Starting phenix.real_space_refine on Mon Apr 15 04:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f66_31474/04_2024/7f66_31474.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 173 5.16 5 C 21339 2.51 5 N 5953 2.21 5 O 6274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33739 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2275 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2275 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2631 Classifications: {'peptide': 335} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 320} Chain breaks: 2 Chain: "D" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2596 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1798 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1869 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "G" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2769 Classifications: {'peptide': 356} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 337} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2765 Classifications: {'peptide': 355} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 336} Chain: "I" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3336 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 4149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4149 Classifications: {'peptide': 591} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 152} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 18, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 338 Chain: "K" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "N" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1818 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 122} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 204 Chain: "O" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2210 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 956 Unresolved non-hydrogen angles: 1216 Unresolved non-hydrogen dihedrals: 757 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 11, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 391 Time building chain proxies: 17.56, per 1000 atoms: 0.52 Number of scatterers: 33739 At special positions: 0 Unit cell: (156.681, 208.079, 179.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 173 16.00 O 6274 8.00 N 5953 7.00 C 21339 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.74 Conformation dependent library (CDL) restraints added in 6.4 seconds 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 43 sheets defined 46.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.687A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.578A pdb=" N ALA A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.751A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 116 removed outlier: 4.560A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.758A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.574A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.754A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.023A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.570A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 41 through 59 removed outlier: 3.991A pdb=" N GLU B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 removed outlier: 3.827A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.348A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.634A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 223 removed outlier: 3.709A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.725A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 292 through 303 removed outlier: 3.906A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.653A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.425A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.572A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 removed outlier: 4.048A pdb=" N GLN C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.578A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.262A pdb=" N SER C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.701A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 270 through 274' Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.957A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.510A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.619A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.617A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.260A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.564A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 274 " --> pdb=" O MET D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 274' Processing helix chain 'D' and resid 296 through 304 removed outlier: 4.027A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 removed outlier: 3.568A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.860A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 46 removed outlier: 3.793A pdb=" N VAL E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.582A pdb=" N GLU E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.626A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.552A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 235 Processing helix chain 'E' and resid 277 through 292 removed outlier: 3.788A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.556A pdb=" N LEU F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 4.263A pdb=" N GLU F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.386A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.640A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 235 removed outlier: 4.897A pdb=" N ILE F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'F' and resid 277 through 292 removed outlier: 4.087A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.664A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.837A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET G 196 " --> pdb=" O THR G 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.766A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 327 removed outlier: 4.986A pdb=" N LEU G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS G 326 " --> pdb=" O PHE G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 353 removed outlier: 3.581A pdb=" N GLY G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 380 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.690A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 398 No H-bonds generated for 'chain 'G' and resid 396 through 398' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 493 through 497 removed outlier: 3.574A pdb=" N VAL G 497 " --> pdb=" O PRO G 494 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 519 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.789A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.248A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 327 removed outlier: 5.005A pdb=" N LEU H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS H 326 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 353 Processing helix chain 'H' and resid 368 through 380 removed outlier: 4.092A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.633A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 511 through 519 Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.535A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.810A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 322 through 326 removed outlier: 3.737A pdb=" N ASN I 326 " --> pdb=" O PRO I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.587A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.731A pdb=" N ASP J 62 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.523A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.678A pdb=" N CYS J 112 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 176 Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.725A pdb=" N GLN J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY J 233 " --> pdb=" O SER J 229 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 228 through 234' Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.860A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 322 through 326 removed outlier: 3.720A pdb=" N ASN J 326 " --> pdb=" O PRO J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 550 through 568 Processing helix chain 'J' and resid 570 through 585 Processing helix chain 'J' and resid 588 through 606 Proline residue: J 604 - end of helix Processing helix chain 'J' and resid 613 through 628 removed outlier: 3.723A pdb=" N TYR J 617 " --> pdb=" O ASP J 613 " (cutoff:3.500A) Proline residue: J 623 - end of helix Processing helix chain 'J' and resid 628 through 636 Processing helix chain 'J' and resid 638 through 656 Processing helix chain 'J' and resid 659 through 661 No H-bonds generated for 'chain 'J' and resid 659 through 661' Processing helix chain 'J' and resid 662 through 673 Processing helix chain 'J' and resid 677 through 687 Processing helix chain 'J' and resid 693 through 699 Processing helix chain 'J' and resid 700 through 715 Processing helix chain 'K' and resid 1 through 3 No H-bonds generated for 'chain 'K' and resid 1 through 3' Processing helix chain 'K' and resid 18 through 23 removed outlier: 4.023A pdb=" N SER K 23 " --> pdb=" O HIS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.779A pdb=" N TYR K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 4.410A pdb=" N ALA K 94 " --> pdb=" O PHE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.316A pdb=" N TRP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.674A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 158 through 178 Processing helix chain 'K' and resid 180 through 184 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'L' and resid 1 through 3 No H-bonds generated for 'chain 'L' and resid 1 through 3' Processing helix chain 'L' and resid 60 through 66 removed outlier: 3.763A pdb=" N PHE L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.244A pdb=" N ARG L 99 " --> pdb=" O SER L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 119 removed outlier: 4.009A pdb=" N TRP L 119 " --> pdb=" O LYS L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.558A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 141 No H-bonds generated for 'chain 'L' and resid 139 through 141' Processing helix chain 'L' and resid 142 through 154 Processing helix chain 'L' and resid 158 through 178 Processing helix chain 'L' and resid 180 through 184 Processing helix chain 'L' and resid 188 through 204 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 48 through 50 No H-bonds generated for 'chain 'N' and resid 48 through 50' Processing helix chain 'N' and resid 57 through 61 removed outlier: 3.623A pdb=" N LEU N 61 " --> pdb=" O ILE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 118 Processing helix chain 'N' and resid 122 through 142 removed outlier: 3.673A pdb=" N LEU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP N 135 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL N 136 " --> pdb=" O ARG N 132 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 158 removed outlier: 4.226A pdb=" N SER N 157 " --> pdb=" O LYS N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 164 removed outlier: 3.792A pdb=" N SER N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 183 Processing helix chain 'N' and resid 202 through 217 removed outlier: 3.788A pdb=" N CYS N 217 " --> pdb=" O ALA N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 242 through 264 removed outlier: 3.672A pdb=" N SER N 248 " --> pdb=" O THR N 244 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 13 Processing helix chain 'S' and resid 53 through 62 removed outlier: 4.356A pdb=" N VAL S 57 " --> pdb=" O GLY S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 146 removed outlier: 3.950A pdb=" N LEU S 141 " --> pdb=" O GLY S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 179 removed outlier: 3.980A pdb=" N GLN S 169 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 214 removed outlier: 3.647A pdb=" N GLN S 212 " --> pdb=" O LEU S 208 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 243 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 6.302A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR A 127 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 124 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 194 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU A 126 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY A 196 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.655A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.677A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 214 " --> pdb=" O ARG H 483 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU H 485 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL C 216 " --> pdb=" O LEU H 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.324A pdb=" N SER C 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LEU H 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLY H 404 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR H 336 " --> pdb=" O GLY H 404 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.575A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.316A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR G 336 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY G 404 " --> pdb=" O TYR G 336 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL G 401 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS G 437 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 403 " --> pdb=" O CYS G 437 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 76 through 79 removed outlier: 6.203A pdb=" N VAL E 51 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE E 78 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 53 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER E 105 " --> pdb=" O HIS E 203 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N HIS E 203 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 172 removed outlier: 6.446A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE E 157 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AB5, first strand: chain 'F' and resid 76 through 78 removed outlier: 8.888A pdb=" N ILE F 52 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN F 4 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU F 104 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA F 202 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ARG F 133 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU F 204 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.412A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET F 170 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE F 157 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL J 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG J 211 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'H' and resid 466 through 467 removed outlier: 4.005A pdb=" N HIS H 470 " --> pdb=" O ARG H 467 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 119 through 124 removed outlier: 6.579A pdb=" N THR I 91 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS I 247 " --> pdb=" O LYS I 186 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LYS I 186 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE I 249 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'I' and resid 336 through 338 removed outlier: 3.667A pdb=" N ILE I 342 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.532A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR I 424 " --> pdb=" O LEU I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 384 through 385 removed outlier: 6.397A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 119 through 124 removed outlier: 4.238A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS J 247 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AC9, first strand: chain 'J' and resid 336 through 338 removed outlier: 3.790A pdb=" N ILE J 342 " --> pdb=" O SER J 338 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU J 412 " --> pdb=" O LEU J 431 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL J 448 " --> pdb=" O GLU J 458 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.398A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE J 373 " --> pdb=" O LEU J 391 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.487A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'K' and resid 5 through 13 removed outlier: 5.098A pdb=" N TYR K 5 " --> pdb=" O LYS K 32 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LYS K 32 " --> pdb=" O TYR K 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE K 7 " --> pdb=" O TYR K 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 37 through 41 removed outlier: 4.420A pdb=" N ASP K 37 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD6, first strand: chain 'L' and resid 5 through 13 removed outlier: 5.226A pdb=" N TYR L 5 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS L 32 " --> pdb=" O TYR L 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE L 7 " --> pdb=" O TYR L 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 44 through 47 removed outlier: 8.833A pdb=" N TRP L 74 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR L 40 " --> pdb=" O TRP L 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 52 through 54 removed outlier: 5.798A pdb=" N ARG L 52 " --> pdb=" O LEU L 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'N' and resid 19 through 26 removed outlier: 7.158A pdb=" N TYR N 32 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE N 26 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL N 33 " --> pdb=" O GLY N 43 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLU N 42 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU N 84 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET N 44 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER N 85 " --> pdb=" O VAL N 72 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL N 72 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 225 through 230 removed outlier: 3.674A pdb=" N THR N 237 " --> pdb=" O LYS N 225 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG N 233 " --> pdb=" O ILE N 229 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP N 193 " --> pdb=" O GLU N 273 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU N 273 " --> pdb=" O ASP N 193 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU N 195 " --> pdb=" O GLN N 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN N 271 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA N 197 " --> pdb=" O ASN N 269 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN N 269 " --> pdb=" O ALA N 197 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 42 through 45 removed outlier: 4.024A pdb=" N ILE S 42 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU S 126 " --> pdb=" O LYS S 90 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS S 90 " --> pdb=" O LEU S 126 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 158 through 159 removed outlier: 5.802A pdb=" N LEU S 188 " --> pdb=" O ILE S 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'S' and resid 282 through 283 removed outlier: 6.496A pdb=" N VAL S 357 " --> pdb=" O ARG S 297 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL S 296 " --> pdb=" O SER S 316 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N SER S 316 " --> pdb=" O VAL S 296 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE S 314 " --> pdb=" O PRO S 298 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 288 through 289 Processing sheet with id=AE6, first strand: chain 'S' and resid 411 through 412 removed outlier: 9.149A pdb=" N VAL S 403 " --> pdb=" O ARG S 446 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG S 446 " --> pdb=" O VAL S 403 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN S 407 " --> pdb=" O ALA S 442 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU S 443 " --> pdb=" O ILE S 454 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 411 through 412 removed outlier: 6.596A pdb=" N LYS S 426 " --> pdb=" O SER S 418 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR S 369 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N ASN S 431 " --> pdb=" O ILE S 367 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ILE S 367 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE S 368 " --> pdb=" O THR S 464 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR S 464 " --> pdb=" O PHE S 368 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU S 370 " --> pdb=" O GLY S 462 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY S 462 " --> pdb=" O GLU S 370 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU S 372 " --> pdb=" O ARG S 460 " (cutoff:3.500A) 1578 hydrogen bonds defined for protein. 4434 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: 13.76 Time building geometry restraints manager: 14.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10914 1.34 - 1.45: 3872 1.45 - 1.57: 19263 1.57 - 1.69: 1 1.69 - 1.81: 264 Bond restraints: 34314 Sorted by residual: bond pdb=" CA ASP B 85 " pdb=" C ASP B 85 " ideal model delta sigma weight residual 1.521 1.486 0.036 1.17e-02 7.31e+03 9.30e+00 bond pdb=" CB PRO F 79 " pdb=" CG PRO F 79 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.86e+00 bond pdb=" C ASP B 85 " pdb=" O ASP B 85 " ideal model delta sigma weight residual 1.236 1.217 0.018 1.14e-02 7.69e+03 2.59e+00 bond pdb=" CA TYR B 86 " pdb=" C TYR B 86 " ideal model delta sigma weight residual 1.522 1.501 0.022 1.36e-02 5.41e+03 2.56e+00 bond pdb=" N SER B 84 " pdb=" CA SER B 84 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.77e-02 3.19e+03 1.94e+00 ... (remaining 34309 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.06: 464 104.06 - 111.55: 16090 111.55 - 119.03: 11808 119.03 - 126.52: 17859 126.52 - 134.01: 371 Bond angle restraints: 46592 Sorted by residual: angle pdb=" N GLU B 82 " pdb=" CA GLU B 82 " pdb=" C GLU B 82 " ideal model delta sigma weight residual 111.36 120.72 -9.36 1.09e+00 8.42e-01 7.38e+01 angle pdb=" N TYR B 83 " pdb=" CA TYR B 83 " pdb=" C TYR B 83 " ideal model delta sigma weight residual 112.68 120.60 -7.92 1.33e+00 5.65e-01 3.55e+01 angle pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" CD PRO F 79 " ideal model delta sigma weight residual 112.00 104.61 7.39 1.40e+00 5.10e-01 2.78e+01 angle pdb=" N ASP B 85 " pdb=" CA ASP B 85 " pdb=" C ASP B 85 " ideal model delta sigma weight residual 108.41 101.57 6.84 1.63e+00 3.76e-01 1.76e+01 angle pdb=" CA LEU J 283 " pdb=" CB LEU J 283 " pdb=" CG LEU J 283 " ideal model delta sigma weight residual 116.30 130.63 -14.33 3.50e+00 8.16e-02 1.68e+01 ... (remaining 46587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 19169 17.80 - 35.60: 1333 35.60 - 53.39: 198 53.39 - 71.19: 37 71.19 - 88.99: 12 Dihedral angle restraints: 20749 sinusoidal: 7461 harmonic: 13288 Sorted by residual: dihedral pdb=" CA LEU H 499 " pdb=" C LEU H 499 " pdb=" N VAL H 500 " pdb=" CA VAL H 500 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA LEU G 499 " pdb=" C LEU G 499 " pdb=" N VAL G 500 " pdb=" CA VAL G 500 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" N SER B 84 " pdb=" C SER B 84 " pdb=" CA SER B 84 " pdb=" CB SER B 84 " ideal model delta harmonic sigma weight residual 122.80 132.47 -9.67 0 2.50e+00 1.60e-01 1.50e+01 ... (remaining 20746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5132 0.091 - 0.183: 370 0.183 - 0.274: 1 0.274 - 0.365: 0 0.365 - 0.457: 2 Chirality restraints: 5505 Sorted by residual: chirality pdb=" CA TYR B 83 " pdb=" N TYR B 83 " pdb=" C TYR B 83 " pdb=" CB TYR B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA SER B 84 " pdb=" N SER B 84 " pdb=" C SER B 84 " pdb=" CB SER B 84 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA GLU B 82 " pdb=" N GLU B 82 " pdb=" C GLU B 82 " pdb=" CB GLU B 82 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 5502 not shown) Planarity restraints: 6023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 78 " 0.092 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO F 79 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO F 79 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO F 79 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 28 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 29 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 29 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 29 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 119 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO L 120 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " 0.036 5.00e-02 4.00e+02 ... (remaining 6020 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 325 2.65 - 3.21: 31190 3.21 - 3.78: 50791 3.78 - 4.34: 70403 4.34 - 4.90: 117726 Nonbonded interactions: 270435 Sorted by model distance: nonbonded pdb=" OG SER A 232 " pdb=" OD1 ASP A 287 " model vdw 2.091 2.440 nonbonded pdb=" OD1 ASN G 223 " pdb=" OH TYR G 441 " model vdw 2.167 2.440 nonbonded pdb=" O HIS A 128 " pdb=" OG1 THR A 153 " model vdw 2.175 2.440 nonbonded pdb=" OG1 THR F 110 " pdb=" NZ LYS F 268 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR J 128 " pdb=" OD2 ASP J 137 " model vdw 2.235 2.440 ... (remaining 270430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 305)) selection = (chain 'B' and (resid 0 through 43 or (resid 44 and (name N or name CA or name C \ )) or resid 45 through 305)) } ncs_group { reference = (chain 'C' and (resid 9 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 84 \ through 98 or resid 106 through 115 or resid 121 through 351)) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 55 or (resid 56 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 270 or (resid 271 throug \ h 286 and (name N or name CA or name C or name O or name CB )) or resid 287 thro \ ugh 295)) selection = (chain 'F' and (resid 1 through 10 or resid 27 through 63 or (resid 64 through 7 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 73 through 7 \ 9 or (resid 80 through 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 through 136 or resid 155 through 295)) } ncs_group { reference = (chain 'G' and resid 166 through 520) selection = (chain 'H' and (resid 166 through 291 or (resid 292 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ )) or resi \ d 293 through 520)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.460 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: 0.000 Extract box with map and model: 15.420 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 90.320 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.002 0.098 34314 Z= 0.170 Angle : 0.519 14.334 46592 Z= 0.280 Chirality : 0.044 0.457 5505 Planarity : 0.004 0.134 6023 Dihedral : 12.561 88.988 12109 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4481 helix: 1.84 (0.13), residues: 1776 sheet: -0.42 (0.23), residues: 546 loop : -0.66 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 135 HIS 0.003 0.001 HIS D 160 PHE 0.035 0.001 PHE B 239 TYR 0.018 0.001 TYR B 83 ARG 0.003 0.000 ARG H 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 4.150 Fit side-chains revert: symmetry clash REVERT: B 170 HIS cc_start: 0.8358 (t-90) cc_final: 0.7994 (t-90) REVERT: D 124 PHE cc_start: 0.8180 (m-10) cc_final: 0.7901 (m-10) REVERT: E 218 ASN cc_start: 0.7971 (m110) cc_final: 0.7560 (m-40) REVERT: F 94 TYR cc_start: 0.8423 (t80) cc_final: 0.8153 (t80) REVERT: F 214 PHE cc_start: 0.8630 (t80) cc_final: 0.8270 (t80) REVERT: F 218 ASN cc_start: 0.8198 (m110) cc_final: 0.7996 (m-40) REVERT: K 127 GLU cc_start: 0.7950 (pt0) cc_final: 0.7661 (pm20) REVERT: K 182 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8390 (pp20) REVERT: K 192 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7908 (mt-10) REVERT: L 84 LYS cc_start: 0.8675 (mmpt) cc_final: 0.8243 (mmpt) REVERT: L 141 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8246 (tp-100) REVERT: N 17 ASP cc_start: 0.6899 (m-30) cc_final: 0.6359 (m-30) REVERT: N 68 GLU cc_start: 0.6834 (tp30) cc_final: 0.6591 (tp30) REVERT: N 93 GLU cc_start: 0.7576 (mp0) cc_final: 0.7320 (mp0) REVERT: N 95 ILE cc_start: 0.8950 (pt) cc_final: 0.8629 (pp) REVERT: N 96 LYS cc_start: 0.8498 (ptpt) cc_final: 0.7994 (ptpt) REVERT: N 105 LYS cc_start: 0.8640 (tptm) cc_final: 0.8314 (tptm) REVERT: S 375 TYR cc_start: 0.7963 (p90) cc_final: 0.7748 (p90) outliers start: 0 outliers final: 1 residues processed: 401 average time/residue: 1.5895 time to fit residues: 757.1796 Evaluate side-chains 306 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 0.8980 chunk 341 optimal weight: 50.0000 chunk 189 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 352 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 262 optimal weight: 6.9990 chunk 408 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN H 194 GLN H 431 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 91 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34314 Z= 0.205 Angle : 0.522 17.122 46592 Z= 0.270 Chirality : 0.043 0.209 5505 Planarity : 0.004 0.076 6023 Dihedral : 3.990 26.925 4884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 1.08 % Allowed : 8.23 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4481 helix: 2.12 (0.13), residues: 1782 sheet: -0.48 (0.21), residues: 659 loop : -0.52 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 37 HIS 0.004 0.001 HIS F 115 PHE 0.033 0.001 PHE L 90 TYR 0.017 0.001 TYR L 65 ARG 0.008 0.000 ARG H 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 335 time to evaluate : 3.973 Fit side-chains REVERT: B 4 LYS cc_start: 0.8673 (mppt) cc_final: 0.8420 (mppt) REVERT: B 170 HIS cc_start: 0.8336 (t-90) cc_final: 0.7973 (t-90) REVERT: D 186 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8221 (mptt) REVERT: E 218 ASN cc_start: 0.7679 (m110) cc_final: 0.7416 (m-40) REVERT: F 8 MET cc_start: 0.8390 (mmm) cc_final: 0.8188 (mmt) REVERT: F 50 GLU cc_start: 0.8173 (pp20) cc_final: 0.7712 (tm-30) REVERT: F 94 TYR cc_start: 0.8562 (t80) cc_final: 0.8333 (t80) REVERT: F 214 PHE cc_start: 0.8550 (t80) cc_final: 0.8328 (t80) REVERT: F 218 ASN cc_start: 0.7922 (m110) cc_final: 0.7651 (m110) REVERT: I 199 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7410 (t0) REVERT: K 127 GLU cc_start: 0.7912 (pt0) cc_final: 0.7595 (pm20) REVERT: K 182 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8233 (pp20) REVERT: K 183 HIS cc_start: 0.8497 (m90) cc_final: 0.7963 (m90) REVERT: K 192 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8087 (mt-10) REVERT: L 84 LYS cc_start: 0.8709 (mmpt) cc_final: 0.8279 (mmpt) REVERT: N 14 GLU cc_start: 0.6856 (pp20) cc_final: 0.6310 (pp20) REVERT: N 68 GLU cc_start: 0.6782 (tp30) cc_final: 0.6505 (tp30) REVERT: N 93 GLU cc_start: 0.7705 (mp0) cc_final: 0.7467 (mp0) REVERT: N 95 ILE cc_start: 0.8905 (pt) cc_final: 0.8527 (pp) REVERT: N 99 ASP cc_start: 0.8168 (p0) cc_final: 0.7836 (p0) REVERT: N 105 LYS cc_start: 0.8606 (tptm) cc_final: 0.8333 (tptm) REVERT: S 452 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8079 (mtp85) outliers start: 36 outliers final: 13 residues processed: 344 average time/residue: 1.5927 time to fit residues: 651.9433 Evaluate side-chains 305 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 290 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 340 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 409 optimal weight: 40.0000 chunk 442 optimal weight: 0.0040 chunk 364 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 328 optimal weight: 30.0000 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN G 422 GLN I 232 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34314 Z= 0.259 Angle : 0.525 17.012 46592 Z= 0.271 Chirality : 0.044 0.176 5505 Planarity : 0.004 0.063 6023 Dihedral : 3.998 19.291 4882 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.93 % Favored : 95.05 % Rotamer: Outliers : 1.32 % Allowed : 10.72 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 4481 helix: 2.14 (0.13), residues: 1785 sheet: -0.44 (0.21), residues: 646 loop : -0.58 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 37 HIS 0.005 0.001 HIS D 349 PHE 0.021 0.001 PHE D 177 TYR 0.036 0.001 TYR B 83 ARG 0.005 0.000 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 4.107 Fit side-chains REVERT: B 4 LYS cc_start: 0.8715 (mppt) cc_final: 0.8403 (mppt) REVERT: B 170 HIS cc_start: 0.8339 (t-90) cc_final: 0.7985 (t-90) REVERT: D 186 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8224 (mptt) REVERT: E 1 MET cc_start: 0.8238 (tpp) cc_final: 0.8032 (tpt) REVERT: E 218 ASN cc_start: 0.7787 (m110) cc_final: 0.7512 (m-40) REVERT: F 214 PHE cc_start: 0.8594 (t80) cc_final: 0.8367 (t80) REVERT: F 218 ASN cc_start: 0.7933 (m110) cc_final: 0.7630 (m110) REVERT: F 269 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: G 415 MET cc_start: 0.8395 (ttm) cc_final: 0.8193 (ttp) REVERT: I 199 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7393 (t0) REVERT: K 49 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: K 127 GLU cc_start: 0.7928 (pt0) cc_final: 0.7617 (pm20) REVERT: K 182 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8208 (pp20) REVERT: K 183 HIS cc_start: 0.8510 (m90) cc_final: 0.7942 (m90) REVERT: K 192 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8099 (mt-10) REVERT: L 84 LYS cc_start: 0.8730 (mmpt) cc_final: 0.8301 (mmpt) REVERT: N 14 GLU cc_start: 0.6489 (pp20) cc_final: 0.6263 (pp20) REVERT: N 17 ASP cc_start: 0.6031 (m-30) cc_final: 0.5816 (m-30) REVERT: N 64 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7607 (mt) REVERT: N 68 GLU cc_start: 0.6841 (tp30) cc_final: 0.6546 (tp30) REVERT: N 92 GLU cc_start: 0.8342 (mp0) cc_final: 0.8120 (pm20) REVERT: N 93 GLU cc_start: 0.7691 (mp0) cc_final: 0.7309 (mp0) REVERT: N 105 LYS cc_start: 0.8571 (tptm) cc_final: 0.8290 (tptm) REVERT: S 375 TYR cc_start: 0.7866 (p90) cc_final: 0.7640 (p90) REVERT: S 452 ARG cc_start: 0.8702 (ttm110) cc_final: 0.8263 (mtp85) outliers start: 44 outliers final: 20 residues processed: 332 average time/residue: 1.5947 time to fit residues: 631.2049 Evaluate side-chains 312 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 287 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 412 SER Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 274 optimal weight: 1.9990 chunk 410 optimal weight: 20.0000 chunk 434 optimal weight: 30.0000 chunk 214 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN D 132 ASN I 232 GLN N 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34314 Z= 0.292 Angle : 0.534 17.046 46592 Z= 0.276 Chirality : 0.044 0.180 5505 Planarity : 0.004 0.064 6023 Dihedral : 4.075 19.684 4882 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 1.80 % Allowed : 12.30 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4481 helix: 2.16 (0.13), residues: 1776 sheet: -0.48 (0.21), residues: 636 loop : -0.64 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 111 HIS 0.006 0.001 HIS D 349 PHE 0.022 0.001 PHE D 177 TYR 0.036 0.001 TYR B 83 ARG 0.005 0.000 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 295 time to evaluate : 4.162 Fit side-chains revert: symmetry clash REVERT: A 14 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8484 (mmm) REVERT: A 93 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8727 (mtp) REVERT: B 170 HIS cc_start: 0.8336 (t-90) cc_final: 0.7966 (t-90) REVERT: D 186 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8221 (mptt) REVERT: E 218 ASN cc_start: 0.7814 (m110) cc_final: 0.7574 (m-40) REVERT: F 49 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: F 217 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.4192 (pm20) REVERT: F 218 ASN cc_start: 0.8012 (m110) cc_final: 0.7404 (m110) REVERT: F 269 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: G 415 MET cc_start: 0.8443 (ttm) cc_final: 0.8234 (ttp) REVERT: H 415 MET cc_start: 0.8535 (ttm) cc_final: 0.8013 (ttm) REVERT: I 199 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7426 (t0) REVERT: K 49 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8560 (mt-10) REVERT: K 127 GLU cc_start: 0.7911 (pt0) cc_final: 0.7596 (pm20) REVERT: K 182 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8431 (tm-30) REVERT: L 84 LYS cc_start: 0.8771 (mmpt) cc_final: 0.8317 (mmpt) REVERT: N 64 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7581 (mt) REVERT: N 68 GLU cc_start: 0.6852 (tp30) cc_final: 0.6504 (tp30) REVERT: N 105 LYS cc_start: 0.8561 (tptm) cc_final: 0.8301 (tptm) REVERT: S 375 TYR cc_start: 0.7876 (p90) cc_final: 0.7665 (p90) REVERT: S 452 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8383 (mmt90) outliers start: 60 outliers final: 24 residues processed: 326 average time/residue: 1.5318 time to fit residues: 597.6471 Evaluate side-chains 326 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 412 SER Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 323 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 371 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 222 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 232 GLN N 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34314 Z= 0.173 Angle : 0.496 16.405 46592 Z= 0.255 Chirality : 0.043 0.171 5505 Planarity : 0.004 0.060 6023 Dihedral : 3.915 18.739 4882 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 1.74 % Allowed : 13.47 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4481 helix: 2.29 (0.13), residues: 1770 sheet: -0.34 (0.21), residues: 618 loop : -0.60 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 37 HIS 0.004 0.001 HIS E 115 PHE 0.024 0.001 PHE D 177 TYR 0.030 0.001 TYR B 83 ARG 0.004 0.000 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 320 time to evaluate : 4.245 Fit side-chains revert: symmetry clash REVERT: A 14 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8525 (mmm) REVERT: A 93 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8699 (mtp) REVERT: B 170 HIS cc_start: 0.8327 (t-90) cc_final: 0.8009 (t70) REVERT: E 218 ASN cc_start: 0.7810 (m110) cc_final: 0.7572 (m-40) REVERT: F 217 GLU cc_start: 0.4347 (OUTLIER) cc_final: 0.4089 (pm20) REVERT: F 218 ASN cc_start: 0.7959 (m110) cc_final: 0.7574 (m-40) REVERT: F 269 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: I 199 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7393 (t0) REVERT: J 143 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8972 (mt) REVERT: J 163 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7829 (ttm-80) REVERT: K 49 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: K 127 GLU cc_start: 0.7900 (pt0) cc_final: 0.7579 (pm20) REVERT: K 182 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8401 (tm-30) REVERT: L 60 SER cc_start: 0.7914 (t) cc_final: 0.7710 (p) REVERT: L 84 LYS cc_start: 0.8729 (mmpt) cc_final: 0.8294 (mmpt) REVERT: L 183 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.7708 (m90) REVERT: N 64 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7627 (mt) REVERT: N 93 GLU cc_start: 0.7836 (mp0) cc_final: 0.7513 (mp0) REVERT: N 105 LYS cc_start: 0.8559 (tptm) cc_final: 0.8313 (tptm) REVERT: N 120 TYR cc_start: 0.7144 (m-10) cc_final: 0.6828 (m-10) REVERT: S 375 TYR cc_start: 0.7868 (p90) cc_final: 0.7666 (p90) outliers start: 58 outliers final: 22 residues processed: 346 average time/residue: 1.6502 time to fit residues: 693.4412 Evaluate side-chains 322 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 412 SER Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 420 VAL Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 0.6980 chunk 391 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 435 optimal weight: 30.0000 chunk 361 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN I 232 GLN N 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 34314 Z= 0.164 Angle : 0.492 16.605 46592 Z= 0.253 Chirality : 0.043 0.171 5505 Planarity : 0.004 0.059 6023 Dihedral : 3.834 22.061 4882 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 1.74 % Allowed : 14.25 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4481 helix: 2.37 (0.13), residues: 1769 sheet: -0.30 (0.21), residues: 618 loop : -0.56 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 37 HIS 0.004 0.001 HIS E 115 PHE 0.022 0.001 PHE D 177 TYR 0.035 0.001 TYR B 83 ARG 0.004 0.000 ARG H 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 326 time to evaluate : 4.157 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8698 (mtp) REVERT: A 169 CYS cc_start: 0.8193 (m) cc_final: 0.7931 (m) REVERT: B 170 HIS cc_start: 0.8332 (t-90) cc_final: 0.8019 (t70) REVERT: D 186 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8195 (mptt) REVERT: E 218 ASN cc_start: 0.7843 (m110) cc_final: 0.7613 (m-40) REVERT: F 49 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: F 173 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: F 217 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.4281 (pm20) REVERT: F 218 ASN cc_start: 0.7957 (m110) cc_final: 0.7551 (m-40) REVERT: F 269 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: J 143 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8988 (mt) REVERT: J 163 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7836 (ttm-80) REVERT: K 127 GLU cc_start: 0.7892 (pt0) cc_final: 0.7587 (pm20) REVERT: K 149 TYR cc_start: 0.8831 (t80) cc_final: 0.8626 (t80) REVERT: K 182 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8469 (tm-30) REVERT: K 184 TYR cc_start: 0.8183 (m-80) cc_final: 0.7889 (m-10) REVERT: L 60 SER cc_start: 0.7901 (t) cc_final: 0.7694 (p) REVERT: L 84 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8310 (mmpt) REVERT: N 64 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7636 (mt) REVERT: N 68 GLU cc_start: 0.7034 (tp30) cc_final: 0.6661 (tp30) REVERT: N 93 GLU cc_start: 0.7893 (mp0) cc_final: 0.7475 (mp0) REVERT: N 105 LYS cc_start: 0.8552 (tptm) cc_final: 0.8310 (tptm) REVERT: S 375 TYR cc_start: 0.7901 (p90) cc_final: 0.7673 (p90) REVERT: S 418 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7768 (p) REVERT: S 452 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8474 (mmt90) outliers start: 58 outliers final: 26 residues processed: 355 average time/residue: 1.5452 time to fit residues: 655.8339 Evaluate side-chains 337 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 412 SER Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 420 VAL Chi-restraints excluded: chain S residue 430 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 317 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 433 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 222 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN I 232 GLN L 141 GLN L 145 GLN N 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 34314 Z= 0.519 Angle : 0.643 16.765 46592 Z= 0.329 Chirality : 0.049 0.193 5505 Planarity : 0.005 0.062 6023 Dihedral : 4.386 22.426 4882 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.80 % Favored : 94.18 % Rotamer: Outliers : 1.98 % Allowed : 14.85 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4481 helix: 1.96 (0.13), residues: 1786 sheet: -0.53 (0.21), residues: 626 loop : -0.80 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 111 HIS 0.008 0.001 HIS D 349 PHE 0.022 0.002 PHE C 177 TYR 0.044 0.002 TYR B 83 ARG 0.005 0.001 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 298 time to evaluate : 3.914 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8692 (mppt) cc_final: 0.8393 (mppt) REVERT: C 58 MET cc_start: 0.8818 (mtp) cc_final: 0.8608 (mtp) REVERT: D 203 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.7868 (tpt) REVERT: E 132 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8450 (mtp) REVERT: F 49 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: F 217 GLU cc_start: 0.4790 (OUTLIER) cc_final: 0.4493 (pm20) REVERT: F 218 ASN cc_start: 0.7999 (m110) cc_final: 0.7526 (m-40) REVERT: F 269 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: J 143 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8998 (mt) REVERT: J 163 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7870 (ttm-80) REVERT: K 49 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: K 127 GLU cc_start: 0.7932 (pt0) cc_final: 0.7584 (pm20) REVERT: K 182 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8485 (tm-30) REVERT: K 184 TYR cc_start: 0.8465 (m-80) cc_final: 0.8175 (m-80) REVERT: L 32 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8613 (pttm) REVERT: L 84 LYS cc_start: 0.8824 (mmpt) cc_final: 0.8461 (mmpt) REVERT: L 183 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.7988 (m90) REVERT: N 64 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7519 (mp) REVERT: N 68 GLU cc_start: 0.7098 (tp30) cc_final: 0.6774 (tp30) REVERT: N 73 ILE cc_start: 0.6513 (mt) cc_final: 0.6183 (pt) REVERT: N 105 LYS cc_start: 0.8512 (tptm) cc_final: 0.8270 (tptm) REVERT: N 120 TYR cc_start: 0.7326 (m-10) cc_final: 0.7048 (m-10) REVERT: S 375 TYR cc_start: 0.7928 (p90) cc_final: 0.7724 (p90) REVERT: S 452 ARG cc_start: 0.8689 (mmm160) cc_final: 0.8467 (mmt90) outliers start: 66 outliers final: 34 residues processed: 333 average time/residue: 1.4874 time to fit residues: 595.3367 Evaluate side-chains 327 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 283 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 415 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 172 GLN Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 430 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 259 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 214 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 340 optimal weight: 8.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN H 431 ASN N 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34314 Z= 0.166 Angle : 0.519 17.473 46592 Z= 0.265 Chirality : 0.043 0.215 5505 Planarity : 0.004 0.060 6023 Dihedral : 4.057 23.324 4882 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.40 % Favored : 95.58 % Rotamer: Outliers : 1.29 % Allowed : 15.92 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4481 helix: 2.27 (0.13), residues: 1766 sheet: -0.33 (0.22), residues: 610 loop : -0.66 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 37 HIS 0.004 0.001 HIS E 115 PHE 0.025 0.001 PHE D 177 TYR 0.031 0.001 TYR B 83 ARG 0.004 0.000 ARG J 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 312 time to evaluate : 3.922 Fit side-chains revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8624 (mppt) cc_final: 0.8321 (mppt) REVERT: F 49 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: F 218 ASN cc_start: 0.7992 (m110) cc_final: 0.7543 (m-40) REVERT: F 269 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: J 143 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9025 (mt) REVERT: J 163 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7840 (ttm-80) REVERT: K 127 GLU cc_start: 0.7917 (pt0) cc_final: 0.7592 (pm20) REVERT: K 182 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8520 (tm-30) REVERT: K 184 TYR cc_start: 0.8431 (m-80) cc_final: 0.8205 (m-80) REVERT: L 84 LYS cc_start: 0.8762 (mmpt) cc_final: 0.8407 (mmpt) REVERT: L 183 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7841 (m90) REVERT: N 64 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7582 (mt) REVERT: N 68 GLU cc_start: 0.7053 (tp30) cc_final: 0.6660 (tp30) REVERT: N 73 ILE cc_start: 0.6441 (mt) cc_final: 0.6103 (pt) REVERT: N 105 LYS cc_start: 0.8537 (tptm) cc_final: 0.8262 (tptm) REVERT: N 120 TYR cc_start: 0.7319 (m-10) cc_final: 0.6995 (m-10) REVERT: S 375 TYR cc_start: 0.7896 (p90) cc_final: 0.7694 (p90) REVERT: S 418 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7781 (p) outliers start: 43 outliers final: 23 residues processed: 336 average time/residue: 1.5115 time to fit residues: 608.7809 Evaluate side-chains 331 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 302 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 415 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 412 SER Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 430 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 9.9990 chunk 415 optimal weight: 30.0000 chunk 379 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 402 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN F 236 GLN G 422 GLN H 431 ASN L 141 GLN L 145 GLN N 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 34314 Z= 0.381 Angle : 0.583 17.263 46592 Z= 0.298 Chirality : 0.046 0.204 5505 Planarity : 0.004 0.061 6023 Dihedral : 4.224 22.747 4882 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 1.38 % Allowed : 15.95 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4481 helix: 2.11 (0.13), residues: 1782 sheet: -0.48 (0.21), residues: 624 loop : -0.74 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 111 HIS 0.006 0.001 HIS D 160 PHE 0.021 0.001 PHE D 177 TYR 0.039 0.002 TYR N 120 ARG 0.004 0.000 ARG J 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 300 time to evaluate : 4.296 Fit side-chains REVERT: B 4 LYS cc_start: 0.8616 (mppt) cc_final: 0.8332 (mppt) REVERT: F 49 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: F 218 ASN cc_start: 0.8005 (m110) cc_final: 0.7478 (m-40) REVERT: F 269 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: J 143 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9007 (mt) REVERT: J 163 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7857 (ttm-80) REVERT: K 49 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: K 127 GLU cc_start: 0.7921 (pt0) cc_final: 0.7583 (pm20) REVERT: K 182 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8527 (tm-30) REVERT: K 184 TYR cc_start: 0.8507 (m-80) cc_final: 0.8256 (m-80) REVERT: L 32 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8641 (pttm) REVERT: L 84 LYS cc_start: 0.8811 (mmpt) cc_final: 0.8471 (mmpt) REVERT: L 86 MET cc_start: 0.8254 (ppp) cc_final: 0.8044 (ppp) REVERT: L 183 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7815 (m90) REVERT: N 64 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7581 (mp) REVERT: N 68 GLU cc_start: 0.7027 (tp30) cc_final: 0.6710 (tp30) REVERT: N 73 ILE cc_start: 0.6559 (mt) cc_final: 0.6261 (pt) REVERT: N 105 LYS cc_start: 0.8537 (tptm) cc_final: 0.8300 (tptm) REVERT: N 113 HIS cc_start: 0.7706 (t70) cc_final: 0.7436 (t70) REVERT: N 120 TYR cc_start: 0.7350 (m-10) cc_final: 0.7127 (m-10) outliers start: 46 outliers final: 29 residues processed: 324 average time/residue: 1.5387 time to fit residues: 596.2718 Evaluate side-chains 341 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain H residue 418 VAL Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 415 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 49 GLU Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 183 HIS Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 420 VAL Chi-restraints excluded: chain S residue 430 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 0.7980 chunk 427 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 297 optimal weight: 0.0970 chunk 448 optimal weight: 6.9990 chunk 412 optimal weight: 20.0000 chunk 356 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 275 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 GLN H 431 ASN L 145 GLN N 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34314 Z= 0.164 Angle : 0.521 17.277 46592 Z= 0.265 Chirality : 0.043 0.203 5505 Planarity : 0.004 0.060 6023 Dihedral : 3.991 21.701 4882 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 1.17 % Allowed : 16.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4481 helix: 2.31 (0.13), residues: 1771 sheet: -0.32 (0.21), residues: 625 loop : -0.63 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 456 HIS 0.004 0.001 HIS E 115 PHE 0.024 0.001 PHE D 177 TYR 0.030 0.001 TYR B 83 ARG 0.005 0.000 ARG K 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8962 Ramachandran restraints generated. 4481 Oldfield, 0 Emsley, 4481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 3.894 Fit side-chains revert: symmetry clash REVERT: A 169 CYS cc_start: 0.8189 (m) cc_final: 0.7929 (m) REVERT: B 4 LYS cc_start: 0.8600 (mppt) cc_final: 0.8308 (mppt) REVERT: B 170 HIS cc_start: 0.8324 (t70) cc_final: 0.8021 (t70) REVERT: F 49 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: F 173 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: F 218 ASN cc_start: 0.7956 (m110) cc_final: 0.7457 (m-40) REVERT: F 269 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: J 143 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9009 (mt) REVERT: J 163 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7826 (ttm-80) REVERT: K 127 GLU cc_start: 0.7926 (pt0) cc_final: 0.7608 (pm20) REVERT: L 32 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8592 (pttm) REVERT: L 84 LYS cc_start: 0.8735 (mmpt) cc_final: 0.8353 (mmpt) REVERT: N 64 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7565 (mt) REVERT: N 68 GLU cc_start: 0.7016 (tp30) cc_final: 0.6558 (tp30) REVERT: N 73 ILE cc_start: 0.6370 (mt) cc_final: 0.6076 (pt) REVERT: N 93 GLU cc_start: 0.7941 (mp0) cc_final: 0.7650 (mp0) REVERT: N 105 LYS cc_start: 0.8511 (tptm) cc_final: 0.8281 (tptm) REVERT: S 418 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7821 (p) outliers start: 39 outliers final: 26 residues processed: 339 average time/residue: 1.5948 time to fit residues: 645.5802 Evaluate side-chains 338 residues out of total 3980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 485 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 415 ASP Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain S residue 346 THR Chi-restraints excluded: chain S residue 413 THR Chi-restraints excluded: chain S residue 418 SER Chi-restraints excluded: chain S residue 420 VAL Chi-restraints excluded: chain S residue 430 THR Chi-restraints excluded: chain S residue 454 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 9.9990 chunk 380 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 GLN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075721 restraints weight = 70701.908| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.66 r_work: 0.2980 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34314 Z= 0.307 Angle : 0.566 17.099 46592 Z= 0.287 Chirality : 0.045 0.179 5505 Planarity : 0.004 0.061 6023 Dihedral : 4.099 22.378 4882 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 1.26 % Allowed : 16.43 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.13), residues: 4481 helix: 2.21 (0.13), residues: 1782 sheet: -0.44 (0.21), residues: 634 loop : -0.69 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 451 HIS 0.005 0.001 HIS D 349 PHE 0.022 0.001 PHE D 177 TYR 0.057 0.001 TYR N 120 ARG 0.012 0.000 ARG J 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12128.44 seconds wall clock time: 220 minutes 40.39 seconds (13240.39 seconds total)