Starting phenix.real_space_refine on Mon Sep 30 03:00:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/09_2024/8ihr_35453.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 Zn 16 6.06 5 S 72 5.16 5 C 15184 2.51 5 N 4424 2.21 5 O 4528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 15.06, per 1000 atoms: 0.62 Number of scatterers: 24224 At special positions: 0 Unit cell: (138.55, 138.55, 103.7, 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) Zn 16 29.99 S 72 16.00 O 4528 8.00 N 4424 7.00 C 15184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 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: 5.93 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 28 sheets defined 43.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.547A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.607A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.435A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.854A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.676A pdb=" N HIS A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.655A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.551A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.502A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 304 removed outlier: 3.598A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 4.420A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.933A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.545A pdb=" N ALA B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 3.653A pdb=" N GLU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.547A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.503A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.604A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 4.420A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.937A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.589A pdb=" N ALA C 411 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.655A pdb=" N GLU D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.551A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.502A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 304 removed outlier: 3.598A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 4.419A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.932A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.700A pdb=" N HIS D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.545A pdb=" N ALA D 411 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.538A pdb=" N TYR E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 304 removed outlier: 3.651A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 removed outlier: 4.531A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.543A pdb=" N ASN E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.916A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 3.537A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 removed outlier: 3.589A pdb=" N ALA E 411 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 96 through 101 Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.164A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 143 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.531A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 304 removed outlier: 3.639A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 323 removed outlier: 4.528A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.502A pdb=" N ASN F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.912A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 383 removed outlier: 3.539A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 removed outlier: 3.583A pdb=" N ALA F 411 " --> pdb=" O ASP F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 96 through 101 Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.164A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.541A pdb=" N TYR G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 304 removed outlier: 3.651A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 323 removed outlier: 4.528A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.520A pdb=" N ASN G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 362 removed outlier: 3.914A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 383 removed outlier: 3.537A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 removed outlier: 3.588A pdb=" N ALA G 411 " --> pdb=" O ASP G 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 190 through 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.540A pdb=" N TYR H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.639A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 323 removed outlier: 4.527A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.672A pdb=" N ASN H 335 " --> pdb=" O LYS H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 362 removed outlier: 3.917A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 383 removed outlier: 3.540A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA H 378 " --> pdb=" O ALA H 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 removed outlier: 3.590A pdb=" N ALA H 411 " --> pdb=" O ASP H 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 5.174A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.870A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.414A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 398 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 418 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 400 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.329A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.563A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL A 248 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU A 270 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 250 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 56 removed outlier: 5.177A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 13.910A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.891A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.464A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 398 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 418 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 400 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.328A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 248 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU B 270 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 250 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 56 removed outlier: 5.176A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 13.914A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 398 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 418 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 400 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.330A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 248 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU C 270 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA C 250 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 56 removed outlier: 5.176A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 13.919A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.904A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.454A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 398 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL D 418 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA D 400 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.335A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.562A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D 248 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLU D 270 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA D 250 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.537A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.537A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.911A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL E 398 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 418 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA E 400 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.453A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.629A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL E 248 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU E 270 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA E 250 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE E 269 " --> pdb=" O VAL E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.546A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.546A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.907A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 14.309A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.620A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 398 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL F 418 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA F 400 " --> pdb=" O ARG F 416 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.454A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.628A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL F 248 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLU F 270 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA F 250 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 269 " --> pdb=" O VAL F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.540A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.540A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 13.906A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL G 398 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL G 418 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA G 400 " --> pdb=" O ARG G 416 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.455A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.630A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL G 248 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLU G 270 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA G 250 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE G 269 " --> pdb=" O VAL G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.542A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.542A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.904A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 14.309A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.610A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL H 398 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL H 418 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA H 400 " --> pdb=" O ARG H 416 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.452A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.631A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL H 248 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU H 270 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA H 250 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE H 269 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1001 hydrogen bonds defined for protein. 2820 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: 8.43 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4626 1.32 - 1.45: 6097 1.45 - 1.57: 13853 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24704 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX A 210 " pdb=" CX KCX A 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 24699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 32907 2.21 - 4.43: 495 4.43 - 6.64: 59 6.64 - 8.85: 26 8.85 - 11.07: 9 Bond angle restraints: 33496 Sorted by residual: angle pdb=" N VAL C 347 " pdb=" CA VAL C 347 " pdb=" C VAL C 347 " ideal model delta sigma weight residual 111.67 101.21 10.46 9.50e-01 1.11e+00 1.21e+02 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.67 101.42 10.25 9.50e-01 1.11e+00 1.16e+02 angle pdb=" N GLY C 346 " pdb=" CA GLY C 346 " pdb=" C GLY C 346 " ideal model delta sigma weight residual 113.18 102.11 11.07 2.37e+00 1.78e-01 2.18e+01 angle pdb=" C GLN C 345 " pdb=" CA GLN C 345 " pdb=" CB GLN C 345 " ideal model delta sigma weight residual 109.72 117.46 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" C GLN B 345 " pdb=" CA GLN B 345 " pdb=" CB GLN B 345 " ideal model delta sigma weight residual 109.72 117.43 -7.71 1.66e+00 3.63e-01 2.16e+01 ... (remaining 33491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 12882 17.58 - 35.16: 1251 35.16 - 52.74: 368 52.74 - 70.33: 86 70.33 - 87.91: 29 Dihedral angle restraints: 14616 sinusoidal: 5656 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN D 345 " pdb=" C GLN D 345 " pdb=" N GLY D 346 " pdb=" CA GLY D 346 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY F 272 " pdb=" C GLY F 272 " pdb=" N THR F 273 " pdb=" CA THR F 273 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2988 0.057 - 0.114: 610 0.114 - 0.171: 68 0.171 - 0.229: 6 0.229 - 0.286: 8 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA VAL G 347 " pdb=" N VAL G 347 " pdb=" C VAL G 347 " pdb=" CB VAL G 347 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL E 347 " pdb=" N VAL E 347 " pdb=" C VAL E 347 " pdb=" CB VAL E 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA VAL H 347 " pdb=" N VAL H 347 " pdb=" C VAL H 347 " pdb=" CB VAL H 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3677 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 55 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO G 56 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 374 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C ALA E 374 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA E 374 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 375 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 374 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C ALA G 374 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA G 374 " -0.017 2.00e-02 2.50e+03 pdb=" N THR G 375 " -0.016 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 412 2.69 - 3.24: 21978 3.24 - 3.80: 37678 3.80 - 4.35: 54581 4.35 - 4.90: 88592 Nonbonded interactions: 203241 Sorted by model distance: nonbonded pdb=" OQ2 KCX E 210 " pdb="ZN ZN E 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX F 210 " pdb="ZN ZN F 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX G 210 " pdb="ZN ZN G 501 " model vdw 2.139 2.230 nonbonded pdb=" OQ2 KCX H 210 " pdb="ZN ZN H 501 " model vdw 2.139 2.230 nonbonded pdb=" N GLN H 327 " pdb=" OE1 GLN H 327 " model vdw 2.216 3.120 ... (remaining 203236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.440 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24704 Z= 0.252 Angle : 0.669 11.066 33496 Z= 0.401 Chirality : 0.048 0.286 3680 Planarity : 0.005 0.068 4464 Dihedral : 15.866 87.908 8912 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 15.72 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1344 sheet: -0.05 (0.24), residues: 400 loop : -0.90 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.012 0.001 PHE D 294 TYR 0.008 0.001 TYR A 95 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 2.838 Fit side-chains REVERT: E 55 LEU cc_start: 0.8051 (mm) cc_final: 0.7754 (mp) REVERT: E 331 LYS cc_start: 0.8278 (tptt) cc_final: 0.8011 (tttm) REVERT: F 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7747 (mp) REVERT: F 277 ASP cc_start: 0.7809 (m-30) cc_final: 0.7472 (m-30) REVERT: G 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7728 (mp) REVERT: G 277 ASP cc_start: 0.7718 (m-30) cc_final: 0.7409 (m-30) REVERT: H 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7746 (mp) REVERT: H 331 LYS cc_start: 0.8376 (tttm) cc_final: 0.8017 (tptt) outliers start: 17 outliers final: 17 residues processed: 351 average time/residue: 1.5325 time to fit residues: 608.8549 Evaluate side-chains 339 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 322 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24704 Z= 0.157 Angle : 0.526 7.977 33496 Z= 0.282 Chirality : 0.044 0.137 3680 Planarity : 0.004 0.048 4464 Dihedral : 5.335 54.963 3577 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.77 % Allowed : 14.48 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3136 helix: 1.06 (0.15), residues: 1240 sheet: 0.05 (0.24), residues: 400 loop : -0.88 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 289 HIS 0.007 0.001 HIS C 251 PHE 0.013 0.001 PHE C 294 TYR 0.011 0.001 TYR C 95 ARG 0.003 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 324 time to evaluate : 3.045 Fit side-chains REVERT: E 55 LEU cc_start: 0.8083 (mm) cc_final: 0.7839 (mp) REVERT: E 155 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7307 (mmtt) REVERT: F 55 LEU cc_start: 0.8068 (mm) cc_final: 0.7820 (mp) REVERT: F 155 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7301 (mmtt) REVERT: G 55 LEU cc_start: 0.8063 (mm) cc_final: 0.7819 (mp) REVERT: G 155 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7323 (mmtt) REVERT: H 55 LEU cc_start: 0.8081 (mm) cc_final: 0.7831 (mp) REVERT: H 155 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7334 (mmtt) outliers start: 43 outliers final: 30 residues processed: 337 average time/residue: 1.5903 time to fit residues: 606.8686 Evaluate side-chains 353 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 319 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 281 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 24704 Z= 0.338 Angle : 0.646 9.487 33496 Z= 0.352 Chirality : 0.050 0.149 3680 Planarity : 0.005 0.050 4464 Dihedral : 5.508 57.903 3556 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.72 % Allowed : 13.70 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3136 helix: 0.86 (0.14), residues: 1240 sheet: -0.12 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 289 HIS 0.007 0.001 HIS A 271 PHE 0.015 0.002 PHE D 294 TYR 0.014 0.002 TYR C 95 ARG 0.004 0.000 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 310 time to evaluate : 2.836 Fit side-chains REVERT: A 155 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7629 (tmtm) REVERT: B 155 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7556 (tmtm) REVERT: C 155 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7623 (tmtm) REVERT: D 155 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7619 (tmtm) REVERT: E 55 LEU cc_start: 0.8108 (mm) cc_final: 0.7892 (mp) REVERT: E 98 ASP cc_start: 0.7656 (m-30) cc_final: 0.7143 (m-30) REVERT: E 155 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7359 (mmtt) REVERT: E 222 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7574 (mtm180) REVERT: F 55 LEU cc_start: 0.8107 (mm) cc_final: 0.7891 (mp) REVERT: F 155 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7349 (mmtt) REVERT: G 55 LEU cc_start: 0.8096 (mm) cc_final: 0.7880 (mp) REVERT: G 155 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7373 (mmtt) REVERT: G 222 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7546 (mtm180) REVERT: H 55 LEU cc_start: 0.8105 (mm) cc_final: 0.7888 (mp) REVERT: H 98 ASP cc_start: 0.7646 (m-30) cc_final: 0.7134 (m-30) REVERT: H 155 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7382 (mmtt) outliers start: 66 outliers final: 31 residues processed: 331 average time/residue: 1.5434 time to fit residues: 577.6333 Evaluate side-chains 349 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN C 53 GLN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 24704 Z= 0.394 Angle : 0.685 9.779 33496 Z= 0.375 Chirality : 0.052 0.163 3680 Planarity : 0.006 0.049 4464 Dihedral : 5.569 59.294 3553 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.14 % Allowed : 13.66 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3136 helix: 0.70 (0.14), residues: 1240 sheet: -0.22 (0.24), residues: 400 loop : -1.22 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 289 HIS 0.008 0.002 HIS C 271 PHE 0.015 0.003 PHE C 294 TYR 0.015 0.002 TYR D 369 ARG 0.005 0.001 ARG G 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 314 time to evaluate : 2.606 Fit side-chains REVERT: A 155 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7649 (tmtm) REVERT: B 155 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7658 (tmtm) REVERT: C 155 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7663 (tmtm) REVERT: D 155 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7684 (tmtm) REVERT: E 97 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: E 98 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: E 155 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7359 (mmtt) REVERT: E 222 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7572 (mtm180) REVERT: F 97 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: F 155 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7348 (mmtt) REVERT: G 97 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: G 155 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7374 (mmtt) REVERT: G 222 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: H 97 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: H 98 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: H 155 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7383 (mmtt) outliers start: 76 outliers final: 33 residues processed: 345 average time/residue: 1.5618 time to fit residues: 611.4693 Evaluate side-chains 356 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 307 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN E 37 GLN E 53 GLN F 37 GLN F 53 GLN G 37 GLN G 53 GLN H 37 GLN H 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24704 Z= 0.165 Angle : 0.533 8.049 33496 Z= 0.287 Chirality : 0.045 0.138 3680 Planarity : 0.004 0.045 4464 Dihedral : 5.052 54.735 3553 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.76 % Allowed : 14.32 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3136 helix: 1.05 (0.14), residues: 1240 sheet: -0.05 (0.24), residues: 400 loop : -1.09 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.007 0.001 HIS B 251 PHE 0.012 0.001 PHE C 294 TYR 0.009 0.001 TYR A 95 ARG 0.005 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 310 time to evaluate : 2.763 Fit side-chains REVERT: E 97 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: E 98 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: E 155 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: F 97 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: F 155 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7311 (mmtt) REVERT: G 97 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: G 155 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7332 (mmtt) REVERT: G 222 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7477 (mtm180) REVERT: H 97 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: H 98 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: H 155 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7344 (mmtt) outliers start: 67 outliers final: 26 residues processed: 341 average time/residue: 1.5469 time to fit residues: 596.2431 Evaluate side-chains 348 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 24704 Z= 0.414 Angle : 0.698 9.842 33496 Z= 0.383 Chirality : 0.052 0.201 3680 Planarity : 0.006 0.049 4464 Dihedral : 5.573 58.893 3553 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.81 % Allowed : 14.27 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3136 helix: 0.73 (0.14), residues: 1248 sheet: -0.21 (0.24), residues: 400 loop : -1.21 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 289 HIS 0.008 0.002 HIS C 271 PHE 0.017 0.003 PHE C 294 TYR 0.016 0.002 TYR D 369 ARG 0.005 0.001 ARG H 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 308 time to evaluate : 2.806 Fit side-chains REVERT: E 97 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: E 98 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: E 155 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7361 (mmtt) REVERT: F 155 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: G 155 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7375 (mmtt) REVERT: G 222 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7538 (mtm180) REVERT: H 97 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: H 98 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: H 155 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7423 (mmtt) outliers start: 68 outliers final: 35 residues processed: 341 average time/residue: 1.5505 time to fit residues: 596.6338 Evaluate side-chains 343 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 299 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24704 Z= 0.140 Angle : 0.519 7.675 33496 Z= 0.278 Chirality : 0.044 0.145 3680 Planarity : 0.004 0.043 4464 Dihedral : 4.924 51.967 3553 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.31 % Allowed : 15.26 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3136 helix: 1.12 (0.15), residues: 1240 sheet: -0.03 (0.24), residues: 400 loop : -1.06 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.007 0.001 HIS D 251 PHE 0.011 0.001 PHE C 294 TYR 0.008 0.001 TYR A 95 ARG 0.007 0.000 ARG G 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 306 time to evaluate : 2.802 Fit side-chains REVERT: A 97 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: E 97 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: E 98 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: E 155 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7303 (mmtt) REVERT: F 97 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: F 155 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7297 (mmtt) REVERT: G 97 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: G 155 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: H 97 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: H 98 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: H 155 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7349 (mmtt) outliers start: 56 outliers final: 25 residues processed: 326 average time/residue: 1.5457 time to fit residues: 568.6514 Evaluate side-chains 345 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 309 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 236 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 410 ASN C 53 GLN C 410 ASN D 53 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24704 Z= 0.292 Angle : 0.623 9.155 33496 Z= 0.339 Chirality : 0.048 0.191 3680 Planarity : 0.005 0.048 4464 Dihedral : 5.350 56.268 3553 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.35 % Allowed : 15.39 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3136 helix: 0.98 (0.14), residues: 1240 sheet: -0.11 (0.24), residues: 400 loop : -1.15 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 289 HIS 0.007 0.001 HIS D 251 PHE 0.015 0.002 PHE D 294 TYR 0.013 0.002 TYR D 369 ARG 0.008 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 306 time to evaluate : 2.482 Fit side-chains REVERT: A 97 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: E 98 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: E 155 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7358 (mmtt) REVERT: F 155 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7353 (mmtt) REVERT: G 155 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7374 (mmtt) REVERT: H 98 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: H 155 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7384 (mmtt) outliers start: 57 outliers final: 28 residues processed: 332 average time/residue: 1.6252 time to fit residues: 609.7013 Evaluate side-chains 334 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 299 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24704 Z= 0.150 Angle : 0.529 7.860 33496 Z= 0.282 Chirality : 0.044 0.169 3680 Planarity : 0.004 0.043 4464 Dihedral : 4.891 47.504 3553 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 16.13 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3136 helix: 1.20 (0.15), residues: 1240 sheet: 0.05 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.008 0.001 HIS C 251 PHE 0.011 0.001 PHE C 294 TYR 0.008 0.001 TYR A 95 ARG 0.008 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 2.611 Fit side-chains REVERT: A 97 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: E 98 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: E 155 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7308 (mmtt) REVERT: E 331 LYS cc_start: 0.8367 (tttp) cc_final: 0.8016 (tttm) REVERT: F 155 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7305 (mmtt) REVERT: G 155 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7326 (mmtt) REVERT: H 98 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: H 155 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7338 (mmtt) REVERT: H 327 GLN cc_start: 0.7361 (mp10) cc_final: 0.6947 (pt0) outliers start: 44 outliers final: 26 residues processed: 325 average time/residue: 1.5611 time to fit residues: 573.0785 Evaluate side-chains 347 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 314 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN D 53 GLN D 93 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 24704 Z= 0.379 Angle : 0.684 9.591 33496 Z= 0.372 Chirality : 0.051 0.232 3680 Planarity : 0.005 0.048 4464 Dihedral : 5.496 57.455 3553 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.61 % Allowed : 16.58 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3136 helix: 0.84 (0.14), residues: 1248 sheet: -0.13 (0.24), residues: 400 loop : -1.18 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 289 HIS 0.007 0.001 HIS C 271 PHE 0.016 0.003 PHE G 122 TYR 0.015 0.002 TYR D 369 ARG 0.008 0.001 ARG F 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 300 time to evaluate : 2.671 Fit side-chains REVERT: A 97 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: E 98 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: E 155 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7400 (mmtt) REVERT: E 331 LYS cc_start: 0.8463 (tttp) cc_final: 0.8131 (tttm) REVERT: F 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7392 (mmtt) REVERT: G 155 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: H 98 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: H 155 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7426 (mmtt) REVERT: H 331 LYS cc_start: 0.8362 (tttm) cc_final: 0.8155 (pptt) outliers start: 39 outliers final: 30 residues processed: 311 average time/residue: 1.5961 time to fit residues: 559.5850 Evaluate side-chains 336 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.0370 chunk 263 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN B 410 ASN C 53 GLN C 93 GLN C 410 ASN D 53 GLN D 93 GLN D 410 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117878 restraints weight = 23663.247| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.18 r_work: 0.3278 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24704 Z= 0.207 Angle : 0.578 8.415 33496 Z= 0.311 Chirality : 0.046 0.196 3680 Planarity : 0.005 0.046 4464 Dihedral : 5.163 53.732 3553 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.73 % Allowed : 16.25 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3136 helix: 1.03 (0.14), residues: 1240 sheet: -0.04 (0.24), residues: 400 loop : -1.14 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 289 HIS 0.007 0.001 HIS C 251 PHE 0.013 0.002 PHE C 294 TYR 0.011 0.001 TYR D 369 ARG 0.008 0.000 ARG G 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9300.52 seconds wall clock time: 162 minutes 39.40 seconds (9759.40 seconds total)