Starting phenix.real_space_refine on Mon Sep 30 02:17:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/09_2024/8ihq_35452.cif" } resolution = 2.71 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= 0.001 sd= 0.049 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 15112 2.51 5 N 4416 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24128 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.60, per 1000 atoms: 0.61 Number of scatterers: 24128 At special positions: 0 Unit cell: (131.75, 131.75, 104.55, 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 4512 8.00 N 4416 7.00 C 15112 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: 5.62 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " 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 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " 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 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " 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=" NE2 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " 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: 5664 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 40.5% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.515A pdb=" N SER A 96 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.525A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.538A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) 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 305 removed outlier: 3.681A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 354 through 362 removed outlier: 4.051A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.759A pdb=" N ALA A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.901A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.544A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 230 through 244 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 305 removed outlier: 3.538A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.972A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.762A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.541A pdb=" N ALA B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 102 through 120 removed outlier: 3.550A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 190 through 204 Processing helix chain 'C' and resid 230 through 244 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 305 removed outlier: 3.537A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.977A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 removed outlier: 3.761A pdb=" N ALA C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 93 through 97 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.544A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 230 through 244 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 305 removed outlier: 3.538A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.972A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 removed outlier: 3.762A pdb=" N ALA D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.903A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.598A pdb=" N ALA D 411 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 412 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.146A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.504A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.645A 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 305 removed outlier: 3.716A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.761A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 Processing helix chain 'E' and resid 354 through 362 removed outlier: 4.027A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 removed outlier: 3.718A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 removed outlier: 3.872A pdb=" N VAL E 412 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.146A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 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: 3.502A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.649A 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 305 removed outlier: 3.715A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 3.791A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 354 through 362 removed outlier: 4.026A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 removed outlier: 3.723A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 removed outlier: 3.870A pdb=" N VAL F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.146A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 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: 3.651A 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: 3.715A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 removed outlier: 3.804A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 Processing helix chain 'G' and resid 354 through 362 removed outlier: 4.026A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 removed outlier: 3.728A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 removed outlier: 3.874A pdb=" N VAL G 412 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.148A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 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: 3.651A 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 305 removed outlier: 3.717A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 removed outlier: 3.801A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 335 Processing helix chain 'H' and resid 354 through 362 removed outlier: 4.028A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 removed outlier: 3.724A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 removed outlier: 3.875A pdb=" N VAL H 412 " --> pdb=" O ILE H 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 6.570A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 14.176A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.618A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.390A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.942A 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: 6.546A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 56 removed outlier: 6.576A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 14.169A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.620A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.388A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.948A 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: 6.540A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 56 removed outlier: 6.569A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 14.180A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.388A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.945A 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: 6.531A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 56 removed outlier: 6.576A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 13.791A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.994A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.345A 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: 6.389A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.951A 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: 6.555A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 56 removed outlier: 6.588A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 13.514A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.702A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.176A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL E 398 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL E 418 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA E 400 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 426 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.321A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 50 through 56 removed outlier: 6.587A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA F 24 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU F 70 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLN F 26 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP F 72 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY F 28 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL F 74 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU F 30 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU F 76 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 398 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL F 418 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA F 400 " --> pdb=" O ARG F 416 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 426 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.303A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 156 through 157 removed outlier: 6.683A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 50 through 56 removed outlier: 6.609A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 13.506A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 398 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL G 418 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA G 400 " --> pdb=" O ARG G 416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 426 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.325A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 50 through 56 removed outlier: 6.584A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA H 24 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU H 70 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN H 26 " --> pdb=" O LEU H 70 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP H 72 " --> pdb=" O GLN H 26 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY H 28 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL H 74 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU H 30 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU H 76 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL H 398 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL H 418 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA H 400 " --> pdb=" O ARG H 416 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 426 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.322A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 156 through 157 removed outlier: 6.684A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5989 1.33 - 1.45: 4852 1.45 - 1.57: 13639 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24608 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" NZ KCX F 210 " pdb=" CX KCX F 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 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 1.78e+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 1.76e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 32322 1.42 - 2.84: 831 2.84 - 4.26: 162 4.26 - 5.68: 38 5.68 - 7.10: 23 Bond angle restraints: 33376 Sorted by residual: angle pdb=" CA GLY G 179 " pdb=" C GLY G 179 " pdb=" O GLY G 179 " ideal model delta sigma weight residual 122.29 118.22 4.07 8.10e-01 1.52e+00 2.53e+01 angle pdb=" CA GLY E 179 " pdb=" C GLY E 179 " pdb=" O GLY E 179 " ideal model delta sigma weight residual 122.39 118.05 4.34 9.30e-01 1.16e+00 2.18e+01 angle pdb=" N VAL G 178 " pdb=" CA VAL G 178 " pdb=" C VAL G 178 " ideal model delta sigma weight residual 112.96 108.52 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA THR H 230 " pdb=" C THR H 230 " pdb=" O THR H 230 " ideal model delta sigma weight residual 121.72 117.39 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.75 118.27 4.48 1.27e+00 6.20e-01 1.25e+01 ... (remaining 33371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 12701 17.64 - 35.28: 1360 35.28 - 52.91: 377 52.91 - 70.55: 113 70.55 - 88.19: 25 Dihedral angle restraints: 14576 sinusoidal: 5632 harmonic: 8944 Sorted by residual: dihedral pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " pdb=" SG CYS H 75 " pdb=" CB CYS H 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.29 37.29 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.17 37.17 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA GLY E 346 " pdb=" C GLY E 346 " pdb=" N VAL E 347 " pdb=" CA VAL E 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2827 0.050 - 0.100: 645 0.100 - 0.151: 186 0.151 - 0.201: 12 0.201 - 0.251: 2 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU D 70 " pdb=" N LEU D 70 " pdb=" C LEU D 70 " pdb=" CB LEU D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL D 188 " pdb=" N VAL D 188 " pdb=" C VAL D 188 " pdb=" CB VAL D 188 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 3669 not shown) Planarity restraints: 4448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 55 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO D 56 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 55 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 55 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.044 5.00e-02 4.00e+02 ... (remaining 4445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 266 2.66 - 3.22: 20642 3.22 - 3.78: 35742 3.78 - 4.34: 54571 4.34 - 4.90: 89529 Nonbonded interactions: 200750 Sorted by model distance: nonbonded pdb=" OQ1 KCX C 210 " pdb="ZN ZN C 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX A 210 " pdb="ZN ZN A 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX B 210 " pdb="ZN ZN B 501 " model vdw 2.096 2.230 nonbonded pdb=" OQ1 KCX D 210 " pdb="ZN ZN D 501 " model vdw 2.097 2.230 nonbonded pdb=" NZ LYS D 155 " pdb=" O SER D 156 " model vdw 2.243 3.120 ... (remaining 200745 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 55.550 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:18.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 0.085 24608 Z= 0.243 Angle : 0.586 7.097 33376 Z= 0.356 Chirality : 0.046 0.251 3672 Planarity : 0.005 0.082 4448 Dihedral : 16.578 88.189 8888 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.62 % Allowed : 18.96 % Favored : 80.42 % 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: -0.68 (0.14), residues: 3136 helix: 0.01 (0.14), residues: 1320 sheet: 0.35 (0.25), residues: 384 loop : -1.04 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 PHE 0.011 0.001 PHE F 294 TYR 0.009 0.001 TYR C 333 ARG 0.014 0.000 ARG D 281 *********************** 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 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 333 time to evaluate : 2.806 Fit side-chains REVERT: B 281 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7310 (ttp-110) REVERT: C 331 LYS cc_start: 0.7476 (tttp) cc_final: 0.7252 (ttpp) REVERT: D 281 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7245 (ttp-110) REVERT: E 98 ASP cc_start: 0.8069 (t0) cc_final: 0.7609 (m-30) REVERT: E 131 GLU cc_start: 0.7465 (mp0) cc_final: 0.7239 (mp0) REVERT: E 397 ASP cc_start: 0.8441 (m-30) cc_final: 0.8116 (m-30) REVERT: F 98 ASP cc_start: 0.8085 (t0) cc_final: 0.7615 (m-30) REVERT: F 385 ASP cc_start: 0.7668 (p0) cc_final: 0.7108 (t0) REVERT: F 397 ASP cc_start: 0.8419 (m-30) cc_final: 0.8112 (m-30) REVERT: G 26 GLN cc_start: 0.8018 (mt0) cc_final: 0.7731 (mt0) REVERT: G 98 ASP cc_start: 0.8075 (t0) cc_final: 0.7605 (m-30) REVERT: G 335 ASN cc_start: 0.7684 (m-40) cc_final: 0.7352 (m110) REVERT: G 385 ASP cc_start: 0.7720 (p0) cc_final: 0.7187 (t0) REVERT: G 397 ASP cc_start: 0.8462 (m-30) cc_final: 0.8114 (m-30) REVERT: H 26 GLN cc_start: 0.8005 (mt0) cc_final: 0.7736 (mt0) REVERT: H 98 ASP cc_start: 0.8071 (t0) cc_final: 0.7599 (m-30) REVERT: H 385 ASP cc_start: 0.7701 (p0) cc_final: 0.7167 (t0) REVERT: H 397 ASP cc_start: 0.8429 (m-30) cc_final: 0.8122 (m-30) outliers start: 15 outliers final: 9 residues processed: 346 average time/residue: 1.4760 time to fit residues: 577.2425 Evaluate side-chains 326 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 24608 Z= 0.455 Angle : 0.640 7.299 33376 Z= 0.348 Chirality : 0.051 0.151 3672 Planarity : 0.006 0.064 4448 Dihedral : 6.096 53.838 3558 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.10 % Allowed : 16.14 % Favored : 79.76 % 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: -0.75 (0.14), residues: 3136 helix: 0.08 (0.14), residues: 1304 sheet: 1.14 (0.31), residues: 248 loop : -1.26 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 289 HIS 0.007 0.002 HIS D 251 PHE 0.018 0.002 PHE H 294 TYR 0.014 0.003 TYR C 333 ARG 0.004 0.000 ARG B 281 *********************** 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 401 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 302 time to evaluate : 2.728 Fit side-chains REVERT: A 50 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5476 (mtt90) REVERT: A 172 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: B 50 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5485 (mtt90) REVERT: B 172 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: C 50 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.5457 (mtt90) REVERT: C 116 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7790 (mtpt) REVERT: C 172 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: D 50 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5469 (mtt90) REVERT: D 155 LYS cc_start: 0.8013 (tptp) cc_final: 0.7453 (tptp) REVERT: E 98 ASP cc_start: 0.8172 (t0) cc_final: 0.7586 (m-30) REVERT: E 356 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: F 98 ASP cc_start: 0.8186 (t0) cc_final: 0.7589 (m-30) REVERT: F 155 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7348 (mptm) REVERT: F 173 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7234 (tmm-80) REVERT: F 356 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6409 (tp30) REVERT: G 26 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: G 98 ASP cc_start: 0.8172 (t0) cc_final: 0.7577 (m-30) REVERT: G 271 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7810 (m-70) REVERT: G 356 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6377 (tp30) REVERT: H 26 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: H 98 ASP cc_start: 0.8176 (t0) cc_final: 0.7554 (m-30) REVERT: H 356 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6371 (tp30) outliers start: 99 outliers final: 44 residues processed: 366 average time/residue: 1.4988 time to fit residues: 622.1469 Evaluate side-chains 344 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 283 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 42 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24608 Z= 0.183 Angle : 0.484 7.557 33376 Z= 0.256 Chirality : 0.044 0.130 3672 Planarity : 0.005 0.053 4448 Dihedral : 5.424 53.843 3554 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.48 % Allowed : 17.43 % Favored : 80.09 % 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: -0.31 (0.14), residues: 3136 helix: 0.53 (0.14), residues: 1312 sheet: 0.91 (0.29), residues: 304 loop : -1.09 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.006 0.001 HIS G 251 PHE 0.013 0.001 PHE H 294 TYR 0.010 0.001 TYR C 333 ARG 0.005 0.000 ARG B 281 *********************** 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 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 305 time to evaluate : 2.734 Fit side-chains REVERT: A 39 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7587 (mtmt) REVERT: A 50 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6174 (mtt90) REVERT: A 52 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7472 (mtm110) REVERT: A 116 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7121 (mtpt) REVERT: A 222 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7978 (ttt180) REVERT: B 39 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7563 (mtmt) REVERT: B 50 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6185 (mtt90) REVERT: B 52 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7413 (mtm110) REVERT: B 222 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: C 39 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7572 (mtmt) REVERT: C 50 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6176 (mtt90) REVERT: C 222 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7985 (ttt180) REVERT: D 39 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7586 (mtmt) REVERT: D 50 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6168 (mtt90) REVERT: D 155 LYS cc_start: 0.7849 (tptp) cc_final: 0.7591 (tptp) REVERT: D 222 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8036 (ttt180) REVERT: E 52 ARG cc_start: 0.7307 (mmt180) cc_final: 0.7069 (mmt180) REVERT: E 98 ASP cc_start: 0.8134 (t0) cc_final: 0.7454 (m-30) REVERT: E 302 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6299 (mt-10) REVERT: E 356 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6188 (tp30) REVERT: F 98 ASP cc_start: 0.8149 (t0) cc_final: 0.7459 (m-30) REVERT: F 173 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7177 (tmm-80) REVERT: F 302 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: F 356 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6227 (tp30) REVERT: G 98 ASP cc_start: 0.8137 (t0) cc_final: 0.7449 (m-30) REVERT: G 302 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6289 (mt-10) REVERT: G 356 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6188 (tp30) REVERT: H 52 ARG cc_start: 0.7334 (mmt180) cc_final: 0.7098 (mmt180) REVERT: H 98 ASP cc_start: 0.8129 (t0) cc_final: 0.7446 (m-30) REVERT: H 302 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: H 356 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6192 (tp30) outliers start: 60 outliers final: 30 residues processed: 337 average time/residue: 1.5617 time to fit residues: 595.3519 Evaluate side-chains 334 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 286 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.0040 chunk 213 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24608 Z= 0.196 Angle : 0.483 7.716 33376 Z= 0.256 Chirality : 0.044 0.130 3672 Planarity : 0.005 0.048 4448 Dihedral : 5.129 52.526 3545 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.27 % Allowed : 16.64 % Favored : 80.09 % 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: -0.18 (0.14), residues: 3136 helix: 0.69 (0.14), residues: 1312 sheet: 1.02 (0.29), residues: 304 loop : -1.08 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.005 0.001 HIS E 251 PHE 0.013 0.001 PHE H 294 TYR 0.010 0.001 TYR B 333 ARG 0.006 0.000 ARG A 281 *********************** 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 378 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 299 time to evaluate : 2.833 Fit side-chains REVERT: A 39 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7600 (mtmt) REVERT: A 50 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5355 (mtt90) REVERT: A 116 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7176 (mtpt) REVERT: A 222 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: A 327 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6761 (mt0) REVERT: A 356 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 39 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7533 (mtmt) REVERT: B 50 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5371 (mtt90) REVERT: B 222 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7979 (ttt180) REVERT: B 327 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6731 (mt0) REVERT: C 39 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7543 (mtmt) REVERT: C 50 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6126 (mtt90) REVERT: C 222 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7991 (ttt180) REVERT: C 327 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6735 (mt0) REVERT: D 39 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7558 (mtmt) REVERT: D 50 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6112 (mtt90) REVERT: D 155 LYS cc_start: 0.7764 (tptp) cc_final: 0.7558 (tptp) REVERT: D 327 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6692 (mt0) REVERT: E 52 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6998 (mmt180) REVERT: E 98 ASP cc_start: 0.8080 (t0) cc_final: 0.7407 (m-30) REVERT: E 302 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6314 (mt-10) REVERT: E 356 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6200 (tp30) REVERT: F 98 ASP cc_start: 0.8095 (t0) cc_final: 0.7410 (m-30) REVERT: F 235 LYS cc_start: 0.8305 (mttp) cc_final: 0.7961 (mttm) REVERT: F 302 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6310 (mt-10) REVERT: F 356 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6258 (tp30) REVERT: G 52 ARG cc_start: 0.7303 (mmt180) cc_final: 0.6974 (mmt180) REVERT: G 98 ASP cc_start: 0.8081 (t0) cc_final: 0.7400 (m-30) REVERT: G 302 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6314 (mt-10) REVERT: G 356 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6218 (tp30) REVERT: H 52 ARG cc_start: 0.7344 (mmt180) cc_final: 0.7054 (mmt180) REVERT: H 98 ASP cc_start: 0.8076 (t0) cc_final: 0.7397 (m-30) REVERT: H 302 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6320 (mt-10) REVERT: H 356 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6209 (tp30) outliers start: 79 outliers final: 43 residues processed: 352 average time/residue: 1.5327 time to fit residues: 610.7655 Evaluate side-chains 353 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 289 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN C 285 GLN C 404 ASN D 285 GLN E 42 HIS E 53 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS F 176 HIS G 176 HIS H 53 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.004 0.029 24608 Z= 0.267 Angle : 0.528 8.068 33376 Z= 0.281 Chirality : 0.046 0.133 3672 Planarity : 0.005 0.047 4448 Dihedral : 5.351 51.413 3545 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.48 % Allowed : 17.09 % Favored : 79.43 % 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: -0.30 (0.14), residues: 3136 helix: 0.59 (0.14), residues: 1312 sheet: 1.51 (0.31), residues: 248 loop : -1.17 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 289 HIS 0.006 0.001 HIS E 271 PHE 0.014 0.002 PHE G 294 TYR 0.012 0.002 TYR B 333 ARG 0.007 0.000 ARG B 281 *********************** 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 380 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 296 time to evaluate : 2.815 Fit side-chains REVERT: A 50 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6157 (mtt90) REVERT: A 116 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7350 (mtpt) REVERT: A 222 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8019 (ttt180) REVERT: A 327 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: A 356 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: B 50 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6164 (mtt90) REVERT: B 222 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8030 (ttt180) REVERT: B 327 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6770 (mt0) REVERT: C 50 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6180 (mtt90) REVERT: C 222 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8022 (ttt180) REVERT: C 327 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6740 (mt0) REVERT: D 50 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6159 (mtt90) REVERT: D 222 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8035 (ttt180) REVERT: D 327 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6731 (mt0) REVERT: E 52 ARG cc_start: 0.7353 (mmt180) cc_final: 0.7038 (mmt180) REVERT: E 98 ASP cc_start: 0.8142 (t0) cc_final: 0.7440 (m-30) REVERT: E 173 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7336 (tmm-80) REVERT: E 302 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: E 356 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6275 (tp30) REVERT: F 52 ARG cc_start: 0.7393 (mmt180) cc_final: 0.7044 (mmt180) REVERT: F 98 ASP cc_start: 0.8155 (t0) cc_final: 0.7445 (m-30) REVERT: F 173 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7217 (tmm-80) REVERT: F 302 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: F 356 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: G 52 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6982 (mmt180) REVERT: G 98 ASP cc_start: 0.8143 (t0) cc_final: 0.7435 (m-30) REVERT: G 302 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: G 356 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: H 52 ARG cc_start: 0.7385 (mmt180) cc_final: 0.7075 (mmt180) REVERT: H 98 ASP cc_start: 0.8136 (t0) cc_final: 0.7433 (m-30) REVERT: H 173 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7379 (tmm-80) REVERT: H 302 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6355 (mt-10) REVERT: H 356 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6278 (tp30) outliers start: 84 outliers final: 48 residues processed: 354 average time/residue: 1.5515 time to fit residues: 620.4460 Evaluate side-chains 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 292 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 301 optimal weight: 0.0980 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN B 404 ASN C 285 GLN D 285 GLN D 404 ASN E 176 HIS F 176 HIS G 42 HIS G 176 HIS H 42 HIS H 53 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24608 Z= 0.178 Angle : 0.475 7.754 33376 Z= 0.249 Chirality : 0.044 0.130 3672 Planarity : 0.005 0.044 4448 Dihedral : 5.059 52.637 3545 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.15 % Allowed : 17.34 % Favored : 79.51 % 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: -0.12 (0.15), residues: 3136 helix: 0.79 (0.14), residues: 1312 sheet: 0.71 (0.26), residues: 384 loop : -1.11 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.005 0.001 HIS G 251 PHE 0.012 0.001 PHE G 294 TYR 0.009 0.001 TYR B 333 ARG 0.008 0.000 ARG C 281 *********************** 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 378 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 302 time to evaluate : 4.414 Fit side-chains REVERT: A 39 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7577 (mtmt) REVERT: A 50 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.6125 (mtt90) REVERT: A 116 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7186 (mtpt) REVERT: A 222 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7965 (ttt180) REVERT: A 327 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: A 356 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 39 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7551 (mtmt) REVERT: B 50 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6135 (mtt90) REVERT: B 222 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7972 (ttt180) REVERT: B 327 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6792 (mt0) REVERT: C 39 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7517 (mtmt) REVERT: C 50 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6131 (mtt90) REVERT: C 222 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7968 (ttt180) REVERT: C 327 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: C 331 LYS cc_start: 0.7546 (tttp) cc_final: 0.7297 (ttpp) REVERT: D 39 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7543 (mtmt) REVERT: D 50 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6135 (mtt90) REVERT: D 222 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7985 (ttt180) REVERT: D 327 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6751 (mt0) REVERT: E 52 ARG cc_start: 0.7329 (mmt180) cc_final: 0.7027 (mmt180) REVERT: E 98 ASP cc_start: 0.8075 (t0) cc_final: 0.7391 (m-30) REVERT: E 173 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7300 (tmm-80) REVERT: E 235 LYS cc_start: 0.8224 (mttp) cc_final: 0.7881 (mttm) REVERT: E 302 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: E 356 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6229 (tp30) REVERT: F 37 GLN cc_start: 0.8092 (mt0) cc_final: 0.7748 (mm-40) REVERT: F 52 ARG cc_start: 0.7369 (mmt180) cc_final: 0.6989 (mmt180) REVERT: F 98 ASP cc_start: 0.8090 (t0) cc_final: 0.7396 (m-30) REVERT: F 173 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7245 (tmm-80) REVERT: F 235 LYS cc_start: 0.8276 (mttp) cc_final: 0.7937 (mttm) REVERT: F 302 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: F 356 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6264 (tp30) REVERT: G 52 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6997 (mmt180) REVERT: G 98 ASP cc_start: 0.8079 (t0) cc_final: 0.7385 (m-30) REVERT: G 131 GLU cc_start: 0.7529 (mp0) cc_final: 0.7277 (mt-10) REVERT: G 302 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: G 356 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6226 (tp30) REVERT: H 52 ARG cc_start: 0.7356 (mmt180) cc_final: 0.7051 (mmt180) REVERT: H 98 ASP cc_start: 0.8070 (t0) cc_final: 0.7383 (m-30) REVERT: H 173 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7312 (tmm-80) REVERT: H 302 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: H 356 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6242 (tp30) outliers start: 76 outliers final: 45 residues processed: 354 average time/residue: 1.5695 time to fit residues: 628.4199 Evaluate side-chains 357 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 287 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 220 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 0.0050 chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN E 176 HIS F 176 HIS G 176 HIS H 176 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24608 Z= 0.134 Angle : 0.449 7.812 33376 Z= 0.231 Chirality : 0.042 0.126 3672 Planarity : 0.004 0.049 4448 Dihedral : 4.729 53.336 3545 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.02 % Allowed : 17.63 % Favored : 79.35 % 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: 0.09 (0.15), residues: 3136 helix: 0.98 (0.14), residues: 1312 sheet: 0.85 (0.26), residues: 384 loop : -1.02 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.006 0.001 HIS F 251 PHE 0.010 0.001 PHE H 294 TYR 0.008 0.001 TYR B 333 ARG 0.010 0.000 ARG B 281 *********************** 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 383 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 310 time to evaluate : 2.766 Fit side-chains REVERT: A 39 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7607 (mtmt) REVERT: A 50 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.6099 (mtt90) REVERT: A 222 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7912 (ttt180) REVERT: A 356 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: B 39 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7535 (mtmt) REVERT: B 50 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6111 (mtt90) REVERT: B 222 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: B 327 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6646 (mt0) REVERT: C 39 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7540 (mtmt) REVERT: C 50 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6093 (mtt90) REVERT: C 222 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7901 (ttt180) REVERT: C 327 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6645 (mt0) REVERT: D 39 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7553 (mtmt) REVERT: D 50 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6097 (mtt90) REVERT: D 222 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: E 52 ARG cc_start: 0.7343 (mmt180) cc_final: 0.7042 (mmt180) REVERT: E 235 LYS cc_start: 0.8202 (mttp) cc_final: 0.7889 (mttm) REVERT: E 302 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: E 356 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6146 (tp30) REVERT: E 385 ASP cc_start: 0.7583 (p0) cc_final: 0.7003 (t0) REVERT: E 397 ASP cc_start: 0.8400 (m-30) cc_final: 0.8105 (m-30) REVERT: F 37 GLN cc_start: 0.8092 (mt0) cc_final: 0.7756 (mm-40) REVERT: F 52 ARG cc_start: 0.7355 (mmt180) cc_final: 0.6968 (mmt180) REVERT: F 173 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7428 (ttt180) REVERT: F 235 LYS cc_start: 0.8260 (mttp) cc_final: 0.7947 (mttm) REVERT: F 302 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: F 356 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6183 (tp30) REVERT: F 385 ASP cc_start: 0.7429 (p0) cc_final: 0.7055 (t0) REVERT: F 397 ASP cc_start: 0.8383 (m-30) cc_final: 0.8100 (m-30) REVERT: G 131 GLU cc_start: 0.7455 (mp0) cc_final: 0.7204 (mt-10) REVERT: G 302 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: G 356 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6148 (tp30) REVERT: G 385 ASP cc_start: 0.7496 (p0) cc_final: 0.7096 (t0) REVERT: G 397 ASP cc_start: 0.8421 (m-30) cc_final: 0.8116 (m-30) REVERT: H 52 ARG cc_start: 0.7372 (mmt180) cc_final: 0.7063 (mmt180) REVERT: H 173 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7298 (tmm-80) REVERT: H 302 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: H 356 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6156 (tp30) REVERT: H 385 ASP cc_start: 0.7442 (p0) cc_final: 0.7086 (t0) REVERT: H 397 ASP cc_start: 0.8393 (m-30) cc_final: 0.8117 (m-30) outliers start: 73 outliers final: 42 residues processed: 361 average time/residue: 1.5286 time to fit residues: 624.1005 Evaluate side-chains 364 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 301 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 176 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24608 Z= 0.327 Angle : 0.567 8.646 33376 Z= 0.302 Chirality : 0.047 0.140 3672 Planarity : 0.005 0.055 4448 Dihedral : 5.390 51.760 3544 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.77 % Allowed : 18.00 % Favored : 79.22 % 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: -0.21 (0.14), residues: 3136 helix: 0.64 (0.14), residues: 1320 sheet: 1.54 (0.31), residues: 248 loop : -1.10 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 289 HIS 0.006 0.001 HIS H 271 PHE 0.016 0.002 PHE E 294 TYR 0.012 0.002 TYR D 333 ARG 0.011 0.000 ARG D 281 *********************** 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 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 2.985 Fit side-chains REVERT: A 50 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6212 (mtt90) REVERT: A 222 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8046 (ttt180) REVERT: A 356 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 50 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6224 (mtt90) REVERT: B 222 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8040 (ttt180) REVERT: B 327 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: C 50 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6198 (mtt90) REVERT: C 222 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8050 (ttt180) REVERT: C 327 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6746 (mt0) REVERT: D 50 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5405 (mtt90) REVERT: D 222 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8060 (ttt180) REVERT: D 278 GLU cc_start: 0.6489 (tt0) cc_final: 0.6234 (pt0) REVERT: E 52 ARG cc_start: 0.7370 (mmt180) cc_final: 0.7047 (mmt180) REVERT: E 98 ASP cc_start: 0.8138 (t0) cc_final: 0.7576 (m-30) REVERT: E 173 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7349 (tmm-80) REVERT: E 356 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6318 (tp30) REVERT: F 52 ARG cc_start: 0.7395 (mmt180) cc_final: 0.6962 (mmt180) REVERT: F 98 ASP cc_start: 0.8152 (t0) cc_final: 0.7596 (m-30) REVERT: F 173 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7202 (tmm-80) REVERT: F 356 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6356 (tp30) REVERT: G 52 ARG cc_start: 0.7329 (mmt180) cc_final: 0.7015 (mmt180) REVERT: G 98 ASP cc_start: 0.8140 (t0) cc_final: 0.7586 (m-30) REVERT: G 131 GLU cc_start: 0.7522 (mp0) cc_final: 0.7286 (mt-10) REVERT: G 356 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6324 (tp30) REVERT: H 98 ASP cc_start: 0.8133 (t0) cc_final: 0.7583 (m-30) REVERT: H 173 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7352 (tmm-80) REVERT: H 356 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6328 (tp30) outliers start: 67 outliers final: 41 residues processed: 339 average time/residue: 1.5036 time to fit residues: 577.2600 Evaluate side-chains 353 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 294 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL 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: 3.9990 chunk 262 optimal weight: 0.0170 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 253 optimal weight: 0.0470 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 0.0170 overall best weight: 1.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 42 HIS E 176 HIS F 42 HIS F 176 HIS G 176 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24608 Z= 0.215 Angle : 0.509 8.016 33376 Z= 0.267 Chirality : 0.045 0.132 3672 Planarity : 0.005 0.059 4448 Dihedral : 5.148 52.318 3544 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.81 % Allowed : 18.25 % Favored : 78.93 % 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 (0.15), residues: 3136 helix: 0.77 (0.14), residues: 1312 sheet: 0.73 (0.26), residues: 384 loop : -1.14 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.005 0.001 HIS E 271 PHE 0.013 0.001 PHE H 294 TYR 0.010 0.002 TYR C 333 ARG 0.012 0.000 ARG C 281 *********************** 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 365 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 297 time to evaluate : 2.610 Fit side-chains REVERT: A 50 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6137 (mtt90) REVERT: A 116 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7187 (mtpt) REVERT: A 222 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8001 (ttt180) REVERT: A 356 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: B 50 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6150 (mtt90) REVERT: B 222 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8011 (ttt180) REVERT: B 327 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6810 (mt0) REVERT: C 50 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6170 (mtt90) REVERT: C 222 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7994 (ttt180) REVERT: C 327 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6751 (mt0) REVERT: D 50 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6136 (mtt90) REVERT: D 222 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8025 (ttt180) REVERT: D 278 GLU cc_start: 0.6455 (tt0) cc_final: 0.6152 (pt0) REVERT: E 52 ARG cc_start: 0.7337 (mmt180) cc_final: 0.7028 (mmt180) REVERT: E 98 ASP cc_start: 0.8117 (t0) cc_final: 0.7507 (m-30) REVERT: E 173 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7273 (tmm-80) REVERT: E 302 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6353 (mt-10) REVERT: E 356 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6249 (tp30) REVERT: F 52 ARG cc_start: 0.7352 (mmt180) cc_final: 0.6937 (mmt180) REVERT: F 98 ASP cc_start: 0.8135 (t0) cc_final: 0.7517 (m-30) REVERT: F 173 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7282 (tmm-80) REVERT: F 302 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6346 (mt-10) REVERT: F 356 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: G 52 ARG cc_start: 0.7319 (mmt180) cc_final: 0.7014 (mmt180) REVERT: G 98 ASP cc_start: 0.8125 (t0) cc_final: 0.7504 (m-30) REVERT: G 131 GLU cc_start: 0.7516 (mp0) cc_final: 0.7278 (mt-10) REVERT: G 356 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: H 52 ARG cc_start: 0.7326 (mmt180) cc_final: 0.7010 (mmt180) REVERT: H 98 ASP cc_start: 0.8118 (t0) cc_final: 0.7502 (m-30) REVERT: H 173 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7363 (tmm-80) REVERT: H 302 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6360 (mt-10) REVERT: H 356 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6260 (tp30) outliers start: 68 outliers final: 43 residues processed: 345 average time/residue: 1.5201 time to fit residues: 592.7640 Evaluate side-chains 360 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 295 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.0040 chunk 296 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 176 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24608 Z= 0.152 Angle : 0.470 8.164 33376 Z= 0.244 Chirality : 0.043 0.129 3672 Planarity : 0.005 0.059 4448 Dihedral : 4.849 53.107 3544 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.57 % Allowed : 18.71 % Favored : 78.73 % 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: 0.04 (0.15), residues: 3136 helix: 0.94 (0.14), residues: 1312 sheet: 0.85 (0.26), residues: 384 loop : -1.07 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 79 HIS 0.006 0.001 HIS F 251 PHE 0.011 0.001 PHE G 294 TYR 0.009 0.001 TYR C 333 ARG 0.013 0.000 ARG A 281 ********************** 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 363 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 301 time to evaluate : 2.760 Fit side-chains REVERT: A 39 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7547 (mtmt) REVERT: A 50 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6093 (mtt90) REVERT: A 222 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7917 (ttt180) REVERT: A 281 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7271 (ttp-110) REVERT: A 356 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: B 39 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7517 (mtmt) REVERT: B 50 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6108 (mtt90) REVERT: B 222 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7953 (ttt180) REVERT: B 281 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7273 (ttp-110) REVERT: B 331 LYS cc_start: 0.7596 (ttpp) cc_final: 0.6972 (tttp) REVERT: C 39 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7527 (mtmt) REVERT: C 50 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6117 (mtt90) REVERT: C 222 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7919 (ttt180) REVERT: C 281 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7250 (ttp-110) REVERT: D 39 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7536 (mtmt) REVERT: D 50 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6096 (mtt90) REVERT: D 222 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7976 (ttt180) REVERT: D 278 GLU cc_start: 0.6437 (tt0) cc_final: 0.6153 (pt0) REVERT: D 281 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7270 (ttp-110) REVERT: E 52 ARG cc_start: 0.7346 (mmt180) cc_final: 0.7048 (mmt180) REVERT: E 173 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7258 (tmm-80) REVERT: E 235 LYS cc_start: 0.8244 (mttp) cc_final: 0.7888 (mttm) REVERT: E 302 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: E 356 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6144 (tp30) REVERT: E 385 ASP cc_start: 0.7650 (p0) cc_final: 0.7076 (t0) REVERT: F 37 GLN cc_start: 0.8085 (mt0) cc_final: 0.7753 (mm-40) REVERT: F 52 ARG cc_start: 0.7337 (mmt180) cc_final: 0.6943 (mmt180) REVERT: F 173 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7284 (tmm-80) REVERT: F 235 LYS cc_start: 0.8250 (mttp) cc_final: 0.7893 (mttm) REVERT: F 356 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6185 (tp30) REVERT: F 385 ASP cc_start: 0.7419 (p0) cc_final: 0.7059 (t0) REVERT: G 52 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6969 (mmt180) REVERT: G 131 GLU cc_start: 0.7433 (mp0) cc_final: 0.7215 (mt-10) REVERT: G 356 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6148 (tp30) REVERT: G 385 ASP cc_start: 0.7433 (p0) cc_final: 0.7060 (t0) REVERT: G 397 ASP cc_start: 0.8427 (m-30) cc_final: 0.8134 (m-30) REVERT: H 52 ARG cc_start: 0.7315 (mmt180) cc_final: 0.7012 (mmt180) REVERT: H 173 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7339 (tmm-80) REVERT: H 302 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: H 356 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6158 (tp30) REVERT: H 385 ASP cc_start: 0.7392 (p0) cc_final: 0.7072 (t0) outliers start: 62 outliers final: 39 residues processed: 345 average time/residue: 1.5783 time to fit residues: 613.9361 Evaluate side-chains 351 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 294 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Chi-restraints excluded: chain H residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 176 HIS F 176 HIS G 176 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115329 restraints weight = 25165.331| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.36 r_work: 0.3226 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24608 Z= 0.257 Angle : 0.531 8.577 33376 Z= 0.280 Chirality : 0.046 0.132 3672 Planarity : 0.005 0.060 4448 Dihedral : 5.210 51.621 3544 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.77 % Allowed : 18.46 % Favored : 78.77 % 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: -0.13 (0.15), residues: 3136 helix: 0.80 (0.14), residues: 1312 sheet: 0.72 (0.26), residues: 384 loop : -1.13 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 289 HIS 0.006 0.001 HIS H 271 PHE 0.013 0.002 PHE G 294 TYR 0.011 0.002 TYR A 333 ARG 0.012 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9269.61 seconds wall clock time: 166 minutes 0.74 seconds (9960.74 seconds total)