 207 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8145 (t70) REVERT: i 73 TRP cc_start: 0.6772 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: k 73 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: j 73 TRP cc_start: 0.6664 (OUTLIER) cc_final: 0.6191 (m-10) REVERT: l 73 TRP cc_start: 0.6680 (OUTLIER) cc_final: 0.6207 (m-10) REVERT: e 89 MET cc_start: 0.4430 (ptt) cc_final: 0.4002 (ptt) outliers start: 129 outliers final: 50 residues processed: 681 average time/residue: 0.8396 time to fit residues: 678.3190 Evaluate side-chains 581 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 519 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 63 SER Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 101 ASN Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 394 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 446 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 441 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 211 ASN A 448 GLN B 146 HIS B 211 ASN B 448 GLN C 146 HIS C 211 ASN C 448 GLN D 146 HIS D 211 ASN D 448 GLN E 146 HIS E 211 ASN E 448 GLN F 146 HIS F 211 ASN F 448 GLN G 146 HIS G 211 ASN G 448 GLN H 146 HIS H 211 ASN H 448 GLN I 131 GLN J 131 GLN K 131 GLN L 131 GLN M 131 GLN N 105 ASN N 131 GLN O 131 GLN P 105 ASN P 131 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.129489 restraints weight = 22821.982| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.18 r_work: 0.3185 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 1.11 restraints_weight: 0.2500 r_work: 0.3008 rms_B_bonded: 2.23 restraints_weight: 0.1250 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 40876 Z= 0.268 Angle : 0.747 5.839 55484 Z= 0.408 Chirality : 0.050 0.179 5992 Planarity : 0.005 0.036 7120 Dihedral : 10.322 179.054 5881 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.57 % Allowed : 10.15 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.03 (0.11), residues: 4816 helix: 1.35 (0.12), residues: 1912 sheet: -0.33 (0.17), residues: 792 loop : -1.08 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 315 TYR 0.015 0.002 TYR G 89 PHE 0.017 0.002 PHE H 405 TRP 0.012 0.002 TRP H 218 HIS 0.006 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00481 (40876) covalent geometry : angle 0.74711 (55484) hydrogen bonds : bond 0.09021 ( 1685) hydrogen bonds : angle 4.71684 ( 4557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 507 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8260 (t70) REVERT: A 308 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7806 (ttpp) REVERT: B 207 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8259 (t70) REVERT: B 308 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7800 (ttpp) REVERT: C 207 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8262 (t70) REVERT: C 308 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7843 (ttpp) REVERT: D 207 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8273 (t70) REVERT: D 308 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7792 (ttpp) REVERT: E 207 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8236 (t70) REVERT: E 308 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7809 (ttpp) REVERT: F 207 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8277 (t70) REVERT: F 308 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7834 (ttpp) REVERT: G 207 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (t70) REVERT: G 308 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7801 (ttpp) REVERT: H 207 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8252 (t70) REVERT: H 308 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7801 (ttpp) REVERT: I 70 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: J 66 PHE cc_start: 0.7876 (t80) cc_final: 0.7644 (t80) REVERT: J 70 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: L 66 PHE cc_start: 0.7862 (t80) cc_final: 0.7636 (t80) REVERT: L 70 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: N 70 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: O 66 PHE cc_start: 0.7884 (t80) cc_final: 0.7642 (t80) REVERT: O 70 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: i 73 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6080 (m-90) REVERT: k 73 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6103 (m-90) REVERT: j 73 TRP cc_start: 0.6747 (OUTLIER) cc_final: 0.6167 (m-90) REVERT: j 76 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5440 (ttt180) REVERT: l 73 TRP cc_start: 0.6746 (OUTLIER) cc_final: 0.6169 (m-90) REVERT: a 91 GLN cc_start: 0.4295 (OUTLIER) cc_final: 0.3933 (pp30) outliers start: 105 outliers final: 54 residues processed: 604 average time/residue: 0.8258 time to fit residues: 588.8910 Evaluate side-chains 582 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 501 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 308 LYS Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 89 MET Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 88 SER Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 91 GLN Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 85 GLU Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 469 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN I 131 GLN J 131 GLN K 131 GLN L 131 GLN M 131 GLN N 105 ASN N 131 GLN O 131 GLN P 105 ASN P 131 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133976 restraints weight = 23125.660| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 0.18 r_work: 0.3242 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work: 0.3040 rms_B_bonded: 2.66 restraints_weight: 0.1250 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40876 Z= 0.183 Angle : 0.611 5.310 55484 Z= 0.332 Chirality : 0.046 0.175 5992 Planarity : 0.004 0.037 7120 Dihedral : 9.757 178.891 5872 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.91 % Allowed : 10.76 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.48 (0.12), residues: 4816 helix: 1.90 (0.12), residues: 1864 sheet: -0.16 (0.17), residues: 792 loop : -0.91 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 451 TYR 0.011 0.002 TYR H 89 PHE 0.017 0.002 PHE F 203 TRP 0.012 0.001 TRP D 218 HIS 0.004 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00318 (40876) covalent geometry : angle 0.61106 (55484) hydrogen bonds : bond 0.06730 ( 1685) hydrogen bonds : angle 4.34660 ( 4557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 511 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8425 (t70) REVERT: B 207 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8423 (t70) REVERT: C 207 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8413 (t70) REVERT: D 207 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8443 (t70) REVERT: E 207 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8393 (t70) REVERT: F 207 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8445 (t70) REVERT: G 207 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8432 (t70) REVERT: H 207 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8421 (t70) REVERT: i 73 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.6164 (m-90) REVERT: k 73 TRP cc_start: 0.6841 (OUTLIER) cc_final: 0.6156 (m-90) REVERT: j 73 TRP cc_start: 0.6828 (OUTLIER) cc_final: 0.6215 (m-90) REVERT: j 76 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.5599 (ttt180) REVERT: l 73 TRP cc_start: 0.6805 (OUTLIER) cc_final: 0.6204 (m-90) REVERT: a 91 GLN cc_start: 0.4406 (OUTLIER) cc_final: 0.3981 (pp30) outliers start: 78 outliers final: 44 residues processed: 582 average time/residue: 0.9014 time to fit residues: 615.8746 Evaluate side-chains 572 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 514 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain K residue 101 ASN Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain g residue 85 GLU Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 85 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain e residue 85 GLU Chi-restraints excluded: chain e residue 91 GLN Chi-restraints excluded: chain d residue 88 SER Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain b residue 85 GLU Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain a residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 399 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 335 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN N 105 ASN P 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131708 restraints weight = 22865.952| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.18 r_work: 0.3207 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.3013 rms_B_bonded: 2.57 restraints_weight: 0.1250 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 40876 Z= 0.216 Angle : 0.665 5.591 55484 Z= 0.361 Chirality : 0.047 0.178 5992 Planarity : 0.005 0.036 7120 Dihedral : 9.825 179.026 5859 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.81 % Allowed : 10.96 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.40 (0.12), residues: 4816 helix: 1.78 (0.12), residues: 1864 sheet: -0.16 (0.17), residues: 792 loop : -0.91 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 451 TYR 0.012 0.002 TYR H 89 PHE 0.018 0.002 PHE H 203 TRP 0.012 0.001 TRP B 218 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00380 (40876) covalent geometry : angle 0.66501 (55484) hydrogen bonds : bond 0.07882 ( 1685) hydrogen bonds : angle 4.47172 ( 4557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 511 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8283 (t70) REVERT: A 308 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: B 207 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8278 (t70) REVERT: B 308 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7796 (ttpp) REVERT: C 207 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8269 (t70) REVERT: C 308 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7842 (ttpp) REVERT: D 207 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (t70) REVERT: D 308 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7786 (ttpp) REVERT: E 207 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8247 (t70) REVERT: E 308 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7795 (ttpp) REVERT: F 207 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8295 (t70) REVERT: F 308 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7831 (ttpp) REVERT: G 207 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8286 (t70) REVERT: G 308 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7797 (ttpp) REVERT: H 207 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8270 (t70) REVERT: H 308 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7798 (ttpp) REVERT: K 70 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: M 70 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: N 70 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: P 70 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: i 73 TRP cc_start: 0.6811 (OUTLIER) cc_final: 0.6112 (m-90) REVERT: i 76 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5444 (ttt180) REVERT: k 73 TRP cc_start: 0.6804 (OUTLIER) cc_final: 0.6088 (m-90) REVERT: j 73 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.6185 (m-90) REVERT: j 76 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5557 (ttt180) REVERT: l 73 TRP cc_start: 0.6800 (OUTLIER) cc_final: 0.6127 (m-90) outliers start: 74 outliers final: 31 residues processed: 575 average time/residue: 0.9883 time to fit residues: 665.3296 Evaluate side-chains 568 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 511 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 308 LYS Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain g residue 91 GLN Chi-restraints excluded: chain f residue 91 GLN Chi-restraints excluded: chain d residue 85 GLU Chi-restraints excluded: chain d residue 91 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 162 optimal weight: 0.8980 chunk 255 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 462 optimal weight: 6.9990 chunk 344 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 471 optimal weight: 2.9990 chunk 285 optimal weight: 0.1980 chunk 362 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 368 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN N 105 ASN P 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.147258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.139221 restraints weight = 23629.312| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.18 r_work: 0.3307 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 1.11 restraints_weight: 0.2500 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.1250 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 40876 Z= 0.128 Angle : 0.525 4.913 55484 Z= 0.283 Chirality : 0.043 0.174 5992 Planarity : 0.004 0.038 7120 Dihedral : 9.046 177.920 5829 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.50 % Allowed : 11.25 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.77 (0.12), residues: 4816 helix: 2.36 (0.12), residues: 1808 sheet: 0.01 (0.18), residues: 792 loop : -0.89 (0.11), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 451 TYR 0.010 0.001 TYR P 110 PHE 0.010 0.001 PHE E 203 TRP 0.012 0.001 TRP H 218 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00222 (40876) covalent geometry : angle 0.52512 (55484) hydrogen bonds : bond 0.05007 ( 1685) hydrogen bonds : angle 4.02448 ( 4557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 527 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7061 (mtt180) REVERT: A 207 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (t70) REVERT: B 207 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (t70) REVERT: C 207 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8325 (t70) REVERT: C 308 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8031 (ttpt) REVERT: D 207 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8356 (t70) REVERT: E 207 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8313 (t70) REVERT: F 207 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8358 (t70) REVERT: G 207 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8334 (t70) REVERT: G 448 GLN cc_start: 0.8257 (tp40) cc_final: 0.7997 (tp-100) REVERT: H 207 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8330 (t70) REVERT: i 73 TRP cc_start: 0.6848 (OUTLIER) cc_final: 0.6058 (m-90) REVERT: i 76 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5419 (ttt180) REVERT: k 73 TRP cc_start: 0.7009 (OUTLIER) cc_final: 0.6227 (m-90) REVERT: j 73 TRP cc_start: 0.6993 (OUTLIER) cc_final: 0.6294 (m-90) REVERT: j 76 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.5439 (ttt180) REVERT: l 73 TRP cc_start: 0.6771 (OUTLIER) cc_final: 0.6123 (m-90) outliers start: 61 outliers final: 32 residues processed: 577 average time/residue: 0.9300 time to fit residues: 634.0567 Evaluate side-chains 561 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 514 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain K residue 101 ASN Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain d residue 85 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 172 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 313 optimal weight: 0.9990 chunk 472 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 441 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 396 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN L 105 ASN N 105 ASN P 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.138114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.130266 restraints weight = 22756.747| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.18 r_work: 0.3193 rms_B_bonded: 0.61 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3019 rms_B_bonded: 2.17 restraints_weight: 0.1250 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 40876 Z= 0.251 Angle : 0.713 5.751 55484 Z= 0.387 Chirality : 0.049 0.179 5992 Planarity : 0.005 0.035 7120 Dihedral : 9.743 179.271 5820 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 10.81 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.49 (0.11), residues: 4816 helix: 1.97 (0.12), residues: 1816 sheet: -0.14 (0.18), residues: 792 loop : -0.91 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 315 TYR 0.012 0.002 TYR H 89 PHE 0.021 0.002 PHE A 203 TRP 0.011 0.002 TRP A 218 HIS 0.005 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00451 (40876) covalent geometry : angle 0.71293 (55484) hydrogen bonds : bond 0.08625 ( 1685) hydrogen bonds : angle 4.53293 ( 4557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 510 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 189 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8455 (t80) REVERT: A 207 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8251 (t70) REVERT: A 308 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7813 (ttpp) REVERT: B 123 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8325 (t) REVERT: B 189 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (t80) REVERT: B 207 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8246 (t70) REVERT: B 308 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: C 123 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8325 (t) REVERT: C 189 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8486 (t80) REVERT: C 207 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8236 (t70) REVERT: C 308 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7838 (ttpp) REVERT: D 123 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8328 (t) REVERT: D 189 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8475 (t80) REVERT: D 207 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8250 (t70) REVERT: D 308 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7798 (ttpp) REVERT: E 123 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8318 (t) REVERT: E 189 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8475 (t80) REVERT: E 207 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8219 (t70) REVERT: E 308 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7801 (ttpp) REVERT: F 123 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8319 (t) REVERT: F 189 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8486 (t80) REVERT: F 207 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8256 (t70) REVERT: F 308 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: G 123 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8328 (t) REVERT: G 189 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.8463 (t80) REVERT: G 207 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8257 (t70) REVERT: G 308 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7809 (ttpp) REVERT: H 123 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8319 (t) REVERT: H 189 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8481 (t80) REVERT: H 207 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8228 (t70) REVERT: H 308 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7811 (ttpp) REVERT: I 70 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: J 70 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: K 70 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: L 70 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: M 70 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: N 70 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: O 70 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: P 70 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: i 73 TRP cc_start: 0.7042 (OUTLIER) cc_final: 0.6193 (m-90) REVERT: i 76 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5368 (ttt180) REVERT: k 73 TRP cc_start: 0.7033 (OUTLIER) cc_final: 0.6199 (m-90) REVERT: j 73 TRP cc_start: 0.7007 (OUTLIER) cc_final: 0.6276 (m-90) REVERT: j 76 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5454 (ttt180) REVERT: l 73 TRP cc_start: 0.6989 (OUTLIER) cc_final: 0.6277 (m-90) outliers start: 76 outliers final: 17 residues processed: 579 average time/residue: 0.9969 time to fit residues: 675.1650 Evaluate side-chains 567 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 504 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 308 LYS Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 308 LYS Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 308 LYS Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain i residue 76 ARG Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain d residue 85 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 31 optimal weight: 1.9990 chunk 481 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 470 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 430 optimal weight: 9.9990 chunk 466 optimal weight: 0.0370 chunk 230 optimal weight: 10.0000 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN L 105 ASN N 105 ASN P 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.143435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.135313 restraints weight = 23155.124| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.18 r_work: 0.3266 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work: 0.3060 rms_B_bonded: 2.72 restraints_weight: 0.1250 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 40876 Z= 0.163 Angle : 0.579 5.192 55484 Z= 0.314 Chirality : 0.045 0.176 5992 Planarity : 0.004 0.037 7120 Dihedral : 9.247 178.512 5816 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.42 % Allowed : 11.35 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 4816 helix: 2.22 (0.12), residues: 1808 sheet: -0.06 (0.18), residues: 792 loop : -0.90 (0.11), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 90 TYR 0.014 0.001 TYR A 89 PHE 0.014 0.002 PHE E 203 TRP 0.011 0.001 TRP A 218 HIS 0.004 0.001 HIS G 146 Details of bonding type rmsd covalent geometry : bond 0.00283 (40876) covalent geometry : angle 0.57870 (55484) hydrogen bonds : bond 0.06152 ( 1685) hydrogen bonds : angle 4.19406 ( 4557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 514 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8459 (t80) REVERT: A 207 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8435 (t70) REVERT: B 189 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8459 (t80) REVERT: B 207 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8441 (t70) REVERT: C 10 ARG cc_start: 0.7550 (mtt180) cc_final: 0.7078 (mtt180) REVERT: C 189 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8478 (t80) REVERT: C 207 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8424 (t70) REVERT: C 308 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7813 (ttpp) REVERT: D 189 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8463 (t80) REVERT: D 207 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8456 (t70) REVERT: E 10 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7067 (mtt180) REVERT: E 189 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8474 (t80) REVERT: E 207 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8402 (t70) REVERT: F 189 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (t80) REVERT: F 207 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8447 (t70) REVERT: G 189 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8450 (t80) REVERT: G 207 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8436 (t70) REVERT: G 448 GLN cc_start: 0.8242 (tp40) cc_final: 0.8040 (tp-100) REVERT: H 189 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8466 (t80) REVERT: H 207 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8422 (t70) REVERT: K 70 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: M 70 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: N 70 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: P 70 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: i 73 TRP cc_start: 0.7113 (OUTLIER) cc_final: 0.6247 (m-90) REVERT: k 73 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.6231 (m-90) REVERT: j 73 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6325 (m-90) REVERT: j 76 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.5602 (ttt180) REVERT: l 73 TRP cc_start: 0.7044 (OUTLIER) cc_final: 0.6354 (m-90) outliers start: 58 outliers final: 26 residues processed: 565 average time/residue: 0.9779 time to fit residues: 648.0364 Evaluate side-chains 565 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 513 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 101 ASN Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 101 ASN Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 101 ASN Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain d residue 85 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 188 optimal weight: 4.9990 chunk 389 optimal weight: 0.0970 chunk 392 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN L 105 ASN P 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.138204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121881 restraints weight = 22537.157| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.35 r_work: 0.3018 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.2823 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 40876 Z= 0.270 Angle : 0.747 5.883 55484 Z= 0.405 Chirality : 0.050 0.180 5992 Planarity : 0.005 0.034 7120 Dihedral : 9.801 179.636 5816 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.32 % Allowed : 11.54 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.38 (0.11), residues: 4816 helix: 1.84 (0.12), residues: 1816 sheet: -0.21 (0.17), residues: 792 loop : -0.92 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 451 TYR 0.013 0.002 TYR A 89 PHE 0.019 0.003 PHE H 405 TRP 0.012 0.002 TRP H 218 HIS 0.005 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00488 (40876) covalent geometry : angle 0.74671 (55484) hydrogen bonds : bond 0.09068 ( 1685) hydrogen bonds : angle 4.58139 ( 4557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 505 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8494 (t80) REVERT: A 207 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8330 (t70) REVERT: A 308 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7887 (ttpp) REVERT: B 189 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8501 (t80) REVERT: B 207 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8317 (t70) REVERT: B 308 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7886 (ttpp) REVERT: C 189 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8504 (t80) REVERT: C 207 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8319 (t70) REVERT: C 308 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7933 (ttpp) REVERT: D 189 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8499 (t80) REVERT: D 207 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8327 (t70) REVERT: E 189 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8510 (t80) REVERT: E 207 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (t70) REVERT: F 189 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8509 (t80) REVERT: F 207 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8317 (t70) REVERT: G 189 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8506 (t80) REVERT: G 207 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8337 (t70) REVERT: H 189 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (t80) REVERT: H 207 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8295 (t70) REVERT: I 70 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: K 70 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: L 70 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: M 70 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: N 70 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: P 70 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: i 73 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.6925 (m-90) REVERT: k 73 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.6943 (m-90) REVERT: j 73 TRP cc_start: 0.7911 (OUTLIER) cc_final: 0.7013 (m-90) REVERT: j 76 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6364 (ttt180) REVERT: l 73 TRP cc_start: 0.7919 (OUTLIER) cc_final: 0.7020 (m-90) outliers start: 54 outliers final: 19 residues processed: 552 average time/residue: 1.0038 time to fit residues: 647.1967 Evaluate side-chains 544 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain d residue 85 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 91 optimal weight: 9.9990 chunk 208 optimal weight: 0.4980 chunk 319 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 473 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 467 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN L 105 ASN P 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.139978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.124720 restraints weight = 22577.675| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 0.33 r_work: 0.3064 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2873 rms_B_bonded: 2.94 restraints_weight: 0.1250 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 40876 Z= 0.230 Angle : 0.682 5.584 55484 Z= 0.371 Chirality : 0.048 0.177 5992 Planarity : 0.005 0.035 7120 Dihedral : 9.658 179.047 5816 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.25 % Allowed : 12.08 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.43 (0.11), residues: 4816 helix: 1.93 (0.12), residues: 1816 sheet: -0.21 (0.17), residues: 792 loop : -0.93 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 451 TYR 0.011 0.002 TYR A 89 PHE 0.017 0.002 PHE E 203 TRP 0.013 0.001 TRP E 218 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00409 (40876) covalent geometry : angle 0.68249 (55484) hydrogen bonds : bond 0.07982 ( 1685) hydrogen bonds : angle 4.45519 ( 4557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9632 Ramachandran restraints generated. 4816 Oldfield, 0 Emsley, 4816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 496 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8510 (t80) REVERT: A 207 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8297 (t70) REVERT: B 189 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.8515 (t80) REVERT: B 207 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8292 (t70) REVERT: C 123 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8336 (t) REVERT: C 189 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8536 (t80) REVERT: C 207 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8300 (t70) REVERT: C 308 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: D 189 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8530 (t80) REVERT: D 207 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8302 (t70) REVERT: D 308 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7858 (ttpp) REVERT: E 189 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8519 (t80) REVERT: E 207 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8258 (t70) REVERT: F 189 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8532 (t80) REVERT: F 207 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8298 (t70) REVERT: G 189 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (t80) REVERT: G 207 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (t70) REVERT: H 123 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8316 (t) REVERT: H 189 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8534 (t80) REVERT: H 207 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8276 (t70) REVERT: I 27 ILE cc_start: 0.7943 (mt) cc_final: 0.7707 (mm) REVERT: I 70 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: J 27 ILE cc_start: 0.7951 (mt) cc_final: 0.7716 (mm) REVERT: K 27 ILE cc_start: 0.7947 (mt) cc_final: 0.7720 (mm) REVERT: K 70 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: L 27 ILE cc_start: 0.7949 (mt) cc_final: 0.7715 (mm) REVERT: L 70 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: M 70 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: N 70 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: O 27 ILE cc_start: 0.7959 (mt) cc_final: 0.7723 (mm) REVERT: P 27 ILE cc_start: 0.7956 (mt) cc_final: 0.7722 (mm) REVERT: P 70 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: i 73 TRP cc_start: 0.7904 (OUTLIER) cc_final: 0.6854 (m-90) REVERT: k 73 TRP cc_start: 0.7874 (OUTLIER) cc_final: 0.6865 (m-90) REVERT: j 73 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.6974 (m-90) REVERT: j 76 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6303 (ttt180) REVERT: l 73 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.6947 (m-90) outliers start: 51 outliers final: 17 residues processed: 540 average time/residue: 0.9652 time to fit residues: 612.1383 Evaluate side-chains 543 residues out of total 4080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 495 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 308 LYS Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 189 TYR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 189 TYR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 189 TYR Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 456 THR Chi-restraints excluded: chain H residue 90 ARG Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 207 ASP Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain i residue 73 TRP Chi-restraints excluded: chain k residue 73 TRP Chi-restraints excluded: chain j residue 73 TRP Chi-restraints excluded: chain j residue 76 ARG Chi-restraints excluded: chain l residue 73 TRP Chi-restraints excluded: chain h residue 85 GLU Chi-restraints excluded: chain d residue 85 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 195 optimal weight: 0.4980 chunk 414 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 416 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN E 448 GLN F 448 GLN H 448 GLN L 105 ASN P 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.143480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133337 restraints weight = 22927.993| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.30 r_work: 0.3164 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work: 0.2935 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40876 Z= 0.173 Angle : 0.596 5.282 55484 Z= 0.323 Chirality : 0.045 0.177 5992 Planarity : 0.004 0.036 7120 Dihedral : 9.308 178.673 5816 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.27 % Allowed : 11.84 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 aren not related in a simple way. whole: 0.62 (0.12), residues: 4816 helix: 2.14 (0.12), residues: 1816 sheet: -0.10 (0.18), residues: 792 loop : -0.88 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 90 TYR 0.010 0.001 TYR A 89 PHE 0.013 0.002 PHE C 203 TRP 0.011 0.001 TRP A 218 HIS 0.005 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00302 (40876) covalent geometry : angle 0.59602 (55484) hydrogen bonds : bond 0.06412 ( 1685) hydrogen bonds : angle 4.22700 ( 4557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19051.59 seconds wall clock time: 324 minutes 10.18 seconds (19450.18 seconds total)