Starting phenix.real_space_refine on Sat Mar 7 02:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qg0_4543/03_2026/6qg0_4543.map" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 162 5.16 5 C 23526 2.51 5 N 6322 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36980 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 8.15, per 1000 atoms: 0.22 Number of scatterers: 36980 At special positions: 0 Unit cell: (274.7, 167.5, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 P 2 15.00 O 6968 8.00 N 6322 7.00 C 23526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.5 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8992 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 46 sheets defined 34.3% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.917A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.573A pdb=" N ALA A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.546A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.514A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.898A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 removed outlier: 4.382A pdb=" N GLY A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 188 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.560A pdb=" N TYR A 279 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 280 " --> pdb=" O GLN A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.952A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.670A pdb=" N ALA B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.569A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.962A pdb=" N GLN B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 removed outlier: 4.394A pdb=" N GLY B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 188 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.546A pdb=" N TYR B 279 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 280 " --> pdb=" O GLN B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 276 through 280' Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'D' and resid 20 through 31 removed outlier: 3.823A pdb=" N THR D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 55 Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 81 through 108 removed outlier: 3.550A pdb=" N ILE D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.993A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.569A pdb=" N LEU D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.692A pdb=" N PHE D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 360 through 367 removed outlier: 4.004A pdb=" N ILE D 364 " --> pdb=" O PHE D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 4.049A pdb=" N TYR E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 180 through 191 removed outlier: 3.738A pdb=" N VAL E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.693A pdb=" N ASN E 262 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.657A pdb=" N LEU E 288 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 289' Processing helix chain 'E' and resid 402 through 412 removed outlier: 4.153A pdb=" N ARG E 406 " --> pdb=" O MET E 402 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS E 412 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 180 through 191 removed outlier: 3.659A pdb=" N VAL F 184 " --> pdb=" O PRO F 180 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP F 191 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.708A pdb=" N ASN F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.621A pdb=" N LEU F 288 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 289' Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.714A pdb=" N VAL F 408 " --> pdb=" O ALA F 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 409 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 283 removed outlier: 4.054A pdb=" N HIS G 283 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 307 removed outlier: 3.927A pdb=" N CYS G 293 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 334 Processing helix chain 'G' and resid 337 through 354 removed outlier: 3.557A pdb=" N GLY G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 379 removed outlier: 3.704A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 394 removed outlier: 3.743A pdb=" N GLN G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 419 Processing helix chain 'G' and resid 435 through 448 Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'G' and resid 528 through 533 removed outlier: 3.533A pdb=" N ASP G 531 " --> pdb=" O ASP G 528 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL G 533 " --> pdb=" O ASN G 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 283 removed outlier: 3.512A pdb=" N LEU H 275 " --> pdb=" O HIS H 271 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 307 removed outlier: 3.743A pdb=" N CYS H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE H 294 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 334 Processing helix chain 'H' and resid 337 through 354 Processing helix chain 'H' and resid 359 through 379 removed outlier: 3.541A pdb=" N LYS H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 394 removed outlier: 3.623A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 418 Processing helix chain 'H' and resid 435 through 448 Processing helix chain 'H' and resid 458 through 463 removed outlier: 3.678A pdb=" N ILE H 462 " --> pdb=" O SER H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 489 through 499 Processing helix chain 'H' and resid 528 through 533 removed outlier: 3.611A pdb=" N ASP H 531 " --> pdb=" O ASP H 528 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL H 533 " --> pdb=" O ASN H 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 589 removed outlier: 6.039A pdb=" N LYS H 587 " --> pdb=" O GLY H 584 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA H 589 " --> pdb=" O SER H 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 71 removed outlier: 3.899A pdb=" N TYR I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.535A pdb=" N ILE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 126 Processing helix chain 'I' and resid 145 through 157 Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.727A pdb=" N VAL I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 249 removed outlier: 4.434A pdb=" N LEU I 244 " --> pdb=" O SER I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 265 Processing helix chain 'I' and resid 287 through 300 Processing helix chain 'I' and resid 307 through 311 Processing helix chain 'J' and resid 58 through 71 removed outlier: 3.946A pdb=" N TYR J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.518A pdb=" N ILE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'J' and resid 145 through 157 Processing helix chain 'J' and resid 214 through 216 No H-bonds generated for 'chain 'J' and resid 214 through 216' Processing helix chain 'J' and resid 217 through 222 removed outlier: 3.838A pdb=" N VAL J 221 " --> pdb=" O LEU J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 249 removed outlier: 4.410A pdb=" N LEU J 244 " --> pdb=" O SER J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 287 through 300 Processing helix chain 'J' and resid 307 through 311 Processing helix chain 'L' and resid 91 through 112 removed outlier: 4.150A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 119 removed outlier: 3.704A pdb=" N PHE L 119 " --> pdb=" O CYS L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 131 removed outlier: 3.728A pdb=" N LEU L 126 " --> pdb=" O PRO L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 151 removed outlier: 3.731A pdb=" N ILE L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'L' and resid 197 through 209 Processing helix chain 'L' and resid 238 through 259 removed outlier: 4.287A pdb=" N GLU L 242 " --> pdb=" O GLN L 238 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 243 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR L 258 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 259 " --> pdb=" O ILE L 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 201 through 211 removed outlier: 3.592A pdb=" N ALA M 209 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 239 Processing helix chain 'M' and resid 257 through 270 Processing helix chain 'M' and resid 290 through 302 removed outlier: 3.654A pdb=" N VAL M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE M 302 " --> pdb=" O ILE M 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 141 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'N' and resid 201 through 211 removed outlier: 3.570A pdb=" N ALA N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 239 Processing helix chain 'N' and resid 255 through 270 removed outlier: 3.553A pdb=" N ALA N 259 " --> pdb=" O ARG N 255 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 302 removed outlier: 3.657A pdb=" N VAL N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL N 299 " --> pdb=" O ASN N 295 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE N 302 " --> pdb=" O ILE N 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 141 Processing helix chain 'K' and resid 91 through 112 removed outlier: 4.150A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 119 removed outlier: 3.706A pdb=" N PHE K 119 " --> pdb=" O CYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.754A pdb=" N LEU K 126 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.747A pdb=" N ILE K 150 " --> pdb=" O LYS K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 174 Processing helix chain 'K' and resid 197 through 209 Processing helix chain 'K' and resid 238 through 259 removed outlier: 4.171A pdb=" N GLU K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN K 243 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY K 259 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.821A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 81 through 108 removed outlier: 3.548A pdb=" N ILE C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.992A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.566A pdb=" N LEU C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.691A pdb=" N PHE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 360 through 367 removed outlier: 4.001A pdb=" N ILE C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 180 removed outlier: 8.089A pdb=" N ILE A 179 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL A 153 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 8.009A pdb=" N ILE B 179 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL B 153 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.516A pdb=" N ASN B 209 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 355 through 356 removed outlier: 3.546A pdb=" N PHE D 356 " --> pdb=" O TYR D 349 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL D 292 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE D 350 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA D 294 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL D 258 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL D 295 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE D 260 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LEU D 241 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 213 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 243 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL D 215 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 265 removed outlier: 3.638A pdb=" N ASP D 339 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 133 through 136 removed outlier: 3.660A pdb=" N HIS E 134 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA9, first strand: chain 'E' and resid 223 through 225 removed outlier: 6.479A pdb=" N ALA J 184 " --> pdb=" O TYR J 197 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR J 197 " --> pdb=" O ALA J 184 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL J 186 " --> pdb=" O ILE J 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 253 through 255 Processing sheet with id=AB2, first strand: chain 'F' and resid 133 through 136 removed outlier: 6.610A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AB4, first strand: chain 'F' and resid 223 through 225 removed outlier: 6.483A pdb=" N ALA I 184 " --> pdb=" O TYR I 197 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR I 197 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL I 186 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 253 through 255 Processing sheet with id=AB6, first strand: chain 'G' and resid 451 through 455 removed outlier: 6.480A pdb=" N VAL G 426 " --> pdb=" O MET G 452 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA G 454 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 428 " --> pdb=" O ALA G 454 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR G 403 " --> pdb=" O PHE G 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 473 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 451 through 455 removed outlier: 6.480A pdb=" N VAL G 426 " --> pdb=" O MET G 452 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA G 454 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 428 " --> pdb=" O ALA G 454 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR G 403 " --> pdb=" O PHE G 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 473 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL G 470 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS G 506 " --> pdb=" O VAL G 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 472 " --> pdb=" O CYS G 506 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL G 503 " --> pdb=" O PRO G 571 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY G 573 " --> pdb=" O VAL G 503 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 556 through 557 removed outlier: 7.113A pdb=" N GLU G 557 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU C 241 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 213 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 243 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL C 215 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL C 258 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL C 295 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 260 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL C 292 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ILE C 350 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 294 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 356 " --> pdb=" O TYR C 349 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 451 through 455 removed outlier: 6.532A pdb=" N VAL H 426 " --> pdb=" O MET H 452 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA H 454 " --> pdb=" O VAL H 426 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 428 " --> pdb=" O ALA H 454 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR H 403 " --> pdb=" O PHE H 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 473 " --> pdb=" O TYR H 403 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 451 through 455 removed outlier: 6.532A pdb=" N VAL H 426 " --> pdb=" O MET H 452 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ALA H 454 " --> pdb=" O VAL H 426 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 428 " --> pdb=" O ALA H 454 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR H 403 " --> pdb=" O PHE H 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 473 " --> pdb=" O TYR H 403 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL H 470 " --> pdb=" O LEU H 504 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 506 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 472 " --> pdb=" O CYS H 506 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL H 503 " --> pdb=" O LYS H 572 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN H 574 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 505 " --> pdb=" O ASN H 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 103 through 108 removed outlier: 6.600A pdb=" N VAL I 75 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE I 107 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU I 77 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG I 234 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS I 233 " --> pdb=" O CYS I 167 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N CYS I 167 " --> pdb=" O CYS I 233 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE I 235 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR I 165 " --> pdb=" O ILE I 235 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR I 276 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET I 166 " --> pdb=" O TYR I 276 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR I 278 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU I 168 " --> pdb=" O THR I 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 139 through 141 removed outlier: 4.039A pdb=" N LEU I 140 " --> pdb=" O VAL I 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL I 283 " --> pdb=" O LEU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.253A pdb=" N ALA I 344 " --> pdb=" O ILE I 362 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE I 378 " --> pdb=" O ILE I 396 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 331 through 333 Processing sheet with id=AC6, first strand: chain 'I' and resid 338 through 339 removed outlier: 7.631A pdb=" N LYS I 338 " --> pdb=" O ILE I 357 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS I 356 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG I 373 " --> pdb=" O ILE I 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 401 through 402 removed outlier: 6.686A pdb=" N THR I 401 " --> pdb=" O ILE I 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 406 through 407 Processing sheet with id=AC9, first strand: chain 'J' and resid 103 through 108 removed outlier: 6.599A pdb=" N VAL J 75 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE J 107 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU J 77 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ARG J 234 " --> pdb=" O SER J 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 169 " --> pdb=" O ILE J 231 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS J 233 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N CYS J 167 " --> pdb=" O CYS J 233 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE J 235 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR J 165 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR J 276 " --> pdb=" O SER J 164 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET J 166 " --> pdb=" O TYR J 276 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR J 278 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU J 168 " --> pdb=" O THR J 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 139 through 141 removed outlier: 4.052A pdb=" N LEU J 140 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL J 283 " --> pdb=" O LEU J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 319 through 321 removed outlier: 6.262A pdb=" N ALA J 344 " --> pdb=" O ILE J 362 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE J 378 " --> pdb=" O ILE J 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 331 through 333 Processing sheet with id=AD4, first strand: chain 'J' and resid 338 through 339 removed outlier: 7.599A pdb=" N LYS J 338 " --> pdb=" O ILE J 357 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS J 356 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG J 373 " --> pdb=" O ILE J 391 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP J 392 " --> pdb=" O LEU J 408 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 19 through 20 removed outlier: 6.628A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.798A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 219 through 222 Processing sheet with id=AD8, first strand: chain 'M' and resid 168 through 169 removed outlier: 3.819A pdb=" N TYR M 148 " --> pdb=" O GLU M 169 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 143 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA M 145 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS M 188 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE M 147 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL M 186 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR M 105 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 314 through 321 removed outlier: 7.610A pdb=" N ARG M 314 " --> pdb=" O LEU M 343 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU M 343 " --> pdb=" O ARG M 314 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY M 339 " --> pdb=" O ILE M 318 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER M 320 " --> pdb=" O VAL M 337 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL M 337 " --> pdb=" O SER M 320 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE M 342 " --> pdb=" O GLY M 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY M 397 " --> pdb=" O LEU M 380 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU M 380 " --> pdb=" O GLY M 397 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY M 399 " --> pdb=" O VAL M 378 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 347 through 348 removed outlier: 3.504A pdb=" N PHE M 347 " --> pdb=" O ALA M 390 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 425 through 441 removed outlier: 10.591A pdb=" N ILE M 426 " --> pdb=" O SER M 489 " (cutoff:3.500A) removed outlier: 11.446A pdb=" N SER M 489 " --> pdb=" O ILE M 426 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR M 428 " --> pdb=" O LEU M 487 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET M 482 " --> pdb=" O VAL M 478 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL M 478 " --> pdb=" O MET M 482 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR M 488 " --> pdb=" O GLY M 472 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY M 472 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA M 470 " --> pdb=" O PRO M 490 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N ARG M 510 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 11.296A pdb=" N ARG M 439 " --> pdb=" O ARG M 510 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE M 512 " --> pdb=" O LEU M 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 168 through 169 removed outlier: 3.638A pdb=" N TYR N 148 " --> pdb=" O GLU N 169 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA N 143 " --> pdb=" O SER N 190 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER N 190 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA N 145 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS N 188 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE N 147 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL N 186 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR N 105 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA N 214 " --> pdb=" O ILE N 245 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU N 247 " --> pdb=" O ALA N 214 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU N 216 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL N 281 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 246 " --> pdb=" O VAL N 281 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 314 through 321 removed outlier: 7.571A pdb=" N ARG N 314 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU N 343 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY N 339 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER N 320 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL N 337 " --> pdb=" O SER N 320 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE N 342 " --> pdb=" O GLY N 394 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY N 394 " --> pdb=" O ILE N 342 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY N 397 " --> pdb=" O LEU N 380 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU N 380 " --> pdb=" O GLY N 397 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY N 399 " --> pdb=" O VAL N 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 347 through 348 removed outlier: 3.500A pdb=" N PHE N 347 " --> pdb=" O ALA N 390 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 425 through 441 removed outlier: 10.639A pdb=" N ILE N 426 " --> pdb=" O SER N 489 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N SER N 489 " --> pdb=" O ILE N 426 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR N 428 " --> pdb=" O LEU N 487 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET N 482 " --> pdb=" O VAL N 478 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL N 478 " --> pdb=" O MET N 482 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 484 " --> pdb=" O VAL N 476 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR N 488 " --> pdb=" O GLY N 472 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY N 472 " --> pdb=" O THR N 488 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA N 470 " --> pdb=" O PRO N 490 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL N 461 " --> pdb=" O ARG N 504 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG N 504 " --> pdb=" O VAL N 461 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE N 499 " --> pdb=" O TRP N 514 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP N 514 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU N 501 " --> pdb=" O ILE N 512 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N ARG N 510 " --> pdb=" O ARG N 439 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N ARG N 439 " --> pdb=" O ARG N 510 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE N 512 " --> pdb=" O LEU N 437 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 20 removed outlier: 6.629A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.798A pdb=" N LYS K 35 " --> pdb=" O ASN K 23 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 219 through 222 Processing sheet with id=AF1, first strand: chain 'C' and resid 262 through 265 removed outlier: 3.636A pdb=" N ASP C 339 " --> pdb=" O SER C 273 " (cutoff:3.500A) 1329 hydrogen bonds defined for protein. 3768 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: 6.57 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6299 1.32 - 1.45: 9109 1.45 - 1.57: 21943 1.57 - 1.70: 5 1.70 - 1.83: 242 Bond restraints: 37598 Sorted by residual: bond pdb=" N ASN B 89 " pdb=" CA ASN B 89 " ideal model delta sigma weight residual 1.459 1.543 -0.085 1.28e-02 6.10e+03 4.37e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.495 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C ALA B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.334 1.254 0.080 1.42e-02 4.96e+03 3.21e+01 bond pdb=" O1P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 37593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 46612 2.47 - 4.95: 3934 4.95 - 7.42: 293 7.42 - 9.90: 46 9.90 - 12.37: 5 Bond angle restraints: 50890 Sorted by residual: angle pdb=" N ARG N 356 " pdb=" CA ARG N 356 " pdb=" C ARG N 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ARG M 356 " pdb=" CA ARG M 356 " pdb=" C ARG M 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ILE H 501 " pdb=" CA ILE H 501 " pdb=" C ILE H 501 " ideal model delta sigma weight residual 109.02 114.80 -5.78 9.30e-01 1.16e+00 3.86e+01 angle pdb=" CA LEU C 125 " pdb=" C LEU C 125 " pdb=" N GLN C 126 " ideal model delta sigma weight residual 119.56 116.25 3.31 5.80e-01 2.97e+00 3.25e+01 angle pdb=" N ILE A 207 " pdb=" CA ILE A 207 " pdb=" C ILE A 207 " ideal model delta sigma weight residual 108.46 116.34 -7.88 1.49e+00 4.50e-01 2.79e+01 ... (remaining 50885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 19287 16.66 - 33.32: 2680 33.32 - 49.98: 612 49.98 - 66.63: 334 66.63 - 83.29: 69 Dihedral angle restraints: 22982 sinusoidal: 9164 harmonic: 13818 Sorted by residual: dihedral pdb=" C GLN I 289 " pdb=" N GLN I 289 " pdb=" CA GLN I 289 " pdb=" CB GLN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.49 13.89 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" C LEU J 202 " pdb=" N LEU J 202 " pdb=" CA LEU J 202 " pdb=" CB LEU J 202 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLN J 289 " pdb=" N GLN J 289 " pdb=" CA GLN J 289 " pdb=" CB GLN J 289 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 22979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5051 0.109 - 0.217: 800 0.217 - 0.326: 98 0.326 - 0.434: 15 0.434 - 0.543: 8 Chirality restraints: 5972 Sorted by residual: chirality pdb=" CA GLN I 289 " pdb=" N GLN I 289 " pdb=" C GLN I 289 " pdb=" CB GLN I 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA GLN J 289 " pdb=" N GLN J 289 " pdb=" C GLN J 289 " pdb=" CB GLN J 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 5969 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 51 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU L 51 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU L 51 " 0.022 2.00e-02 2.50e+03 pdb=" N SEP L 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 249 " -0.016 2.00e-02 2.50e+03 2.35e-02 9.66e+00 pdb=" CG PHE C 249 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE C 249 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 249 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 249 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 249 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 24 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C VAL K 24 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL K 24 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN K 25 " 0.018 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 3 1.96 - 2.69: 236 2.69 - 3.43: 46814 3.43 - 4.16: 82659 4.16 - 4.90: 142491 Nonbonded interactions: 272203 Sorted by model distance: nonbonded pdb=" CD GLN L 26 " pdb=" CA ALA L 32 " model vdw 1.219 2.960 nonbonded pdb=" NE2 GLN L 26 " pdb=" C ALA L 32 " model vdw 1.845 2.680 nonbonded pdb=" OE1 GLN L 26 " pdb=" CA ALA L 32 " model vdw 1.886 3.470 nonbonded pdb=" OE1 GLN L 25 " pdb=" CE LYS L 35 " model vdw 1.983 3.440 nonbonded pdb=" NE2 GLN L 26 " pdb=" N ALA L 32 " model vdw 1.994 2.560 ... (remaining 272198 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.380 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.450 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.010 0.655 37601 Z= 0.711 Angle : 1.399 12.373 50890 Z= 0.896 Chirality : 0.083 0.543 5972 Planarity : 0.005 0.047 6496 Dihedral : 18.074 83.294 13990 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.97 % Favored : 87.59 % Rotamer: Outliers : 5.91 % Allowed : 12.82 % Favored : 81.27 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.10), residues: 4632 helix: -2.05 (0.10), residues: 1536 sheet: -0.65 (0.19), residues: 606 loop : -2.53 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 486 TYR 0.022 0.003 TYR G 469 PHE 0.042 0.003 PHE C 249 TRP 0.030 0.003 TRP B 87 HIS 0.008 0.001 HIS H 475 Details of bonding type rmsd covalent geometry : bond 0.00893 (37598) covalent geometry : angle 1.39921 (50890) hydrogen bonds : bond 0.25978 ( 1315) hydrogen bonds : angle 8.45544 ( 3768) Misc. bond : bond 0.39343 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 1183 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 THR cc_start: 0.6364 (m) cc_final: 0.6132 (t) REVERT: A 24 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5822 (tp) REVERT: A 41 THR cc_start: 0.7137 (p) cc_final: 0.5969 (t) REVERT: A 86 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5311 (m-30) REVERT: A 96 GLU cc_start: 0.5832 (tt0) cc_final: 0.5455 (pt0) REVERT: A 123 ASP cc_start: 0.7709 (t70) cc_final: 0.7184 (t70) REVERT: A 151 CYS cc_start: 0.6279 (m) cc_final: 0.6066 (m) REVERT: A 207 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 228 TYR cc_start: 0.7590 (m-80) cc_final: 0.6557 (m-80) REVERT: A 237 VAL cc_start: 0.5030 (OUTLIER) cc_final: 0.4577 (t) REVERT: A 239 MET cc_start: 0.6408 (mtp) cc_final: 0.6036 (tpp) REVERT: A 249 MET cc_start: 0.6372 (mtm) cc_final: 0.5125 (ttp) REVERT: A 258 ARG cc_start: 0.8091 (mmp-170) cc_final: 0.7702 (tmt170) REVERT: B 20 MET cc_start: 0.2635 (mmt) cc_final: 0.2075 (tpt) REVERT: B 24 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5310 (tp) REVERT: B 37 LYS cc_start: 0.3770 (OUTLIER) cc_final: 0.3421 (tptp) REVERT: B 41 THR cc_start: 0.7753 (p) cc_final: 0.6749 (t) REVERT: B 45 MET cc_start: 0.4029 (tpt) cc_final: 0.3567 (ptt) REVERT: B 91 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6611 (mmtp) REVERT: B 106 LYS cc_start: 0.8062 (mttt) cc_final: 0.7850 (tmtt) REVERT: B 123 ASP cc_start: 0.7503 (t70) cc_final: 0.7026 (t0) REVERT: B 145 LYS cc_start: 0.9323 (mmtt) cc_final: 0.8993 (mmtp) REVERT: B 148 ARG cc_start: 0.6652 (ttp80) cc_final: 0.6384 (ptt180) REVERT: B 195 PHE cc_start: 0.6335 (m-80) cc_final: 0.5957 (m-10) REVERT: B 228 TYR cc_start: 0.7652 (m-80) cc_final: 0.6495 (m-80) REVERT: B 239 MET cc_start: 0.6813 (mtp) cc_final: 0.6015 (tpp) REVERT: B 249 MET cc_start: 0.5951 (mtm) cc_final: 0.5024 (ttp) REVERT: B 258 ARG cc_start: 0.8067 (mmp-170) cc_final: 0.7666 (tmt170) REVERT: D 63 LEU cc_start: 0.8713 (tp) cc_final: 0.8477 (tp) REVERT: D 76 LYS cc_start: 0.8315 (mttt) cc_final: 0.7915 (mttp) REVERT: D 150 TYR cc_start: 0.8750 (t80) cc_final: 0.8248 (p90) REVERT: D 169 ASP cc_start: 0.8853 (m-30) cc_final: 0.8308 (t0) REVERT: D 198 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6008 (mmtt) REVERT: D 224 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8059 (tptp) REVERT: D 227 HIS cc_start: 0.8106 (m170) cc_final: 0.7502 (m-70) REVERT: D 315 PHE cc_start: 0.7409 (m-80) cc_final: 0.7083 (m-80) REVERT: D 319 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 330 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.5058 (mpp-170) REVERT: E 141 ILE cc_start: 0.4174 (OUTLIER) cc_final: 0.3481 (mm) REVERT: E 162 ARG cc_start: 0.5055 (mtt180) cc_final: 0.4505 (tpt170) REVERT: E 261 TRP cc_start: 0.8698 (m100) cc_final: 0.7849 (p-90) REVERT: E 272 LEU cc_start: 0.8418 (mt) cc_final: 0.8119 (mt) REVERT: E 302 LYS cc_start: 0.9135 (pttt) cc_final: 0.8509 (ptpp) REVERT: F 141 ILE cc_start: 0.3021 (OUTLIER) cc_final: 0.2563 (mp) REVERT: F 162 ARG cc_start: 0.4437 (mtt180) cc_final: 0.4064 (ptm160) REVERT: F 188 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7858 (mtt180) REVERT: F 197 MET cc_start: 0.8450 (mmt) cc_final: 0.8023 (tpp) REVERT: F 261 TRP cc_start: 0.8848 (m100) cc_final: 0.7776 (p-90) REVERT: F 269 SER cc_start: 0.9022 (m) cc_final: 0.8805 (p) REVERT: F 294 SER cc_start: 0.7411 (p) cc_final: 0.6913 (t) REVERT: F 302 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8404 (ptpp) REVERT: G 284 TYR cc_start: 0.7611 (t80) cc_final: 0.7188 (t80) REVERT: G 328 ASP cc_start: 0.5598 (m-30) cc_final: 0.5166 (m-30) REVERT: G 350 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7994 (mm-30) REVERT: G 365 LYS cc_start: 0.7796 (tttt) cc_final: 0.7293 (mmtm) REVERT: G 407 LYS cc_start: 0.7945 (tttt) cc_final: 0.7512 (tttp) REVERT: G 411 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8335 (mt-10) REVERT: G 456 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8167 (mt) REVERT: G 486 ARG cc_start: 0.7069 (mtm180) cc_final: 0.4778 (ttm-80) REVERT: G 495 SER cc_start: 0.8750 (p) cc_final: 0.8543 (p) REVERT: G 516 VAL cc_start: 0.5341 (OUTLIER) cc_final: 0.4892 (m) REVERT: G 528 ASP cc_start: 0.7731 (m-30) cc_final: 0.7460 (m-30) REVERT: G 529 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8336 (Cg_exo) REVERT: G 550 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6409 (tp) REVERT: H 396 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7349 (mp0) REVERT: H 407 LYS cc_start: 0.7672 (tttt) cc_final: 0.7227 (tttp) REVERT: H 411 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8290 (mt-10) REVERT: H 435 PHE cc_start: 0.7990 (m-80) cc_final: 0.7721 (m-80) REVERT: H 436 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8708 (mt-10) REVERT: H 439 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8990 (mptt) REVERT: H 456 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8580 (mt) REVERT: H 461 THR cc_start: 0.8733 (p) cc_final: 0.7389 (p) REVERT: H 528 ASP cc_start: 0.8011 (m-30) cc_final: 0.7644 (m-30) REVERT: H 568 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8152 (tm-30) REVERT: H 593 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7111 (mp0) REVERT: I 32 LEU cc_start: 0.8355 (mt) cc_final: 0.7882 (mp) REVERT: I 59 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8919 (tp) REVERT: I 73 HIS cc_start: 0.8569 (m-70) cc_final: 0.8335 (m90) REVERT: I 74 GLU cc_start: 0.9364 (tt0) cc_final: 0.9046 (tp30) REVERT: I 114 CYS cc_start: 0.8465 (m) cc_final: 0.8189 (m) REVERT: I 119 MET cc_start: 0.7701 (mmm) cc_final: 0.6933 (tpt) REVERT: I 145 PHE cc_start: 0.8802 (t80) cc_final: 0.8578 (t80) REVERT: I 198 GLN cc_start: 0.9289 (tp40) cc_final: 0.8733 (tm-30) REVERT: I 211 ILE cc_start: 0.8785 (mp) cc_final: 0.8251 (mp) REVERT: I 212 GLN cc_start: 0.9293 (mt0) cc_final: 0.8843 (mp10) REVERT: I 213 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9326 (mp) REVERT: I 237 ILE cc_start: 0.9093 (mt) cc_final: 0.8889 (mm) REVERT: I 313 GLN cc_start: 0.8885 (tt0) cc_final: 0.8255 (tm-30) REVERT: I 321 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6804 (tt0) REVERT: J 32 LEU cc_start: 0.8159 (mt) cc_final: 0.7648 (mp) REVERT: J 37 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8167 (mp0) REVERT: J 59 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8909 (tp) REVERT: J 73 HIS cc_start: 0.8595 (m-70) cc_final: 0.8187 (m90) REVERT: J 74 GLU cc_start: 0.9366 (tt0) cc_final: 0.9012 (tp30) REVERT: J 77 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7510 (mp) REVERT: J 84 ASN cc_start: 0.9405 (m110) cc_final: 0.9203 (p0) REVERT: J 94 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7802 (mmtt) REVERT: J 95 TRP cc_start: 0.8299 (m100) cc_final: 0.7532 (m100) REVERT: J 119 MET cc_start: 0.7929 (mmm) cc_final: 0.7559 (tpt) REVERT: J 170 LYS cc_start: 0.7705 (mptt) cc_final: 0.7009 (tmtt) REVERT: J 198 GLN cc_start: 0.9155 (tp40) cc_final: 0.8573 (tm-30) REVERT: J 211 ILE cc_start: 0.9051 (mp) cc_final: 0.8844 (mp) REVERT: J 308 LEU cc_start: 0.8259 (mt) cc_final: 0.7879 (tp) REVERT: J 313 GLN cc_start: 0.8917 (tt0) cc_final: 0.8341 (tm-30) REVERT: J 321 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6743 (tt0) REVERT: L 6 CYS cc_start: 0.2664 (t) cc_final: 0.2330 (p) REVERT: L 9 TYR cc_start: 0.3665 (m-80) cc_final: 0.3298 (m-80) REVERT: L 84 ASP cc_start: 0.6182 (m-30) cc_final: 0.5377 (m-30) REVERT: L 124 GLU cc_start: 0.5709 (pp20) cc_final: 0.5439 (tp30) REVERT: L 125 GLU cc_start: 0.7036 (tt0) cc_final: 0.6493 (pp20) REVERT: L 163 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.3029 (mmtt) REVERT: L 238 GLN cc_start: 0.3607 (pt0) cc_final: 0.2933 (mm110) REVERT: M 187 ARG cc_start: 0.5351 (mtm-85) cc_final: 0.5125 (tpt170) REVERT: M 192 VAL cc_start: 0.1983 (t) cc_final: 0.1462 (p) REVERT: M 239 MET cc_start: -0.1996 (mtp) cc_final: -0.2660 (tpp) REVERT: M 318 ILE cc_start: 0.2883 (OUTLIER) cc_final: 0.2228 (mm) REVERT: M 331 GLU cc_start: -0.1318 (mt-10) cc_final: -0.1821 (mm-30) REVERT: M 354 GLU cc_start: -0.2161 (OUTLIER) cc_final: -0.2409 (pm20) REVERT: M 411 ARG cc_start: 0.4437 (mtt-85) cc_final: 0.4081 (tpt170) REVERT: M 430 ILE cc_start: 0.5647 (pt) cc_final: 0.5297 (mm) REVERT: M 443 VAL cc_start: -0.2522 (OUTLIER) cc_final: -0.2773 (p) REVERT: M 452 LYS cc_start: 0.0451 (tttt) cc_final: 0.0002 (ptpt) REVERT: M 462 LEU cc_start: 0.2263 (OUTLIER) cc_final: 0.1261 (mm) REVERT: M 463 MET cc_start: 0.0326 (ttp) cc_final: -0.1235 (mmm) REVERT: N 211 MET cc_start: -0.2662 (mtp) cc_final: -0.3073 (mtm) REVERT: N 228 GLN cc_start: -0.0994 (OUTLIER) cc_final: -0.1370 (tp40) REVERT: N 311 ILE cc_start: 0.2593 (OUTLIER) cc_final: 0.2315 (pt) REVERT: N 318 ILE cc_start: 0.0892 (OUTLIER) cc_final: 0.0444 (mm) REVERT: N 406 LEU cc_start: 0.0744 (OUTLIER) cc_final: 0.0342 (tp) REVERT: N 430 ILE cc_start: 0.5972 (pt) cc_final: 0.5739 (mm) REVERT: N 462 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.2575 (mm) REVERT: N 463 MET cc_start: 0.1461 (ttp) cc_final: -0.0155 (mmm) REVERT: N 499 ILE cc_start: -0.2999 (mt) cc_final: -0.3295 (mt) REVERT: K 6 CYS cc_start: 0.3285 (t) cc_final: 0.1816 (t) REVERT: K 60 GLN cc_start: 0.5401 (pt0) cc_final: 0.5068 (mm-40) REVERT: K 79 GLU cc_start: 0.5083 (OUTLIER) cc_final: 0.4823 (pt0) REVERT: K 84 ASP cc_start: 0.5118 (m-30) cc_final: 0.4421 (m-30) REVERT: K 124 GLU cc_start: 0.5219 (pp20) cc_final: 0.4907 (tp30) REVERT: K 220 VAL cc_start: 0.3485 (t) cc_final: 0.2735 (p) REVERT: C 56 ARG cc_start: 0.8990 (mmp80) cc_final: 0.8738 (tmm160) REVERT: C 63 LEU cc_start: 0.8431 (tp) cc_final: 0.8109 (tp) REVERT: C 76 LYS cc_start: 0.8514 (mttt) cc_final: 0.8036 (mttp) REVERT: C 150 TYR cc_start: 0.8852 (t80) cc_final: 0.8359 (p90) REVERT: C 169 ASP cc_start: 0.8826 (m-30) cc_final: 0.8278 (t0) REVERT: C 224 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8156 (tptp) REVERT: C 319 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 330 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5209 (mpp-170) outliers start: 241 outliers final: 57 residues processed: 1337 average time/residue: 0.2333 time to fit residues: 503.0214 Evaluate side-chains 831 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 744 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 8.9990 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 110 ASN A 144 ASN A 164 GLN A 222 ASN D 10 HIS D 183 HIS D 221 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 237 ASN E 14 ASN E 59 GLN E 262 ASN E 308 ASN E 309 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN G 280 HIS G 301 GLN G 384 GLN G 389 ASN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 ASN H 253 ASN H 280 HIS H 384 GLN ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN H 539 ASN I 73 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN I 296 GLN I 429 ASN J 73 HIS J 247 GLN J 296 GLN J 371 ASN J 409 ASN J 429 ASN L 103 GLN M 98 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 HIS M 197 HIS M 286 GLN M 415 GLN N 98 GLN N 197 HIS ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN N 465 ASN K 25 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN K 103 GLN K 243 GLN C 10 HIS C 61 ASN C 183 HIS C 221 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.245475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.197241 restraints weight = 72063.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.191418 restraints weight = 73170.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.193106 restraints weight = 53245.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.194681 restraints weight = 39088.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.195302 restraints weight = 32038.860| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4484 r_free = 0.4484 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37601 Z= 0.190 Angle : 0.777 14.080 50890 Z= 0.408 Chirality : 0.049 0.382 5972 Planarity : 0.006 0.086 6496 Dihedral : 5.981 80.184 5048 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.64 % Favored : 90.28 % Rotamer: Outliers : 0.27 % Allowed : 4.34 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.11), residues: 4632 helix: 0.03 (0.12), residues: 1550 sheet: -0.27 (0.20), residues: 578 loop : -2.43 (0.11), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 486 TYR 0.035 0.002 TYR G 322 PHE 0.036 0.002 PHE H 554 TRP 0.016 0.002 TRP J 302 HIS 0.016 0.002 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00420 (37598) covalent geometry : angle 0.77749 (50890) hydrogen bonds : bond 0.04955 ( 1315) hydrogen bonds : angle 5.42007 ( 3768) Misc. bond : bond 0.00498 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 903 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.0747 (tpt) cc_final: 0.0422 (tpt) REVERT: A 74 MET cc_start: 0.9036 (mmp) cc_final: 0.8746 (mmp) REVERT: A 79 ARG cc_start: 0.6941 (tmm160) cc_final: 0.6512 (tmm160) REVERT: A 96 GLU cc_start: 0.6061 (tt0) cc_final: 0.5490 (pt0) REVERT: A 228 TYR cc_start: 0.6599 (m-80) cc_final: 0.6342 (m-80) REVERT: A 249 MET cc_start: 0.3169 (mtm) cc_final: 0.2014 (ttp) REVERT: B 54 GLU cc_start: 0.7575 (mp0) cc_final: 0.7227 (pt0) REVERT: B 74 MET cc_start: 0.9018 (mmp) cc_final: 0.8813 (mmp) REVERT: B 193 LYS cc_start: 0.6449 (mttp) cc_final: 0.6024 (mttp) REVERT: B 228 TYR cc_start: 0.6754 (m-80) cc_final: 0.6022 (m-80) REVERT: B 249 MET cc_start: 0.2535 (mtm) cc_final: 0.1754 (ttp) REVERT: D 95 LEU cc_start: 0.7962 (mt) cc_final: 0.7757 (pp) REVERT: D 319 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 76 MET cc_start: 0.6658 (ptt) cc_final: 0.6434 (ptm) REVERT: E 102 GLU cc_start: 0.5794 (mm-30) cc_final: 0.5250 (mm-30) REVERT: E 139 LYS cc_start: 0.4757 (mttt) cc_final: 0.4249 (mmtt) REVERT: E 186 GLN cc_start: 0.8507 (pt0) cc_final: 0.8073 (mm-40) REVERT: E 262 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (t0) REVERT: E 282 PHE cc_start: 0.6304 (p90) cc_final: 0.5068 (p90) REVERT: F 184 VAL cc_start: 0.8094 (t) cc_final: 0.7180 (p) REVERT: F 185 ASP cc_start: 0.7609 (m-30) cc_final: 0.6900 (m-30) REVERT: F 188 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7377 (mtt180) REVERT: F 226 TYR cc_start: 0.7428 (t80) cc_final: 0.6646 (t80) REVERT: G 328 ASP cc_start: 0.4819 (m-30) cc_final: 0.4104 (m-30) REVERT: G 365 LYS cc_start: 0.7976 (tttt) cc_final: 0.7289 (mmtm) REVERT: G 411 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7124 (mt-10) REVERT: G 435 PHE cc_start: 0.7893 (m-80) cc_final: 0.7512 (m-80) REVERT: G 486 ARG cc_start: 0.6443 (mtt90) cc_final: 0.5880 (mtm-85) REVERT: H 252 ASP cc_start: 0.5437 (p0) cc_final: 0.5174 (p0) REVERT: H 328 ASP cc_start: 0.4787 (m-30) cc_final: 0.4032 (m-30) REVERT: H 340 MET cc_start: 0.6968 (mtp) cc_final: 0.6518 (mmm) REVERT: H 411 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6996 (mt-10) REVERT: H 436 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7363 (mt-10) REVERT: H 445 ARG cc_start: 0.7506 (ptt-90) cc_final: 0.7098 (ptt-90) REVERT: H 507 CYS cc_start: 0.8096 (t) cc_final: 0.7625 (t) REVERT: H 515 ARG cc_start: 0.6391 (ptm160) cc_final: 0.5959 (ttt-90) REVERT: H 518 LEU cc_start: 0.7769 (mt) cc_final: 0.7512 (mp) REVERT: H 593 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6955 (mp0) REVERT: I 87 ASN cc_start: 0.8055 (m-40) cc_final: 0.7627 (m-40) REVERT: I 395 LEU cc_start: 0.8150 (mp) cc_final: 0.7777 (tt) REVERT: J 120 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7539 (mtt180) REVERT: J 170 LYS cc_start: 0.7830 (mptt) cc_final: 0.7382 (tmtt) REVERT: L 6 CYS cc_start: 0.5666 (t) cc_final: 0.4492 (t) REVERT: L 21 MET cc_start: 0.0761 (mmt) cc_final: 0.0231 (mpp) REVERT: L 99 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: L 238 GLN cc_start: 0.4011 (pt0) cc_final: 0.2977 (mm-40) REVERT: M 331 GLU cc_start: -0.0417 (mt-10) cc_final: -0.1253 (mm-30) REVERT: M 452 LYS cc_start: 0.1069 (tttt) cc_final: 0.0135 (ptpt) REVERT: M 463 MET cc_start: -0.1676 (ttp) cc_final: -0.2650 (mmm) REVERT: N 331 GLU cc_start: -0.0452 (mt-10) cc_final: -0.1071 (mm-30) REVERT: N 462 LEU cc_start: 0.2967 (mt) cc_final: 0.2643 (mm) REVERT: N 463 MET cc_start: 0.0707 (ttp) cc_final: -0.0985 (mmt) REVERT: K 6 CYS cc_start: 0.5213 (t) cc_final: 0.4002 (t) REVERT: K 21 MET cc_start: 0.4781 (mmm) cc_final: 0.4452 (mpp) REVERT: K 54 ARG cc_start: 0.5531 (mmm160) cc_final: 0.5289 (mmm160) REVERT: C 104 MET cc_start: 0.5020 (tmm) cc_final: 0.2924 (tpp) REVERT: C 227 HIS cc_start: 0.7882 (m170) cc_final: 0.7463 (m-70) REVERT: C 319 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 337 ILE cc_start: 0.7545 (mt) cc_final: 0.7312 (mt) outliers start: 11 outliers final: 3 residues processed: 910 average time/residue: 0.2173 time to fit residues: 324.8266 Evaluate side-chains 637 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 632 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 128 optimal weight: 8.9990 chunk 403 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 292 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN B 47 ASN B 110 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN D 33 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN G 253 ASN G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN G 517 GLN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN G 546 ASN H 416 ASN H 446 ASN H 475 HIS H 500 ASN I 28 GLN I 241 HIS ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 ASN I 376 ASN I 388 ASN J 56 ASN J 241 HIS J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 376 ASN J 388 ASN L 25 GLN M 433 ASN N 108 HIS ** N 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.236818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.186147 restraints weight = 71701.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.180909 restraints weight = 67540.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.183181 restraints weight = 51984.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.182765 restraints weight = 45360.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.183607 restraints weight = 36178.261| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 37601 Z= 0.267 Angle : 0.791 8.901 50890 Z= 0.411 Chirality : 0.050 0.282 5972 Planarity : 0.006 0.067 6496 Dihedral : 6.107 80.518 5048 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.95 % Allowed : 9.65 % Favored : 89.40 % Rotamer: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4632 helix: 0.25 (0.13), residues: 1552 sheet: -0.20 (0.21), residues: 580 loop : -2.42 (0.11), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 238 TYR 0.025 0.002 TYR J 274 PHE 0.026 0.002 PHE B 236 TRP 0.014 0.002 TRP I 302 HIS 0.011 0.002 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00589 (37598) covalent geometry : angle 0.79114 (50890) hydrogen bonds : bond 0.04599 ( 1315) hydrogen bonds : angle 5.32108 ( 3768) Misc. bond : bond 0.00052 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 788 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.1039 (tpt) cc_final: 0.0753 (tpt) REVERT: A 66 LEU cc_start: 0.5740 (mt) cc_final: 0.5377 (mt) REVERT: A 70 CYS cc_start: 0.8235 (m) cc_final: 0.7829 (p) REVERT: A 96 GLU cc_start: 0.6270 (tt0) cc_final: 0.5475 (pt0) REVERT: A 120 ILE cc_start: 0.7086 (mp) cc_final: 0.6421 (tt) REVERT: A 228 TYR cc_start: 0.6558 (m-80) cc_final: 0.5477 (m-80) REVERT: A 249 MET cc_start: 0.2593 (mtm) cc_final: 0.2373 (ttp) REVERT: B 54 GLU cc_start: 0.7487 (mp0) cc_final: 0.7178 (pt0) REVERT: B 78 LEU cc_start: 0.8106 (mt) cc_final: 0.7744 (mt) REVERT: B 228 TYR cc_start: 0.7177 (m-80) cc_final: 0.6796 (m-80) REVERT: B 249 MET cc_start: 0.3081 (mtm) cc_final: 0.2789 (ttp) REVERT: D 23 ASP cc_start: 0.7296 (m-30) cc_final: 0.7068 (m-30) REVERT: D 222 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7624 (m-40) REVERT: D 246 SER cc_start: 0.9147 (p) cc_final: 0.8669 (t) REVERT: D 275 ASN cc_start: 0.8308 (p0) cc_final: 0.7994 (p0) REVERT: E 102 GLU cc_start: 0.5763 (mm-30) cc_final: 0.5300 (mm-30) REVERT: E 139 LYS cc_start: 0.4967 (mttt) cc_final: 0.4414 (mmtt) REVERT: G 328 ASP cc_start: 0.4846 (m-30) cc_final: 0.4180 (m-30) REVERT: G 365 LYS cc_start: 0.8065 (tttt) cc_final: 0.7325 (mmtm) REVERT: G 486 ARG cc_start: 0.6677 (mtt90) cc_final: 0.6120 (mtt90) REVERT: G 562 LYS cc_start: 0.7155 (tptp) cc_final: 0.6856 (tptt) REVERT: H 328 ASP cc_start: 0.5291 (m-30) cc_final: 0.4503 (m-30) REVERT: H 365 LYS cc_start: 0.8052 (tttt) cc_final: 0.7703 (mmtt) REVERT: H 436 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7306 (mt-10) REVERT: H 445 ARG cc_start: 0.7500 (ptt-90) cc_final: 0.6995 (ptt-90) REVERT: H 506 CYS cc_start: 0.7055 (m) cc_final: 0.6750 (m) REVERT: H 510 LEU cc_start: 0.7908 (tp) cc_final: 0.7651 (tp) REVERT: H 515 ARG cc_start: 0.6458 (ptm160) cc_final: 0.6200 (ptm160) REVERT: I 49 ARG cc_start: 0.7654 (ttp80) cc_final: 0.6754 (tmt170) REVERT: I 87 ASN cc_start: 0.8356 (m-40) cc_final: 0.8099 (m-40) REVERT: I 138 ASP cc_start: 0.5640 (m-30) cc_final: 0.5138 (m-30) REVERT: J 87 ASN cc_start: 0.8332 (m-40) cc_final: 0.7654 (m-40) REVERT: J 94 LYS cc_start: 0.9197 (ptmm) cc_final: 0.8821 (ptmm) REVERT: J 120 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7661 (mtt180) REVERT: L 238 GLN cc_start: 0.4606 (pt0) cc_final: 0.3520 (mm110) REVERT: M 331 GLU cc_start: -0.0220 (mt-10) cc_final: -0.1101 (tp30) REVERT: M 452 LYS cc_start: 0.0470 (tttt) cc_final: -0.0431 (ptpt) REVERT: N 331 GLU cc_start: -0.0071 (mt-10) cc_final: -0.0599 (mm-30) REVERT: N 462 LEU cc_start: 0.3280 (mt) cc_final: 0.2822 (mm) REVERT: N 463 MET cc_start: -0.0667 (ttp) cc_final: -0.1894 (mmt) REVERT: K 21 MET cc_start: 0.4719 (mmm) cc_final: 0.4321 (mpp) REVERT: K 36 LEU cc_start: 0.6901 (tp) cc_final: 0.6602 (tp) REVERT: K 82 TYR cc_start: 0.3723 (m-80) cc_final: 0.3488 (m-80) REVERT: K 235 LEU cc_start: 0.3084 (tp) cc_final: 0.2613 (pp) outliers start: 11 outliers final: 5 residues processed: 796 average time/residue: 0.2157 time to fit residues: 282.9750 Evaluate side-chains 619 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 613 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 32 optimal weight: 9.9990 chunk 268 optimal weight: 0.7980 chunk 312 optimal weight: 30.0000 chunk 146 optimal weight: 40.0000 chunk 107 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 299 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 359 optimal weight: 8.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN D 72 ASN D 237 ASN D 368 ASN E 274 ASN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN G 480 ASN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN J 249 ASN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 415 GLN N 433 ASN K 26 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 368 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.238708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.189548 restraints weight = 71596.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.185216 restraints weight = 70120.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.186968 restraints weight = 58194.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.187188 restraints weight = 44480.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.188626 restraints weight = 35639.085| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37601 Z= 0.185 Angle : 0.704 8.475 50890 Z= 0.365 Chirality : 0.048 0.258 5972 Planarity : 0.005 0.062 6496 Dihedral : 5.943 82.133 5048 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.94 % Favored : 90.22 % Rotamer: Outliers : 0.15 % Allowed : 3.90 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4632 helix: 0.50 (0.13), residues: 1566 sheet: -0.60 (0.20), residues: 640 loop : -2.36 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 90 TYR 0.018 0.002 TYR K 33 PHE 0.024 0.002 PHE I 102 TRP 0.031 0.002 TRP B 303 HIS 0.017 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00413 (37598) covalent geometry : angle 0.70403 (50890) hydrogen bonds : bond 0.03985 ( 1315) hydrogen bonds : angle 5.05444 ( 3768) Misc. bond : bond 0.01602 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 766 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.0800 (tpt) cc_final: 0.0563 (tpt) REVERT: A 70 CYS cc_start: 0.8045 (m) cc_final: 0.7669 (p) REVERT: A 74 MET cc_start: 0.8830 (mmp) cc_final: 0.8621 (mmp) REVERT: A 193 LYS cc_start: 0.6867 (mttp) cc_final: 0.6659 (mttp) REVERT: A 249 MET cc_start: 0.2845 (mtm) cc_final: 0.2085 (ttp) REVERT: B 20 MET cc_start: 0.0955 (tpt) cc_final: 0.0511 (tpt) REVERT: B 122 ASP cc_start: 0.7606 (p0) cc_final: 0.7215 (p0) REVERT: B 228 TYR cc_start: 0.6861 (m-80) cc_final: 0.6530 (m-80) REVERT: B 249 MET cc_start: 0.3557 (mtm) cc_final: 0.2512 (ttp) REVERT: D 246 SER cc_start: 0.9143 (p) cc_final: 0.8830 (t) REVERT: E 76 MET cc_start: 0.6733 (ptt) cc_final: 0.6504 (pmm) REVERT: E 139 LYS cc_start: 0.5074 (mttt) cc_final: 0.4549 (mmtt) REVERT: E 197 MET cc_start: 0.7613 (tpt) cc_final: 0.7305 (tpt) REVERT: F 198 THR cc_start: 0.5100 (p) cc_final: 0.4797 (p) REVERT: F 278 TYR cc_start: 0.3279 (m-80) cc_final: 0.2606 (m-80) REVERT: G 284 TYR cc_start: 0.6857 (t80) cc_final: 0.6262 (t80) REVERT: G 328 ASP cc_start: 0.4856 (m-30) cc_final: 0.4161 (m-30) REVERT: G 340 MET cc_start: 0.6973 (mtp) cc_final: 0.6346 (mmm) REVERT: G 365 LYS cc_start: 0.7775 (tttt) cc_final: 0.7066 (mmtm) REVERT: G 495 SER cc_start: 0.8735 (p) cc_final: 0.8487 (p) REVERT: H 284 TYR cc_start: 0.7073 (t80) cc_final: 0.6575 (t80) REVERT: H 328 ASP cc_start: 0.5154 (m-30) cc_final: 0.4510 (m-30) REVERT: H 365 LYS cc_start: 0.7961 (tttt) cc_final: 0.7650 (mmtt) REVERT: H 436 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7448 (mt-10) REVERT: H 442 GLU cc_start: 0.7757 (mt-10) cc_final: 0.6771 (mt-10) REVERT: H 445 ARG cc_start: 0.7576 (ptt-90) cc_final: 0.6985 (ppt-90) REVERT: H 495 SER cc_start: 0.8896 (p) cc_final: 0.8680 (p) REVERT: H 506 CYS cc_start: 0.6736 (m) cc_final: 0.6446 (m) REVERT: H 515 ARG cc_start: 0.6507 (ptm160) cc_final: 0.6272 (ptm160) REVERT: I 49 ARG cc_start: 0.7374 (ttp80) cc_final: 0.6550 (tmt170) REVERT: I 319 SER cc_start: 0.7968 (p) cc_final: 0.7705 (p) REVERT: J 87 ASN cc_start: 0.8188 (m-40) cc_final: 0.7334 (m-40) REVERT: J 185 PHE cc_start: 0.8418 (m-80) cc_final: 0.8171 (m-80) REVERT: L 238 GLN cc_start: 0.4501 (pt0) cc_final: 0.3544 (mm110) REVERT: M 331 GLU cc_start: -0.0291 (mt-10) cc_final: -0.1193 (tp30) REVERT: N 331 GLU cc_start: -0.0118 (mt-10) cc_final: -0.0476 (mm-30) REVERT: N 462 LEU cc_start: 0.3357 (mt) cc_final: 0.2972 (mm) REVERT: N 463 MET cc_start: -0.0590 (ttp) cc_final: -0.1589 (mmt) REVERT: K 21 MET cc_start: 0.4484 (mmm) cc_final: 0.4270 (mpp) REVERT: C 224 LYS cc_start: 0.8465 (tttp) cc_final: 0.8240 (tptt) outliers start: 6 outliers final: 2 residues processed: 771 average time/residue: 0.2174 time to fit residues: 279.6231 Evaluate side-chains 612 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 610 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 157 optimal weight: 0.9980 chunk 364 optimal weight: 5.9990 chunk 456 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 333 optimal weight: 20.0000 chunk 53 optimal weight: 0.0050 chunk 175 optimal weight: 0.0070 chunk 124 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 overall best weight: 1.1014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 47 ASN B 62 ASN B 222 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 219 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN G 517 GLN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.242177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.195003 restraints weight = 71247.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.191549 restraints weight = 71882.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.191732 restraints weight = 66152.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.192916 restraints weight = 51530.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.194203 restraints weight = 39093.035| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37601 Z= 0.135 Angle : 0.658 8.213 50890 Z= 0.339 Chirality : 0.047 0.261 5972 Planarity : 0.005 0.097 6496 Dihedral : 5.706 79.239 5048 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.98 % Favored : 90.22 % Rotamer: Outliers : 0.02 % Allowed : 2.53 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.12), residues: 4632 helix: 0.73 (0.13), residues: 1590 sheet: -0.57 (0.20), residues: 650 loop : -2.27 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 558 TYR 0.014 0.002 TYR C 38 PHE 0.022 0.002 PHE A 236 TRP 0.018 0.001 TRP I 95 HIS 0.011 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00309 (37598) covalent geometry : angle 0.65817 (50890) hydrogen bonds : bond 0.03545 ( 1315) hydrogen bonds : angle 4.81089 ( 3768) Misc. bond : bond 0.00290 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 776 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.1076 (tpt) cc_final: 0.0857 (tpt) REVERT: A 70 CYS cc_start: 0.7919 (m) cc_final: 0.7632 (p) REVERT: A 193 LYS cc_start: 0.6676 (mttp) cc_final: 0.6463 (mttp) REVERT: A 249 MET cc_start: 0.2832 (mtm) cc_final: 0.2102 (ttp) REVERT: A 286 ASP cc_start: 0.7205 (p0) cc_final: 0.6579 (p0) REVERT: B 91 LYS cc_start: 0.5605 (mtpp) cc_final: 0.5011 (tttt) REVERT: B 122 ASP cc_start: 0.7661 (p0) cc_final: 0.7340 (p0) REVERT: B 249 MET cc_start: 0.3516 (mtm) cc_final: 0.2894 (ttp) REVERT: D 246 SER cc_start: 0.8890 (p) cc_final: 0.8642 (p) REVERT: E 58 MET cc_start: -0.2558 (tpt) cc_final: -0.2950 (tpt) REVERT: E 139 LYS cc_start: 0.5066 (mttt) cc_final: 0.4574 (mmtt) REVERT: E 167 PHE cc_start: 0.7066 (p90) cc_final: 0.6745 (p90) REVERT: E 282 PHE cc_start: 0.5668 (p90) cc_final: 0.5157 (p90) REVERT: F 198 THR cc_start: 0.4786 (p) cc_final: 0.4478 (p) REVERT: F 278 TYR cc_start: 0.3059 (m-80) cc_final: 0.2426 (m-80) REVERT: G 284 TYR cc_start: 0.6622 (t80) cc_final: 0.6364 (t80) REVERT: G 328 ASP cc_start: 0.4806 (m-30) cc_final: 0.4104 (m-30) REVERT: G 365 LYS cc_start: 0.7789 (tttt) cc_final: 0.7038 (mmtm) REVERT: G 411 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6849 (mt-10) REVERT: G 504 LEU cc_start: 0.7730 (mp) cc_final: 0.7450 (mp) REVERT: G 519 ASP cc_start: 0.7981 (p0) cc_final: 0.7681 (p0) REVERT: G 568 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6520 (tm-30) REVERT: H 328 ASP cc_start: 0.5004 (m-30) cc_final: 0.4324 (m-30) REVERT: H 365 LYS cc_start: 0.8013 (tttt) cc_final: 0.7709 (mmtt) REVERT: H 495 SER cc_start: 0.8803 (p) cc_final: 0.8566 (p) REVERT: H 519 ASP cc_start: 0.8200 (p0) cc_final: 0.7961 (p0) REVERT: I 49 ARG cc_start: 0.7474 (ttp80) cc_final: 0.6986 (tmt170) REVERT: I 87 ASN cc_start: 0.7962 (m-40) cc_final: 0.7566 (m-40) REVERT: I 255 LEU cc_start: 0.6997 (pp) cc_final: 0.6757 (pp) REVERT: J 87 ASN cc_start: 0.8055 (m-40) cc_final: 0.7328 (m-40) REVERT: J 319 SER cc_start: 0.7498 (p) cc_final: 0.6525 (p) REVERT: L 165 VAL cc_start: 0.6842 (t) cc_final: 0.6506 (t) REVERT: L 221 LYS cc_start: -0.1336 (mttt) cc_final: -0.1687 (tptp) REVERT: L 238 GLN cc_start: 0.4422 (pt0) cc_final: 0.3550 (mm110) REVERT: M 331 GLU cc_start: -0.0451 (mt-10) cc_final: -0.1255 (mm-30) REVERT: M 482 MET cc_start: 0.2126 (mtm) cc_final: 0.1805 (mpp) REVERT: N 331 GLU cc_start: -0.0076 (mt-10) cc_final: -0.0572 (mm-30) REVERT: N 462 LEU cc_start: 0.3277 (mt) cc_final: 0.2901 (mm) REVERT: N 463 MET cc_start: -0.0541 (ttp) cc_final: -0.1586 (mmt) REVERT: K 21 MET cc_start: 0.4566 (mmm) cc_final: 0.4327 (mpp) REVERT: C 224 LYS cc_start: 0.8426 (tttp) cc_final: 0.8093 (tptt) outliers start: 1 outliers final: 0 residues processed: 777 average time/residue: 0.2124 time to fit residues: 276.1408 Evaluate side-chains 632 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 388 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS F 220 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 ASN H 301 GLN H 416 ASN H 475 HIS ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN C 33 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.241455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.192212 restraints weight = 70706.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.186539 restraints weight = 62071.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.188618 restraints weight = 50470.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.188867 restraints weight = 41461.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.189382 restraints weight = 34604.298| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37601 Z= 0.138 Angle : 0.654 8.883 50890 Z= 0.336 Chirality : 0.047 0.238 5972 Planarity : 0.005 0.078 6496 Dihedral : 5.568 77.733 5048 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.66 % Favored : 90.61 % Rotamer: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4632 helix: 0.96 (0.14), residues: 1562 sheet: -0.55 (0.19), residues: 698 loop : -2.23 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 486 TYR 0.020 0.002 TYR I 274 PHE 0.032 0.002 PHE B 119 TRP 0.071 0.002 TRP J 302 HIS 0.008 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00316 (37598) covalent geometry : angle 0.65354 (50890) hydrogen bonds : bond 0.03423 ( 1315) hydrogen bonds : angle 4.68963 ( 3768) Misc. bond : bond 0.00087 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 756 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.0997 (tpt) cc_final: 0.0754 (tpt) REVERT: A 70 CYS cc_start: 0.8220 (m) cc_final: 0.7662 (p) REVERT: A 74 MET cc_start: 0.8908 (mmp) cc_final: 0.8651 (mmp) REVERT: A 249 MET cc_start: 0.3463 (mtm) cc_final: 0.2656 (ttp) REVERT: A 286 ASP cc_start: 0.7304 (p0) cc_final: 0.6611 (p0) REVERT: B 228 TYR cc_start: 0.6695 (m-80) cc_final: 0.6475 (m-10) REVERT: B 249 MET cc_start: 0.3738 (mtm) cc_final: 0.3036 (ttp) REVERT: D 104 MET cc_start: 0.2842 (tpp) cc_final: 0.2116 (tmm) REVERT: D 160 ASP cc_start: 0.8259 (p0) cc_final: 0.7858 (p0) REVERT: D 246 SER cc_start: 0.8981 (p) cc_final: 0.8678 (p) REVERT: E 58 MET cc_start: -0.2616 (tpt) cc_final: -0.2903 (tpt) REVERT: E 76 MET cc_start: 0.6816 (ptt) cc_final: 0.6267 (pmm) REVERT: E 139 LYS cc_start: 0.5094 (mttt) cc_final: 0.4589 (mmtt) REVERT: F 91 GLU cc_start: 0.1788 (pm20) cc_final: 0.0853 (tt0) REVERT: F 198 THR cc_start: 0.4764 (p) cc_final: 0.4427 (p) REVERT: F 278 TYR cc_start: 0.2746 (m-80) cc_final: 0.2455 (m-80) REVERT: G 296 MET cc_start: 0.8523 (tmm) cc_final: 0.8223 (tmm) REVERT: G 328 ASP cc_start: 0.4930 (m-30) cc_final: 0.4206 (m-30) REVERT: G 365 LYS cc_start: 0.7904 (tttt) cc_final: 0.7071 (mmtm) REVERT: H 284 TYR cc_start: 0.6805 (t80) cc_final: 0.6413 (t80) REVERT: H 328 ASP cc_start: 0.5018 (m-30) cc_final: 0.4376 (m-30) REVERT: H 365 LYS cc_start: 0.8379 (tttt) cc_final: 0.7919 (mmtt) REVERT: H 495 SER cc_start: 0.9068 (p) cc_final: 0.8836 (p) REVERT: H 506 CYS cc_start: 0.7198 (m) cc_final: 0.6992 (m) REVERT: I 49 ARG cc_start: 0.7602 (ttp80) cc_final: 0.6927 (tmt170) REVERT: I 87 ASN cc_start: 0.8277 (m-40) cc_final: 0.7930 (m-40) REVERT: I 319 SER cc_start: 0.8011 (p) cc_final: 0.7759 (p) REVERT: J 87 ASN cc_start: 0.8222 (m-40) cc_final: 0.7812 (m-40) REVERT: L 165 VAL cc_start: 0.6660 (t) cc_final: 0.6354 (t) REVERT: L 221 LYS cc_start: -0.1553 (mttt) cc_final: -0.1797 (tptp) REVERT: L 238 GLN cc_start: 0.4516 (pt0) cc_final: 0.3630 (mm110) REVERT: M 331 GLU cc_start: -0.0583 (mt-10) cc_final: -0.1351 (mm-30) REVERT: M 482 MET cc_start: 0.1766 (mtm) cc_final: 0.1483 (mpp) REVERT: N 211 MET cc_start: -0.2791 (mtm) cc_final: -0.2996 (mtm) REVERT: N 331 GLU cc_start: -0.0278 (mt-10) cc_final: -0.0609 (mm-30) REVERT: N 462 LEU cc_start: 0.3622 (mt) cc_final: 0.3107 (mm) REVERT: N 463 MET cc_start: -0.0114 (ttp) cc_final: -0.1328 (mmt) REVERT: K 21 MET cc_start: 0.4427 (mmm) cc_final: 0.3818 (mpp) REVERT: K 22 VAL cc_start: 0.6250 (t) cc_final: 0.5747 (p) REVERT: C 224 LYS cc_start: 0.8410 (tttp) cc_final: 0.7995 (tptt) REVERT: C 362 TYR cc_start: 0.8302 (p90) cc_final: 0.8070 (p90) outliers start: 2 outliers final: 0 residues processed: 758 average time/residue: 0.2140 time to fit residues: 271.8651 Evaluate side-chains 623 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 122 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 433 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 358 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 158 optimal weight: 0.4980 chunk 34 optimal weight: 20.0000 chunk 381 optimal weight: 8.9990 chunk 300 optimal weight: 5.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 HIS M 376 ASN ** M 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 415 GLN N 422 HIS ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.236541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.188073 restraints weight = 71104.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.179327 restraints weight = 60723.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.182521 restraints weight = 59754.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.182373 restraints weight = 43679.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.182933 restraints weight = 35445.296| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 37601 Z= 0.208 Angle : 0.722 10.052 50890 Z= 0.373 Chirality : 0.049 0.295 5972 Planarity : 0.005 0.115 6496 Dihedral : 5.743 76.456 5048 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.43 % Favored : 89.85 % Rotamer: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.12), residues: 4632 helix: 0.70 (0.13), residues: 1560 sheet: -0.41 (0.20), residues: 702 loop : -2.32 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 109 TYR 0.020 0.002 TYR A 166 PHE 0.033 0.002 PHE A 119 TRP 0.054 0.003 TRP A 303 HIS 0.018 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00464 (37598) covalent geometry : angle 0.72166 (50890) hydrogen bonds : bond 0.03851 ( 1315) hydrogen bonds : angle 4.89091 ( 3768) Misc. bond : bond 0.00278 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 742 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8923 (mmp) cc_final: 0.8693 (mmp) REVERT: A 249 MET cc_start: 0.3480 (mtm) cc_final: 0.2656 (ttp) REVERT: B 249 MET cc_start: 0.3722 (mtm) cc_final: 0.3094 (ttp) REVERT: D 23 ASP cc_start: 0.7500 (m-30) cc_final: 0.7299 (m-30) REVERT: D 104 MET cc_start: 0.3141 (tpp) cc_final: 0.2438 (tmm) REVERT: D 160 ASP cc_start: 0.8425 (p0) cc_final: 0.8124 (p0) REVERT: E 58 MET cc_start: -0.2833 (tpt) cc_final: -0.3290 (tpt) REVERT: E 76 MET cc_start: 0.6937 (ptt) cc_final: 0.6158 (pmm) REVERT: E 139 LYS cc_start: 0.5236 (mttt) cc_final: 0.4696 (mmtt) REVERT: F 91 GLU cc_start: 0.1749 (pm20) cc_final: 0.0915 (tt0) REVERT: F 186 GLN cc_start: 0.9083 (pm20) cc_final: 0.8743 (pm20) REVERT: F 270 THR cc_start: 0.6272 (m) cc_final: 0.5887 (p) REVERT: F 278 TYR cc_start: 0.2515 (m-80) cc_final: 0.2109 (m-80) REVERT: G 284 TYR cc_start: 0.7163 (t80) cc_final: 0.6815 (t80) REVERT: G 328 ASP cc_start: 0.5019 (m-30) cc_final: 0.4354 (m-30) REVERT: G 340 MET cc_start: 0.6964 (mtp) cc_final: 0.6379 (mmm) REVERT: G 365 LYS cc_start: 0.7802 (tttt) cc_final: 0.7168 (mmtm) REVERT: G 495 SER cc_start: 0.8881 (p) cc_final: 0.8680 (p) REVERT: G 506 CYS cc_start: 0.7045 (m) cc_final: 0.6811 (m) REVERT: H 284 TYR cc_start: 0.7103 (t80) cc_final: 0.6566 (t80) REVERT: H 328 ASP cc_start: 0.5161 (m-30) cc_final: 0.4417 (m-30) REVERT: H 365 LYS cc_start: 0.8295 (tttt) cc_final: 0.7916 (mmtt) REVERT: H 506 CYS cc_start: 0.7286 (m) cc_final: 0.7064 (m) REVERT: H 519 ASP cc_start: 0.8289 (p0) cc_final: 0.8042 (p0) REVERT: I 49 ARG cc_start: 0.7635 (ttp80) cc_final: 0.6933 (tmt170) REVERT: I 87 ASN cc_start: 0.8116 (m-40) cc_final: 0.7605 (m-40) REVERT: I 319 SER cc_start: 0.8111 (p) cc_final: 0.7809 (p) REVERT: J 87 ASN cc_start: 0.8261 (m-40) cc_final: 0.7576 (m-40) REVERT: J 138 ASP cc_start: 0.5653 (m-30) cc_final: 0.5205 (m-30) REVERT: J 302 TRP cc_start: 0.7276 (m100) cc_final: 0.5366 (m-90) REVERT: J 319 SER cc_start: 0.7737 (p) cc_final: 0.7512 (p) REVERT: L 165 VAL cc_start: 0.6592 (t) cc_final: 0.6283 (t) REVERT: L 221 LYS cc_start: -0.1120 (mttt) cc_final: -0.1608 (pttm) REVERT: L 238 GLN cc_start: 0.4875 (pt0) cc_final: 0.3860 (mm110) REVERT: M 331 GLU cc_start: -0.0557 (mt-10) cc_final: -0.1374 (mm-30) REVERT: N 239 MET cc_start: -0.1936 (ttt) cc_final: -0.2415 (tpp) REVERT: N 462 LEU cc_start: 0.3632 (mt) cc_final: 0.2905 (mm) REVERT: N 463 MET cc_start: -0.0253 (ttp) cc_final: -0.1527 (mmt) REVERT: K 21 MET cc_start: 0.4412 (mmm) cc_final: 0.3915 (mpp) REVERT: C 333 THR cc_start: 0.8252 (p) cc_final: 0.8047 (t) outliers start: 2 outliers final: 0 residues processed: 743 average time/residue: 0.2146 time to fit residues: 266.9563 Evaluate side-chains 620 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 85 optimal weight: 0.6980 chunk 365 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 354 optimal weight: 20.0000 chunk 463 optimal weight: 0.9990 chunk 356 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 435 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN G 480 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN H 500 ASN I 247 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.241125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.194081 restraints weight = 71302.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.190345 restraints weight = 75259.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.191581 restraints weight = 59577.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.191942 restraints weight = 49643.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.193845 restraints weight = 37261.468| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37601 Z= 0.132 Angle : 0.661 8.276 50890 Z= 0.338 Chirality : 0.047 0.240 5972 Planarity : 0.004 0.076 6496 Dihedral : 5.500 74.389 5048 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.51 % Favored : 90.85 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.12), residues: 4632 helix: 0.87 (0.13), residues: 1570 sheet: -0.46 (0.20), residues: 702 loop : -2.19 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 356 TYR 0.023 0.002 TYR C 362 PHE 0.021 0.002 PHE I 416 TRP 0.038 0.002 TRP B 303 HIS 0.013 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00300 (37598) covalent geometry : angle 0.66104 (50890) hydrogen bonds : bond 0.03392 ( 1315) hydrogen bonds : angle 4.64772 ( 3768) Misc. bond : bond 0.00191 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 763 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.3689 (mtt180) cc_final: 0.1787 (tpt-90) REVERT: A 249 MET cc_start: 0.3413 (mtm) cc_final: 0.2808 (ttp) REVERT: B 249 MET cc_start: 0.3761 (mtm) cc_final: 0.3419 (ttp) REVERT: D 104 MET cc_start: 0.3243 (tpp) cc_final: 0.2440 (tmm) REVERT: D 160 ASP cc_start: 0.8219 (p0) cc_final: 0.7862 (p0) REVERT: D 246 SER cc_start: 0.8882 (p) cc_final: 0.8613 (p) REVERT: D 275 ASN cc_start: 0.7177 (p0) cc_final: 0.6785 (p0) REVERT: E 58 MET cc_start: -0.2613 (tpt) cc_final: -0.3087 (tpt) REVERT: E 139 LYS cc_start: 0.5245 (mttt) cc_final: 0.4690 (mmtt) REVERT: F 91 GLU cc_start: 0.2264 (pm20) cc_final: 0.1456 (tt0) REVERT: F 226 TYR cc_start: 0.7990 (t80) cc_final: 0.7655 (t80) REVERT: F 270 THR cc_start: 0.5542 (m) cc_final: 0.5296 (p) REVERT: F 278 TYR cc_start: 0.2573 (m-80) cc_final: 0.2285 (m-80) REVERT: G 284 TYR cc_start: 0.6982 (t80) cc_final: 0.6600 (t80) REVERT: G 300 PHE cc_start: 0.7234 (m-10) cc_final: 0.6915 (m-10) REVERT: G 328 ASP cc_start: 0.4923 (m-30) cc_final: 0.4209 (m-30) REVERT: G 340 MET cc_start: 0.6449 (mtp) cc_final: 0.6115 (mmm) REVERT: G 365 LYS cc_start: 0.7832 (tttt) cc_final: 0.7193 (mmtm) REVERT: G 495 SER cc_start: 0.8906 (p) cc_final: 0.8620 (p) REVERT: H 284 TYR cc_start: 0.6882 (t80) cc_final: 0.6448 (t80) REVERT: H 328 ASP cc_start: 0.4871 (m-30) cc_final: 0.4203 (m-30) REVERT: H 365 LYS cc_start: 0.8189 (tttt) cc_final: 0.7843 (mmtt) REVERT: H 486 ARG cc_start: 0.6321 (mtm-85) cc_final: 0.5811 (mtm-85) REVERT: H 495 SER cc_start: 0.8903 (p) cc_final: 0.8672 (p) REVERT: H 519 ASP cc_start: 0.8020 (p0) cc_final: 0.7736 (p0) REVERT: I 49 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7209 (tmt170) REVERT: I 138 ASP cc_start: 0.6468 (m-30) cc_final: 0.5685 (m-30) REVERT: I 319 SER cc_start: 0.7920 (p) cc_final: 0.7624 (p) REVERT: J 87 ASN cc_start: 0.8052 (m-40) cc_final: 0.7527 (m-40) REVERT: J 302 TRP cc_start: 0.6835 (m100) cc_final: 0.5685 (m100) REVERT: J 319 SER cc_start: 0.7691 (p) cc_final: 0.7429 (p) REVERT: L 165 VAL cc_start: 0.6798 (t) cc_final: 0.6462 (t) REVERT: L 221 LYS cc_start: -0.0851 (mttt) cc_final: -0.1351 (pttm) REVERT: L 238 GLN cc_start: 0.4758 (pt0) cc_final: 0.3793 (mm110) REVERT: M 331 GLU cc_start: -0.0263 (mt-10) cc_final: -0.1227 (mm-30) REVERT: N 239 MET cc_start: -0.1923 (ttt) cc_final: -0.2360 (tpp) REVERT: N 331 GLU cc_start: -0.0351 (mt-10) cc_final: -0.0606 (mm-30) REVERT: N 462 LEU cc_start: 0.3451 (mt) cc_final: 0.2983 (mm) REVERT: N 463 MET cc_start: -0.0397 (ttp) cc_final: -0.1573 (mmt) REVERT: C 333 THR cc_start: 0.8169 (p) cc_final: 0.7946 (t) outliers start: 2 outliers final: 0 residues processed: 764 average time/residue: 0.2074 time to fit residues: 265.8186 Evaluate side-chains 623 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 354 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 453 optimal weight: 0.0010 chunk 422 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 359 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 141 HIS B 141 HIS B 161 GLN B 164 GLN D 19 ASN E 4 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN G 517 GLN H 301 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN H 539 ASN I 87 ASN I 247 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.234535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.188004 restraints weight = 70984.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.185043 restraints weight = 73248.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.187026 restraints weight = 56691.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.186701 restraints weight = 48379.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.187106 restraints weight = 41738.888| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37601 Z= 0.222 Angle : 0.755 10.781 50890 Z= 0.388 Chirality : 0.049 0.227 5972 Planarity : 0.005 0.104 6496 Dihedral : 5.823 73.317 5048 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.10 % Favored : 89.23 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4632 helix: 0.55 (0.13), residues: 1568 sheet: -0.45 (0.20), residues: 726 loop : -2.31 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 90 TYR 0.022 0.002 TYR I 318 PHE 0.042 0.002 PHE I 102 TRP 0.058 0.003 TRP I 95 HIS 0.019 0.002 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00498 (37598) covalent geometry : angle 0.75479 (50890) hydrogen bonds : bond 0.03947 ( 1315) hydrogen bonds : angle 4.96018 ( 3768) Misc. bond : bond 0.00198 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 743 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.6416 (m-80) cc_final: 0.6131 (m-80) REVERT: A 249 MET cc_start: 0.3536 (mtm) cc_final: 0.2953 (ttp) REVERT: A 286 ASP cc_start: 0.6842 (p0) cc_final: 0.6127 (p0) REVERT: B 249 MET cc_start: 0.3838 (mtm) cc_final: 0.3421 (ttm) REVERT: B 304 TYR cc_start: 0.4471 (p90) cc_final: 0.4257 (p90) REVERT: D 104 MET cc_start: 0.3471 (tpp) cc_final: 0.2614 (tmm) REVERT: D 160 ASP cc_start: 0.8399 (p0) cc_final: 0.8133 (p0) REVERT: D 246 SER cc_start: 0.9002 (p) cc_final: 0.8572 (t) REVERT: D 275 ASN cc_start: 0.7378 (p0) cc_final: 0.7084 (p0) REVERT: E 58 MET cc_start: -0.2495 (tpt) cc_final: -0.3055 (tpt) REVERT: E 139 LYS cc_start: 0.5309 (mttt) cc_final: 0.4815 (mmtt) REVERT: E 390 THR cc_start: 0.7607 (p) cc_final: 0.7223 (p) REVERT: F 91 GLU cc_start: 0.1708 (pm20) cc_final: 0.1085 (tt0) REVERT: F 198 THR cc_start: 0.4730 (p) cc_final: 0.4203 (p) REVERT: F 270 THR cc_start: 0.6218 (m) cc_final: 0.5851 (p) REVERT: G 274 ILE cc_start: 0.8670 (mp) cc_final: 0.8420 (mp) REVERT: G 328 ASP cc_start: 0.5007 (m-30) cc_final: 0.4265 (m-30) REVERT: G 365 LYS cc_start: 0.7926 (tttt) cc_final: 0.7361 (mmtm) REVERT: G 430 ASP cc_start: 0.7709 (t70) cc_final: 0.7486 (t70) REVERT: H 284 TYR cc_start: 0.6926 (t80) cc_final: 0.6467 (t80) REVERT: H 328 ASP cc_start: 0.5155 (m-30) cc_final: 0.4416 (m-30) REVERT: H 365 LYS cc_start: 0.8104 (tttt) cc_final: 0.7804 (mmtt) REVERT: H 409 LEU cc_start: 0.8508 (mt) cc_final: 0.8214 (mt) REVERT: H 495 SER cc_start: 0.9000 (p) cc_final: 0.8772 (p) REVERT: H 498 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8034 (ttm-80) REVERT: H 506 CYS cc_start: 0.7239 (m) cc_final: 0.6949 (m) REVERT: I 47 LYS cc_start: 0.5910 (mttt) cc_final: 0.5645 (mmtt) REVERT: I 87 ASN cc_start: 0.8263 (m-40) cc_final: 0.7901 (m-40) REVERT: I 288 TRP cc_start: 0.7391 (m100) cc_final: 0.7094 (m100) REVERT: I 319 SER cc_start: 0.8168 (p) cc_final: 0.7843 (p) REVERT: I 357 ILE cc_start: 0.8333 (mt) cc_final: 0.8062 (mp) REVERT: J 49 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7304 (tmt170) REVERT: J 87 ASN cc_start: 0.8154 (m-40) cc_final: 0.7609 (m-40) REVERT: J 138 ASP cc_start: 0.5517 (m-30) cc_final: 0.4642 (m-30) REVERT: J 319 SER cc_start: 0.7932 (p) cc_final: 0.7700 (p) REVERT: L 30 MET cc_start: 0.5238 (tmm) cc_final: 0.4772 (tmm) REVERT: L 43 GLU cc_start: 0.3722 (pt0) cc_final: 0.3472 (mp0) REVERT: L 221 LYS cc_start: -0.0688 (mttt) cc_final: -0.1226 (pttm) REVERT: L 238 GLN cc_start: 0.4790 (pt0) cc_final: 0.3814 (mm-40) REVERT: M 276 ASP cc_start: 0.5957 (m-30) cc_final: 0.5633 (t0) REVERT: M 331 GLU cc_start: -0.0250 (mt-10) cc_final: -0.1212 (mm-30) REVERT: K 82 TYR cc_start: 0.4172 (m-80) cc_final: 0.3602 (m-80) REVERT: C 254 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8649 (mmt90) outliers start: 2 outliers final: 0 residues processed: 744 average time/residue: 0.2036 time to fit residues: 254.4100 Evaluate side-chains 617 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 114 optimal weight: 0.0060 chunk 48 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 446 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 442 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 164 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN H 301 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.238411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.190547 restraints weight = 70624.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.185767 restraints weight = 73289.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.187998 restraints weight = 58768.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.187991 restraints weight = 48162.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188329 restraints weight = 40073.172| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37601 Z= 0.144 Angle : 0.692 10.503 50890 Z= 0.353 Chirality : 0.047 0.226 5972 Planarity : 0.004 0.087 6496 Dihedral : 5.608 71.223 5048 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.98 % Favored : 90.46 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.12), residues: 4632 helix: 0.75 (0.13), residues: 1564 sheet: -0.41 (0.20), residues: 704 loop : -2.24 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 90 TYR 0.028 0.002 TYR H 537 PHE 0.024 0.002 PHE I 102 TRP 0.041 0.002 TRP I 95 HIS 0.019 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00332 (37598) covalent geometry : angle 0.69194 (50890) hydrogen bonds : bond 0.03481 ( 1315) hydrogen bonds : angle 4.75734 ( 3768) Misc. bond : bond 0.00140 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 750 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8754 (mmp) cc_final: 0.8528 (mmp) REVERT: A 249 MET cc_start: 0.3497 (mtm) cc_final: 0.3044 (ttm) REVERT: B 249 MET cc_start: 0.3709 (mtm) cc_final: 0.3495 (ttp) REVERT: B 304 TYR cc_start: 0.4405 (p90) cc_final: 0.4054 (p90) REVERT: D 104 MET cc_start: 0.3240 (tpp) cc_final: 0.2446 (tmm) REVERT: D 246 SER cc_start: 0.8881 (p) cc_final: 0.8584 (p) REVERT: E 139 LYS cc_start: 0.5565 (mttt) cc_final: 0.5059 (mmtt) REVERT: F 91 GLU cc_start: 0.1605 (pm20) cc_final: 0.0966 (tt0) REVERT: F 198 THR cc_start: 0.4638 (p) cc_final: 0.4359 (p) REVERT: F 270 THR cc_start: 0.6052 (m) cc_final: 0.5715 (p) REVERT: F 278 TYR cc_start: 0.2747 (m-80) cc_final: 0.2429 (m-80) REVERT: G 328 ASP cc_start: 0.5000 (m-30) cc_final: 0.4334 (m-30) REVERT: G 340 MET cc_start: 0.6676 (mtp) cc_final: 0.6051 (mmm) REVERT: G 365 LYS cc_start: 0.7852 (tttt) cc_final: 0.7219 (mmtm) REVERT: G 377 GLU cc_start: 0.7934 (pm20) cc_final: 0.7641 (mp0) REVERT: G 435 PHE cc_start: 0.8121 (m-80) cc_final: 0.7697 (m-80) REVERT: G 486 ARG cc_start: 0.6648 (mtt90) cc_final: 0.4428 (mtt90) REVERT: G 495 SER cc_start: 0.8849 (p) cc_final: 0.8599 (p) REVERT: G 504 LEU cc_start: 0.8065 (mp) cc_final: 0.7847 (mp) REVERT: H 365 LYS cc_start: 0.8111 (tttt) cc_final: 0.7796 (mmtt) REVERT: H 409 LEU cc_start: 0.8481 (mt) cc_final: 0.8254 (mt) REVERT: H 506 CYS cc_start: 0.7454 (m) cc_final: 0.7213 (m) REVERT: H 534 ASN cc_start: 0.7516 (p0) cc_final: 0.7200 (p0) REVERT: I 47 LYS cc_start: 0.5726 (mttt) cc_final: 0.5436 (mmtt) REVERT: I 87 ASN cc_start: 0.8169 (m-40) cc_final: 0.7869 (m-40) REVERT: I 319 SER cc_start: 0.8097 (p) cc_final: 0.7832 (p) REVERT: J 87 ASN cc_start: 0.8121 (m-40) cc_final: 0.7599 (m-40) REVERT: J 138 ASP cc_start: 0.6172 (m-30) cc_final: 0.5881 (m-30) REVERT: J 319 SER cc_start: 0.7875 (p) cc_final: 0.7648 (p) REVERT: L 30 MET cc_start: 0.5391 (tmm) cc_final: 0.5090 (tmm) REVERT: L 43 GLU cc_start: 0.3914 (pt0) cc_final: 0.3552 (mp0) REVERT: L 183 LYS cc_start: -0.1031 (mmpt) cc_final: -0.2638 (ptpt) REVERT: L 221 LYS cc_start: -0.0896 (mttt) cc_final: -0.1490 (pttm) REVERT: L 238 GLN cc_start: 0.4949 (pt0) cc_final: 0.3959 (mm110) REVERT: M 276 ASP cc_start: 0.5918 (m-30) cc_final: 0.5511 (t0) REVERT: M 331 GLU cc_start: -0.0178 (mt-10) cc_final: -0.1035 (mm-30) REVERT: N 106 ILE cc_start: -0.0890 (pt) cc_final: -0.1157 (pt) REVERT: N 462 LEU cc_start: 0.4544 (mm) cc_final: 0.3543 (mp) REVERT: N 463 MET cc_start: -0.0865 (ttp) cc_final: -0.2403 (mmt) REVERT: K 82 TYR cc_start: 0.4427 (m-80) cc_final: 0.3883 (m-80) REVERT: K 235 LEU cc_start: 0.2442 (tp) cc_final: 0.1805 (pp) REVERT: C 165 ILE cc_start: 0.9060 (mm) cc_final: 0.8703 (mm) REVERT: C 227 HIS cc_start: 0.7854 (m170) cc_final: 0.7453 (m-70) outliers start: 2 outliers final: 0 residues processed: 751 average time/residue: 0.2012 time to fit residues: 254.9411 Evaluate side-chains 617 residues out of total 4206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 347 optimal weight: 1.9990 chunk 375 optimal weight: 20.0000 chunk 368 optimal weight: 20.0000 chunk 419 optimal weight: 3.9990 chunk 424 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 219 optimal weight: 0.0980 chunk 78 optimal weight: 0.9980 chunk 458 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 GLN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.237790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.190001 restraints weight = 69967.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.185434 restraints weight = 72776.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.187932 restraints weight = 56747.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.187720 restraints weight = 47884.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.188139 restraints weight = 38782.467| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37601 Z= 0.149 Angle : 0.686 11.150 50890 Z= 0.350 Chirality : 0.047 0.213 5972 Planarity : 0.004 0.089 6496 Dihedral : 5.546 70.742 5048 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.11 % Favored : 90.37 % Rotamer: Outliers : 0.02 % Allowed : 0.15 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.12), residues: 4632 helix: 0.78 (0.13), residues: 1564 sheet: -0.58 (0.19), residues: 754 loop : -2.23 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 486 TYR 0.032 0.002 TYR B 228 PHE 0.024 0.002 PHE D 199 TRP 0.039 0.002 TRP I 95 HIS 0.019 0.001 HIS B 129 Details of bonding type rmsd covalent geometry : bond 0.00343 (37598) covalent geometry : angle 0.68554 (50890) hydrogen bonds : bond 0.03520 ( 1315) hydrogen bonds : angle 4.69392 ( 3768) Misc. bond : bond 0.00138 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7102.04 seconds wall clock time: 123 minutes 32.77 seconds (7412.77 seconds total)