Starting phenix.real_space_refine on Thu Sep 26 10:08:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/09_2024/6fo0_4286.cif" } resolution = 4.1 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= 0.008 sd= 0.035 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: 8 Type Number sf(0) Gaussians Fe 6 7.16 5 S 152 5.16 5 Cl 2 4.86 5 C 19850 2.51 5 N 5304 2.21 5 O 5674 1.98 5 F 6 1.80 5 H 30362 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61356 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6753 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "O" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6206 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5933 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "Q" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3751 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "R" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2658 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1710 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "T" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1255 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "U" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1041 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "V" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "W" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 950 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "A" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6753 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6206 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5933 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3751 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "E" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2658 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1710 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1255 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1041 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 950 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "P" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'G8U': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'G8U': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.38, per 1000 atoms: 0.35 Number of scatterers: 61356 At special positions: 0 Unit cell: (125.67, 137.385, 169.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 6 26.01 Cl 2 17.00 S 152 16.00 F 6 9.00 O 5674 8.00 N 5304 7.00 C 19850 6.00 H 30362 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 139 " - pdb=" SG CYS R 158 " distance=2.04 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 68 " distance=2.03 Simple disulfide: pdb=" SG CYS U 40 " - pdb=" SG CYS U 54 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 158 " distance=2.04 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.51 Conformation dependent library (CDL) restraints added in 3.8 seconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 20 sheets defined 56.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'N' and resid 3 through 11 removed outlier: 3.595A pdb=" N GLN N 9 " --> pdb=" O ALA N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 63 removed outlier: 4.256A pdb=" N GLU N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS N 61 " --> pdb=" O TYR N 57 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU N 62 " --> pdb=" O PHE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 81 removed outlier: 3.858A pdb=" N VAL N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 118 removed outlier: 3.793A pdb=" N ALA N 109 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU N 111 " --> pdb=" O PRO N 107 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 112 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA N 114 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 142 removed outlier: 3.687A pdb=" N LYS N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU N 135 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN N 139 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 158 removed outlier: 3.526A pdb=" N PHE N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE N 158 " --> pdb=" O HIS N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 165 removed outlier: 3.615A pdb=" N ALA N 164 " --> pdb=" O THR N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 175 Processing helix chain 'N' and resid 178 through 190 removed outlier: 3.606A pdb=" N ARG N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS N 189 " --> pdb=" O TYR N 185 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR N 190 " --> pdb=" O LEU N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 194 Processing helix chain 'N' and resid 204 through 215 removed outlier: 3.801A pdb=" N LEU N 208 " --> pdb=" O GLU N 204 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP N 210 " --> pdb=" O ARG N 206 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU N 211 " --> pdb=" O GLN N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 219 Processing helix chain 'N' and resid 266 through 278 removed outlier: 3.920A pdb=" N VAL N 272 " --> pdb=" O VAL N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 290 Processing helix chain 'N' and resid 292 through 301 removed outlier: 3.635A pdb=" N ALA N 298 " --> pdb=" O LEU N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 348 Processing helix chain 'N' and resid 350 through 369 removed outlier: 3.963A pdb=" N ARG N 356 " --> pdb=" O SER N 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY N 357 " --> pdb=" O GLU N 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 363 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER N 367 " --> pdb=" O ASN N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 386 removed outlier: 4.523A pdb=" N LEU N 384 " --> pdb=" O GLY N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 401 removed outlier: 3.671A pdb=" N TRP N 395 " --> pdb=" O PRO N 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N 397 " --> pdb=" O ALA N 393 " (cutoff:3.500A) Processing helix chain 'N' and resid 403 through 415 removed outlier: 3.611A pdb=" N VAL N 407 " --> pdb=" O ASP N 403 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG N 408 " --> pdb=" O ALA N 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU N 409 " --> pdb=" O ARG N 405 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER N 412 " --> pdb=" O ARG N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 440 Processing helix chain 'O' and resid 54 through 58 Processing helix chain 'O' and resid 64 through 72 Processing helix chain 'O' and resid 81 through 93 removed outlier: 3.722A pdb=" N THR O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU O 90 " --> pdb=" O THR O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 128 removed outlier: 3.851A pdb=" N LEU O 119 " --> pdb=" O ASP O 115 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN O 125 " --> pdb=" O GLU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 141 removed outlier: 3.822A pdb=" N VAL O 137 " --> pdb=" O ARG O 133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 152 removed outlier: 3.656A pdb=" N ALA O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 152 " --> pdb=" O LYS O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 167 removed outlier: 3.601A pdb=" N VAL O 159 " --> pdb=" O PRO O 155 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU O 161 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 199 removed outlier: 4.639A pdb=" N TYR O 194 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 224 removed outlier: 3.960A pdb=" N LEU O 216 " --> pdb=" O SER O 212 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 280 removed outlier: 3.888A pdb=" N ASN O 270 " --> pdb=" O SER O 266 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL O 274 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS O 277 " --> pdb=" O SER O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 300 Processing helix chain 'O' and resid 333 through 349 removed outlier: 4.560A pdb=" N ALA O 339 " --> pdb=" O ASP O 335 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN O 342 " --> pdb=" O LYS O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 372 removed outlier: 4.059A pdb=" N VAL O 357 " --> pdb=" O SER O 353 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 374 through 389 removed outlier: 3.677A pdb=" N GLU O 381 " --> pdb=" O GLY O 377 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY O 383 " --> pdb=" O LEU O 379 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN O 385 " --> pdb=" O GLU O 381 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA O 386 " --> pdb=" O VAL O 382 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA O 388 " --> pdb=" O SER O 384 " (cutoff:3.500A) Processing helix chain 'O' and resid 394 through 404 Processing helix chain 'O' and resid 409 through 411 No H-bonds generated for 'chain 'O' and resid 409 through 411' Processing helix chain 'O' and resid 413 through 420 Processing helix chain 'P' and resid 10 through 17 Processing helix chain 'P' and resid 29 through 52 removed outlier: 4.278A pdb=" N PHE P 33 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY P 34 " --> pdb=" O TRP P 30 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER P 35 " --> pdb=" O TRP P 31 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU P 37 " --> pdb=" O PHE P 33 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 73 removed outlier: 4.265A pdb=" N PHE P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER P 64 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL P 73 " --> pdb=" O ILE P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 105 removed outlier: 4.183A pdb=" N ILE P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG P 80 " --> pdb=" O GLY P 76 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR P 81 " --> pdb=" O TRP P 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE P 91 " --> pdb=" O ALA P 87 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY P 99 " --> pdb=" O TYR P 95 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY P 101 " --> pdb=" O HIS P 97 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU P 102 " --> pdb=" O VAL P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 108 No H-bonds generated for 'chain 'P' and resid 106 through 108' Processing helix chain 'P' and resid 109 through 133 removed outlier: 3.739A pdb=" N ASN P 114 " --> pdb=" O LEU P 110 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU P 120 " --> pdb=" O GLY P 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE P 128 " --> pdb=" O MET P 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET P 129 " --> pdb=" O ALA P 125 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL P 132 " --> pdb=" O PHE P 128 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU P 133 " --> pdb=" O MET P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 149 removed outlier: 3.516A pdb=" N ILE P 146 " --> pdb=" O GLY P 142 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU P 149 " --> pdb=" O VAL P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 153 Processing helix chain 'P' and resid 156 through 165 Processing helix chain 'P' and resid 171 through 183 removed outlier: 3.666A pdb=" N PHE P 178 " --> pdb=" O THR P 174 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA P 180 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE P 181 " --> pdb=" O ARG P 177 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 202 removed outlier: 3.533A pdb=" N ILE P 188 " --> pdb=" O ILE P 184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU P 200 " --> pdb=" O HIS P 196 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU P 202 " --> pdb=" O LEU P 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 217 removed outlier: 3.667A pdb=" N LYS P 217 " --> pdb=" O ASP P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 246 removed outlier: 3.830A pdb=" N ILE P 226 " --> pdb=" O PRO P 222 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 257 Processing helix chain 'P' and resid 271 through 273 No H-bonds generated for 'chain 'P' and resid 271 through 273' Processing helix chain 'P' and resid 274 through 284 removed outlier: 4.253A pdb=" N ILE P 280 " --> pdb=" O PHE P 276 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 284 " --> pdb=" O ILE P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 304 removed outlier: 4.006A pdb=" N ALA P 293 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU P 301 " --> pdb=" O SER P 297 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA P 302 " --> pdb=" O ILE P 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU P 303 " --> pdb=" O LEU P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 308 removed outlier: 3.910A pdb=" N HIS P 308 " --> pdb=" O PRO P 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 305 through 308' Processing helix chain 'P' and resid 318 through 339 removed outlier: 3.786A pdb=" N ALA P 327 " --> pdb=" O CYS P 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP P 337 " --> pdb=" O LEU P 333 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY P 339 " --> pdb=" O LEU P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 364 removed outlier: 3.560A pdb=" N THR P 349 " --> pdb=" O HIS P 345 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE P 350 " --> pdb=" O PRO P 346 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 353 " --> pdb=" O THR P 349 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL P 356 " --> pdb=" O GLN P 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE P 362 " --> pdb=" O TYR P 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 377 removed outlier: 3.768A pdb=" N GLY P 370 " --> pdb=" O MET P 366 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS P 375 " --> pdb=" O THR P 371 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 377 " --> pdb=" O GLU P 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 removed outlier: 3.506A pdb=" N GLY Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 40 Processing helix chain 'Q' and resid 47 through 51 Processing helix chain 'Q' and resid 57 through 68 removed outlier: 3.691A pdb=" N LEU Q 64 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL Q 68 " --> pdb=" O LEU Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 104 removed outlier: 3.768A pdb=" N ALA Q 101 " --> pdb=" O ASN Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 132 Processing helix chain 'Q' and resid 153 through 157 removed outlier: 4.344A pdb=" N ALA Q 157 " --> pdb=" O PRO Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 194 removed outlier: 3.618A pdb=" N TRP Q 192 " --> pdb=" O THR Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 232 removed outlier: 3.677A pdb=" N ARG Q 203 " --> pdb=" O ASP Q 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU Q 209 " --> pdb=" O GLY Q 205 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 210 " --> pdb=" O LEU Q 206 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU Q 214 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Proline residue: Q 217 - end of helix removed outlier: 4.962A pdb=" N VAL Q 229 " --> pdb=" O HIS Q 225 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 19 Processing helix chain 'R' and resid 28 through 63 removed outlier: 3.572A pdb=" N SER R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER R 56 " --> pdb=" O LYS R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 71 removed outlier: 3.868A pdb=" N LEU R 69 " --> pdb=" O SER R 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET R 71 " --> pdb=" O ASP R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 112 Processing helix chain 'R' and resid 122 through 127 removed outlier: 3.504A pdb=" N ARG R 126 " --> pdb=" O HIS R 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 24 removed outlier: 3.609A pdb=" N ASN S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 37 removed outlier: 3.544A pdb=" N ILE S 37 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 50 removed outlier: 3.946A pdb=" N ALA S 46 " --> pdb=" O ASP S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 72 removed outlier: 3.764A pdb=" N ASP S 57 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG S 61 " --> pdb=" O ASP S 57 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG S 71 " --> pdb=" O ASP S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 86 Processing helix chain 'S' and resid 90 through 107 removed outlier: 3.791A pdb=" N VAL S 97 " --> pdb=" O TYR S 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 43 removed outlier: 3.504A pdb=" N ALA T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 47 Processing helix chain 'T' and resid 48 through 71 removed outlier: 4.279A pdb=" N PHE T 52 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR T 63 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER T 69 " --> pdb=" O GLU T 65 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS T 70 " --> pdb=" O PHE T 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG T 71 " --> pdb=" O GLU T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 25 removed outlier: 4.094A pdb=" N THR U 19 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL U 20 " --> pdb=" O PRO U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 46 Processing helix chain 'U' and resid 54 through 73 removed outlier: 3.864A pdb=" N LEU U 59 " --> pdb=" O THR U 55 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP U 60 " --> pdb=" O GLU U 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS U 67 " --> pdb=" O HIS U 63 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS U 68 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'W' and resid 4 through 13 removed outlier: 3.730A pdb=" N LEU W 12 " --> pdb=" O ARG W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 47 removed outlier: 3.764A pdb=" N ILE W 24 " --> pdb=" O PHE W 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL W 26 " --> pdb=" O LEU W 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 56 removed outlier: 3.680A pdb=" N LYS W 56 " --> pdb=" O LYS W 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.596A pdb=" N GLN A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 removed outlier: 4.258A pdb=" N GLU A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.858A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.794A pdb=" N ALA A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.686A pdb=" N LYS A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.526A pdb=" N PHE A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.613A pdb=" N ALA A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.605A pdb=" N ARG A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.802A pdb=" N LEU A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.921A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.634A pdb=" N ALA A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 348 Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.963A pdb=" N ARG A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.522A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.671A pdb=" N TRP A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.610A pdb=" N VAL A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.721A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 removed outlier: 3.851A pdb=" N LEU B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.823A pdb=" N VAL B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 removed outlier: 3.654A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.601A pdb=" N VAL B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 199 removed outlier: 4.639A pdb=" N TYR B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.960A pdb=" N LEU B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.887A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 333 through 349 removed outlier: 4.561A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 removed outlier: 4.059A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.678A pdb=" N GLU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 413 through 420 Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 29 through 52 removed outlier: 4.277A pdb=" N PHE C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY C 34 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 35 " --> pdb=" O TRP C 31 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 37 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 removed outlier: 4.265A pdb=" N PHE C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 105 removed outlier: 4.184A pdb=" N ILE C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 81 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 133 removed outlier: 3.740A pdb=" N ASN C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 133 " --> pdb=" O MET C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.516A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 171 through 183 removed outlier: 3.665A pdb=" N PHE C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 202 removed outlier: 3.533A pdb=" N ILE C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.666A pdb=" N LYS C 217 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 246 removed outlier: 3.830A pdb=" N ILE C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 274 through 284 removed outlier: 4.252A pdb=" N ILE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 304 removed outlier: 4.008A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 removed outlier: 3.911A pdb=" N HIS C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 318 through 339 removed outlier: 3.785A pdb=" N ALA C 327 " --> pdb=" O CYS C 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 364 removed outlier: 3.560A pdb=" N THR C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 362 " --> pdb=" O TYR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 removed outlier: 3.768A pdb=" N GLY C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.506A pdb=" N GLY D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 40 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.691A pdb=" N LEU D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 104 removed outlier: 3.767A pdb=" N ALA D 101 " --> pdb=" O ASN D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 153 through 157 removed outlier: 4.344A pdb=" N ALA D 157 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.617A pdb=" N TRP D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 232 removed outlier: 3.676A pdb=" N ARG D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Proline residue: D 217 - end of helix removed outlier: 4.961A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.501A pdb=" N VAL E 18 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 63 removed outlier: 3.573A pdb=" N SER E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 71 removed outlier: 3.868A pdb=" N LEU E 69 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.505A pdb=" N ARG E 126 " --> pdb=" O HIS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 24 removed outlier: 3.608A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.546A pdb=" N ILE F 37 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 50 removed outlier: 3.945A pdb=" N ALA F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 72 removed outlier: 3.764A pdb=" N ASP F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 71 " --> pdb=" O ASP F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 90 through 107 removed outlier: 3.790A pdb=" N VAL F 97 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 removed outlier: 3.505A pdb=" N ALA G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 48 through 71 removed outlier: 4.278A pdb=" N PHE G 52 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 4.095A pdb=" N THR H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 20 " --> pdb=" O PRO H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 46 Processing helix chain 'H' and resid 54 through 73 removed outlier: 3.863A pdb=" N LEU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS H 71 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS H 72 " --> pdb=" O CYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'J' and resid 4 through 13 removed outlier: 3.731A pdb=" N LEU J 12 " --> pdb=" O ARG J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 47 removed outlier: 3.766A pdb=" N ILE J 24 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN J 37 " --> pdb=" O ARG J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 56 removed outlier: 3.681A pdb=" N LYS J 56 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 15 through 17 removed outlier: 3.742A pdb=" N ALA N 199 " --> pdb=" O ALA N 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY N 201 " --> pdb=" O GLU N 28 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL N 196 " --> pdb=" O TRP N 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR N 97 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 279 through 280 Processing sheet with id=AA3, first strand: chain 'N' and resid 279 through 280 removed outlier: 3.630A pdb=" N CYS N 326 " --> pdb=" O ALA N 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA N 251 " --> pdb=" O CYS N 326 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Q 234 " --> pdb=" O TYR T 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 25 through 28 removed outlier: 3.840A pdb=" N SER O 37 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR O 27 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE O 35 " --> pdb=" O THR O 27 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL O 34 " --> pdb=" O LEU O 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 208 through 209 removed outlier: 3.731A pdb=" N CYS O 111 " --> pdb=" O SER O 45 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE O 47 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU O 110 " --> pdb=" O LYS O 95 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER V 67 " --> pdb=" O SER V 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 243 through 247 removed outlier: 6.912A pdb=" N ILE O 244 " --> pdb=" O ALA O 426 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY O 428 " --> pdb=" O ILE O 244 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU O 246 " --> pdb=" O GLY O 428 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA O 255 " --> pdb=" O THR O 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 69 through 74 removed outlier: 4.194A pdb=" N PHE Q 81 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 87 through 91 Processing sheet with id=AA9, first strand: chain 'R' and resid 164 through 165 removed outlier: 6.551A pdb=" N HIS R 164 " --> pdb=" O ARG R 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 185 through 189 removed outlier: 4.072A pdb=" N THR R 188 " --> pdb=" O MET R 192 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET R 192 " --> pdb=" O THR R 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.740A pdb=" N ALA A 199 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 201 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 196 " --> pdb=" O TRP A 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 97 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AB4, first strand: chain 'A' and resid 279 through 280 removed outlier: 3.631A pdb=" N CYS A 326 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 251 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE G 14 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 234 " --> pdb=" O TYR G 16 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.842A pdb=" N SER B 37 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 27 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 35 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 34 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.730A pdb=" N CYS B 111 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 47 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 110 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL I 68 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER I 67 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.911A pdb=" N ILE B 244 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N GLY B 428 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 246 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 255 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 69 through 74 removed outlier: 4.193A pdb=" N PHE D 81 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 87 through 91 Processing sheet with id=AC1, first strand: chain 'E' and resid 164 through 165 removed outlier: 6.551A pdb=" N HIS E 164 " --> pdb=" O ARG E 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 189 removed outlier: 4.072A pdb=" N THR E 188 " --> pdb=" O MET E 192 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) 1429 hydrogen bonds defined for protein. 4002 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: 20.80 Time building geometry restraints manager: 15.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.10: 30310 1.10 - 1.38: 12437 1.38 - 1.65: 19121 1.65 - 1.92: 242 1.92 - 2.20: 22 Bond restraints: 62132 Sorted by residual: bond pdb=" N ARG I 62 " pdb=" H1 ARG I 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N ARG V 62 " pdb=" H1 ARG V 62 " ideal model delta sigma weight residual 0.960 0.863 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C18 G8U C 503 " pdb=" O23 G8U C 503 " ideal model delta sigma weight residual 1.328 1.397 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C VAL O 186 " pdb=" N THR O 187 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.19e+01 bond pdb=" C18 G8U P 503 " pdb=" O23 G8U P 503 " ideal model delta sigma weight residual 1.328 1.397 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 62127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.80: 112014 7.80 - 15.60: 28 15.60 - 23.40: 13 23.40 - 31.20: 39 31.20 - 38.99: 10 Bond angle restraints: 112104 Sorted by residual: angle pdb=" N ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 110.00 71.01 38.99 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C VAL O 186 " pdb=" CA VAL O 186 " pdb=" HA VAL O 186 " ideal model delta sigma weight residual 109.00 71.00 38.00 3.00e+00 1.11e-01 1.60e+02 angle pdb=" N VAL O 186 " pdb=" CA VAL O 186 " pdb=" HA VAL O 186 " ideal model delta sigma weight residual 110.00 72.53 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 109.00 72.91 36.09 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 109.00 74.58 34.42 3.00e+00 1.11e-01 1.32e+02 ... (remaining 112099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 27648 17.69 - 35.38: 1175 35.38 - 53.06: 348 53.06 - 70.75: 121 70.75 - 88.44: 18 Dihedral angle restraints: 29310 sinusoidal: 15760 harmonic: 13550 Sorted by residual: dihedral pdb=" CA GLY E 174 " pdb=" C GLY E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual 180.00 135.97 44.03 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA GLY R 174 " pdb=" C GLY R 174 " pdb=" N PRO R 175 " pdb=" CA PRO R 175 " ideal model delta harmonic sigma weight residual 180.00 136.01 43.99 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA ASN P 15 " pdb=" C ASN P 15 " pdb=" N ASN P 16 " pdb=" CA ASN P 16 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 29307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4639 0.117 - 0.235: 109 0.235 - 0.352: 0 0.352 - 0.469: 0 0.469 - 0.587: 2 Chirality restraints: 4750 Sorted by residual: chirality pdb=" CB VAL I 64 " pdb=" CA VAL I 64 " pdb=" CG1 VAL I 64 " pdb=" CG2 VAL I 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" CB VAL V 64 " pdb=" CA VAL V 64 " pdb=" CG1 VAL V 64 " pdb=" CG2 VAL V 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CB VAL N 39 " pdb=" CA VAL N 39 " pdb=" CG1 VAL N 39 " pdb=" CG2 VAL N 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 4747 not shown) Planarity restraints: 9200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN P 44 " 0.242 2.00e-02 2.50e+03 2.91e-01 1.27e+03 pdb=" CD GLN P 44 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN P 44 " -0.226 2.00e-02 2.50e+03 pdb=" NE2 GLN P 44 " 0.014 2.00e-02 2.50e+03 pdb="HE21 GLN P 44 " -0.439 2.00e-02 2.50e+03 pdb="HE22 GLN P 44 " 0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 44 " -0.240 2.00e-02 2.50e+03 2.86e-01 1.23e+03 pdb=" CD GLN C 44 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN C 44 " 0.224 2.00e-02 2.50e+03 pdb=" NE2 GLN C 44 " -0.014 2.00e-02 2.50e+03 pdb="HE21 GLN C 44 " 0.431 2.00e-02 2.50e+03 pdb="HE22 GLN C 44 " -0.442 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 435 " 0.124 2.00e-02 2.50e+03 1.35e-01 2.74e+02 pdb=" CG ASN N 435 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN N 435 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN N 435 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN N 435 " -0.200 2.00e-02 2.50e+03 pdb="HD22 ASN N 435 " 0.201 2.00e-02 2.50e+03 ... (remaining 9197 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 5588 2.23 - 2.82: 140199 2.82 - 3.41: 153888 3.41 - 4.01: 212329 4.01 - 4.60: 334939 Nonbonded interactions: 846943 Sorted by model distance: nonbonded pdb=" O ILE C 164 " pdb="HH21 ARG C 177 " model vdw 1.636 2.450 nonbonded pdb=" O ILE P 164 " pdb="HH21 ARG P 177 " model vdw 1.638 2.450 nonbonded pdb=" O VAL C 215 " pdb=" HZ3 LYS F 63 " model vdw 1.640 2.450 nonbonded pdb=" O ILE A 277 " pdb=" HG SER A 292 " model vdw 1.644 2.450 nonbonded pdb=" O ILE N 277 " pdb=" HG SER N 292 " model vdw 1.645 2.450 ... (remaining 846938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.830 Extract box with map and model: 1.720 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 97.570 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.012 0.171 31772 Z= 0.758 Angle : 0.962 23.879 43226 Z= 0.478 Chirality : 0.052 0.587 4750 Planarity : 0.006 0.074 5514 Dihedral : 9.174 88.440 11462 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.18 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % 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: -4.55 (0.11), residues: 3850 helix: -3.17 (0.08), residues: 1866 sheet: -3.32 (0.26), residues: 276 loop : -2.64 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 141 HIS 0.017 0.003 HIS B 158 PHE 0.029 0.003 PHE S 26 TYR 0.025 0.003 TYR N 47 ARG 0.011 0.001 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 946 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 946 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 294 LEU cc_start: 0.8949 (tp) cc_final: 0.8624 (tp) REVERT: P 70 CYS cc_start: 0.8373 (m) cc_final: 0.8076 (t) REVERT: P 96 MET cc_start: 0.7855 (mmt) cc_final: 0.7555 (mmm) REVERT: P 190 MET cc_start: 0.7731 (ttp) cc_final: 0.7514 (ttp) REVERT: P 287 LYS cc_start: 0.8592 (tttt) cc_final: 0.8384 (tptm) REVERT: P 311 LYS cc_start: 0.8874 (mttm) cc_final: 0.8465 (mtpp) REVERT: P 349 THR cc_start: 0.8627 (m) cc_final: 0.8398 (t) REVERT: Q 44 ASP cc_start: 0.7772 (m-30) cc_final: 0.7567 (t0) REVERT: Q 66 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6815 (mm-30) REVERT: Q 77 ASP cc_start: 0.8095 (m-30) cc_final: 0.7383 (t0) REVERT: Q 166 ASN cc_start: 0.8295 (t0) cc_final: 0.7939 (t0) REVERT: R 23 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7165 (mmtt) REVERT: R 186 GLU cc_start: 0.7783 (tt0) cc_final: 0.7421 (tm-30) REVERT: S 44 LYS cc_start: 0.9035 (mttt) cc_final: 0.8700 (mtmt) REVERT: S 60 PHE cc_start: 0.8391 (t80) cc_final: 0.8158 (t80) REVERT: S 109 LYS cc_start: 0.8560 (mttt) cc_final: 0.8295 (mttt) REVERT: T 24 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7070 (tpt170) REVERT: B 63 LEU cc_start: 0.8547 (mt) cc_final: 0.8233 (tp) REVERT: B 132 PHE cc_start: 0.8491 (m-10) cc_final: 0.8269 (m-10) REVERT: B 243 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6508 (tm-30) REVERT: C 70 CYS cc_start: 0.8356 (m) cc_final: 0.8150 (t) REVERT: C 96 MET cc_start: 0.7866 (mmt) cc_final: 0.7430 (mmm) REVERT: C 155 TYR cc_start: 0.6272 (m-10) cc_final: 0.6062 (t80) REVERT: C 172 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8319 (tttp) REVERT: C 311 LYS cc_start: 0.8802 (mttm) cc_final: 0.8367 (mtpp) REVERT: D 22 ASP cc_start: 0.7132 (t0) cc_final: 0.6700 (t0) REVERT: D 66 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6715 (mm-30) REVERT: D 77 ASP cc_start: 0.8259 (m-30) cc_final: 0.7298 (t0) REVERT: D 153 PHE cc_start: 0.8101 (t80) cc_final: 0.7777 (t80) REVERT: D 228 SER cc_start: 0.9148 (p) cc_final: 0.8741 (t) REVERT: E 23 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7387 (mmtt) REVERT: E 131 GLU cc_start: 0.6813 (pm20) cc_final: 0.6520 (tp30) REVERT: E 186 GLU cc_start: 0.7920 (tt0) cc_final: 0.7403 (tm-30) REVERT: F 14 GLU cc_start: 0.8049 (tp30) cc_final: 0.7713 (tm-30) REVERT: F 109 LYS cc_start: 0.8370 (mttt) cc_final: 0.8084 (mttt) REVERT: G 24 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7052 (tpt170) REVERT: J 16 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6911 (tpt170) outliers start: 0 outliers final: 0 residues processed: 946 average time/residue: 0.9954 time to fit residues: 1398.5046 Evaluate side-chains 471 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 297 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 GLN ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 ASN Q 31 GLN Q 75 ASN R 53 ASN A 252 HIS B 125 ASN D 31 GLN E 53 ASN H 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 31772 Z= 0.267 Angle : 0.678 12.833 43226 Z= 0.350 Chirality : 0.046 1.374 4750 Planarity : 0.006 0.060 5514 Dihedral : 7.884 89.717 4322 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -3.00 (0.13), residues: 3850 helix: -1.67 (0.10), residues: 1938 sheet: -2.34 (0.28), residues: 296 loop : -2.17 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 379 HIS 0.006 0.001 HIS C 68 PHE 0.016 0.001 PHE T 21 TYR 0.015 0.001 TYR Q 33 ARG 0.014 0.001 ARG J 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 671 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7975 (mt-10) REVERT: N 386 TYR cc_start: 0.6163 (m-80) cc_final: 0.5449 (m-80) REVERT: N 433 ASP cc_start: 0.6644 (t70) cc_final: 0.6383 (t0) REVERT: O 99 THR cc_start: 0.8897 (m) cc_final: 0.8472 (p) REVERT: O 146 ILE cc_start: 0.8077 (mt) cc_final: 0.7707 (tp) REVERT: P 96 MET cc_start: 0.7601 (mmt) cc_final: 0.7146 (mmm) REVERT: P 228 ASP cc_start: 0.8406 (m-30) cc_final: 0.8182 (m-30) REVERT: P 287 LYS cc_start: 0.8437 (tttt) cc_final: 0.8210 (tptm) REVERT: P 311 LYS cc_start: 0.8935 (mttm) cc_final: 0.8561 (mtpp) REVERT: Q 44 ASP cc_start: 0.7514 (m-30) cc_final: 0.7290 (t0) REVERT: Q 66 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7241 (mm-30) REVERT: Q 150 ASN cc_start: 0.8723 (t0) cc_final: 0.8379 (t0) REVERT: Q 153 PHE cc_start: 0.8306 (t80) cc_final: 0.7939 (t80) REVERT: Q 166 ASN cc_start: 0.8258 (t0) cc_final: 0.7904 (t0) REVERT: Q 222 MET cc_start: 0.8848 (mtp) cc_final: 0.7925 (mmm) REVERT: R 2 HIS cc_start: 0.7432 (p-80) cc_final: 0.7229 (p-80) REVERT: R 23 LYS cc_start: 0.7463 (mmtm) cc_final: 0.7156 (mmtt) REVERT: R 40 THR cc_start: 0.9343 (m) cc_final: 0.9085 (m) REVERT: R 186 GLU cc_start: 0.7859 (tt0) cc_final: 0.7352 (tm-30) REVERT: S 44 LYS cc_start: 0.8906 (mttt) cc_final: 0.8671 (mtmt) REVERT: S 60 PHE cc_start: 0.8501 (t80) cc_final: 0.8182 (t80) REVERT: S 109 LYS cc_start: 0.8427 (mttt) cc_final: 0.8213 (mttt) REVERT: T 24 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7005 (tpt170) REVERT: V 70 LEU cc_start: 0.8712 (tp) cc_final: 0.8397 (tp) REVERT: W 33 ARG cc_start: 0.6752 (ttm170) cc_final: 0.6139 (mmp-170) REVERT: A 195 MET cc_start: 0.8018 (mtp) cc_final: 0.7454 (ttm) REVERT: B 146 ILE cc_start: 0.8546 (mm) cc_final: 0.8168 (tp) REVERT: B 243 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6456 (tm-30) REVERT: B 261 SER cc_start: 0.7820 (t) cc_final: 0.7455 (p) REVERT: C 53 MET cc_start: 0.8284 (mtm) cc_final: 0.7756 (mtt) REVERT: C 96 MET cc_start: 0.7631 (mmt) cc_final: 0.7062 (mmm) REVERT: C 155 TYR cc_start: 0.6321 (m-10) cc_final: 0.6051 (t80) REVERT: C 172 LYS cc_start: 0.8572 (ttpt) cc_final: 0.7891 (tttp) REVERT: C 311 LYS cc_start: 0.8903 (mttm) cc_final: 0.8545 (mtpp) REVERT: C 323 CYS cc_start: 0.8233 (m) cc_final: 0.7816 (t) REVERT: D 66 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6823 (tp30) REVERT: D 222 MET cc_start: 0.9020 (mtp) cc_final: 0.7950 (mmm) REVERT: E 2 HIS cc_start: 0.7109 (p-80) cc_final: 0.6837 (p-80) REVERT: E 23 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7370 (mmtt) REVERT: E 40 THR cc_start: 0.9246 (m) cc_final: 0.8837 (p) REVERT: E 131 GLU cc_start: 0.6703 (pm20) cc_final: 0.6433 (tp30) REVERT: E 186 GLU cc_start: 0.7857 (tt0) cc_final: 0.7258 (tm-30) REVERT: G 24 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7049 (tpt170) REVERT: H 24 CYS cc_start: 0.5014 (t) cc_final: 0.4599 (t) REVERT: J 16 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.7056 (tpt170) REVERT: J 18 SER cc_start: 0.8433 (p) cc_final: 0.8062 (p) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.8042 time to fit residues: 853.7508 Evaluate side-chains 454 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 373 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 GLN N 94 HIS N 173 ASN N 252 HIS Q 75 ASN R 57 GLN U 23 GLN U 26 GLN A 18 GLN A 173 ASN E 57 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 31772 Z= 0.386 Angle : 0.697 12.167 43226 Z= 0.357 Chirality : 0.047 1.426 4750 Planarity : 0.005 0.078 5514 Dihedral : 7.458 89.373 4322 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.45 % Rotamer: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -2.36 (0.13), residues: 3850 helix: -0.88 (0.11), residues: 1914 sheet: -2.49 (0.27), residues: 324 loop : -2.12 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 165 HIS 0.011 0.002 HIS D 198 PHE 0.024 0.002 PHE E 187 TYR 0.018 0.002 TYR A 434 ARG 0.009 0.001 ARG N 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 628 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 45 SER cc_start: 0.8883 (p) cc_final: 0.8597 (t) REVERT: N 195 MET cc_start: 0.8042 (mtp) cc_final: 0.7593 (ttm) REVERT: N 294 LEU cc_start: 0.9331 (tp) cc_final: 0.9100 (tp) REVERT: N 443 TRP cc_start: 0.7999 (t-100) cc_final: 0.7701 (t-100) REVERT: O 146 ILE cc_start: 0.8278 (mt) cc_final: 0.7907 (tp) REVERT: O 223 PHE cc_start: 0.6527 (m-80) cc_final: 0.6211 (m-80) REVERT: P 44 GLN cc_start: 0.8514 (tt0) cc_final: 0.7567 (mm110) REVERT: P 96 MET cc_start: 0.7963 (mmt) cc_final: 0.7670 (mmm) REVERT: P 172 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7890 (tttp) REVERT: P 287 LYS cc_start: 0.8569 (tttt) cc_final: 0.8205 (tptm) REVERT: P 303 LEU cc_start: 0.8760 (tp) cc_final: 0.8343 (tt) REVERT: P 311 LYS cc_start: 0.9088 (mttm) cc_final: 0.8872 (mtpp) REVERT: Q 66 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7314 (tp30) REVERT: Q 153 PHE cc_start: 0.8287 (t80) cc_final: 0.7984 (t80) REVERT: Q 166 ASN cc_start: 0.8477 (t0) cc_final: 0.7880 (t0) REVERT: R 23 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7456 (mmtt) REVERT: S 41 ASP cc_start: 0.8573 (p0) cc_final: 0.8168 (p0) REVERT: T 24 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7135 (tpt170) REVERT: V 70 LEU cc_start: 0.9023 (tp) cc_final: 0.8672 (tp) REVERT: W 33 ARG cc_start: 0.7089 (ttm170) cc_final: 0.6387 (mmp-170) REVERT: A 45 SER cc_start: 0.8705 (p) cc_final: 0.8127 (t) REVERT: A 48 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 146 ILE cc_start: 0.8762 (mm) cc_final: 0.8438 (tp) REVERT: B 223 PHE cc_start: 0.6411 (m-80) cc_final: 0.5997 (m-80) REVERT: B 243 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6469 (tm-30) REVERT: B 261 SER cc_start: 0.8014 (t) cc_final: 0.7809 (p) REVERT: C 96 MET cc_start: 0.7966 (mmt) cc_final: 0.7605 (mmm) REVERT: C 311 LYS cc_start: 0.9154 (mttm) cc_final: 0.8790 (mtpp) REVERT: C 315 MET cc_start: 0.8560 (mmt) cc_final: 0.7304 (mmp) REVERT: C 323 CYS cc_start: 0.8231 (m) cc_final: 0.7919 (t) REVERT: D 22 ASP cc_start: 0.6928 (m-30) cc_final: 0.6681 (m-30) REVERT: D 166 ASN cc_start: 0.8218 (m-40) cc_final: 0.7994 (t0) REVERT: D 222 MET cc_start: 0.9181 (mtp) cc_final: 0.8940 (mtp) REVERT: E 23 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7531 (mmtt) REVERT: E 131 GLU cc_start: 0.6847 (pm20) cc_final: 0.6476 (tp30) REVERT: G 24 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7110 (tpt170) REVERT: J 16 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7101 (tpt170) REVERT: J 18 SER cc_start: 0.8395 (p) cc_final: 0.8102 (p) outliers start: 1 outliers final: 1 residues processed: 628 average time/residue: 0.8563 time to fit residues: 858.4081 Evaluate side-chains 444 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 346 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 ASN Q 200 HIS R 53 ASN A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 31772 Z= 0.377 Angle : 0.665 12.465 43226 Z= 0.342 Chirality : 0.047 1.434 4750 Planarity : 0.005 0.055 5514 Dihedral : 7.177 89.332 4322 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3850 helix: -0.59 (0.11), residues: 1914 sheet: -2.29 (0.28), residues: 312 loop : -2.04 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 379 HIS 0.010 0.001 HIS Q 198 PHE 0.022 0.002 PHE C 274 TYR 0.017 0.002 TYR P 278 ARG 0.012 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 591 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 3.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 195 MET cc_start: 0.7888 (mtp) cc_final: 0.7614 (ttm) REVERT: O 146 ILE cc_start: 0.8374 (mt) cc_final: 0.7994 (tp) REVERT: O 223 PHE cc_start: 0.6565 (m-80) cc_final: 0.6355 (m-80) REVERT: P 96 MET cc_start: 0.8040 (mmt) cc_final: 0.7650 (mmm) REVERT: P 172 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8273 (tttp) REVERT: P 287 LYS cc_start: 0.8601 (tttt) cc_final: 0.8256 (tptm) REVERT: P 311 LYS cc_start: 0.9171 (mttm) cc_final: 0.8747 (mtpp) REVERT: Q 66 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7498 (tp30) REVERT: Q 75 ASN cc_start: 0.7226 (m-40) cc_final: 0.6946 (m-40) REVERT: Q 80 MET cc_start: 0.7635 (mmm) cc_final: 0.7346 (mmm) REVERT: Q 153 PHE cc_start: 0.8283 (t80) cc_final: 0.8000 (t80) REVERT: Q 166 ASN cc_start: 0.8338 (t0) cc_final: 0.7922 (t0) REVERT: R 2 HIS cc_start: 0.7458 (p-80) cc_final: 0.7239 (p-80) REVERT: R 23 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7485 (mmtt) REVERT: R 116 GLN cc_start: 0.6469 (tt0) cc_final: 0.6193 (tm-30) REVERT: S 41 ASP cc_start: 0.8631 (p0) cc_final: 0.8175 (p0) REVERT: T 24 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7141 (tpt170) REVERT: U 27 LEU cc_start: 0.7822 (tp) cc_final: 0.7557 (mt) REVERT: V 70 LEU cc_start: 0.9082 (tp) cc_final: 0.8741 (tp) REVERT: A 45 SER cc_start: 0.8874 (p) cc_final: 0.8400 (t) REVERT: B 146 ILE cc_start: 0.8809 (mm) cc_final: 0.8482 (tp) REVERT: B 223 PHE cc_start: 0.6725 (m-80) cc_final: 0.6347 (m-80) REVERT: B 261 SER cc_start: 0.7956 (t) cc_final: 0.7620 (p) REVERT: C 96 MET cc_start: 0.8055 (mmt) cc_final: 0.7617 (mmm) REVERT: C 172 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8376 (tttp) REVERT: C 311 LYS cc_start: 0.9226 (mttm) cc_final: 0.8846 (mtpp) REVERT: E 131 GLU cc_start: 0.6841 (pm20) cc_final: 0.6517 (tp30) REVERT: G 24 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7151 (tpt170) REVERT: J 16 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7219 (tpt170) REVERT: J 18 SER cc_start: 0.8407 (p) cc_final: 0.8126 (p) outliers start: 0 outliers final: 0 residues processed: 591 average time/residue: 0.9160 time to fit residues: 860.7996 Evaluate side-chains 427 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN Q 200 HIS R 57 GLN A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 31772 Z= 0.321 Angle : 0.624 11.577 43226 Z= 0.318 Chirality : 0.046 1.444 4750 Planarity : 0.005 0.076 5514 Dihedral : 6.992 89.265 4322 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3850 helix: -0.29 (0.12), residues: 1918 sheet: -2.19 (0.27), residues: 334 loop : -1.87 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 379 HIS 0.008 0.001 HIS D 41 PHE 0.018 0.001 PHE C 18 TYR 0.014 0.002 TYR B 341 ARG 0.008 0.001 ARG C 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 553 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 195 MET cc_start: 0.7986 (mtp) cc_final: 0.7608 (ttm) REVERT: O 146 ILE cc_start: 0.8479 (mt) cc_final: 0.8080 (tp) REVERT: P 96 MET cc_start: 0.7989 (mmt) cc_final: 0.7562 (mmm) REVERT: P 139 SER cc_start: 0.9135 (m) cc_final: 0.8907 (m) REVERT: P 287 LYS cc_start: 0.8574 (tttt) cc_final: 0.8305 (tptm) REVERT: P 311 LYS cc_start: 0.9177 (mttm) cc_final: 0.8793 (mtpp) REVERT: P 323 CYS cc_start: 0.8230 (m) cc_final: 0.8024 (t) REVERT: Q 75 ASN cc_start: 0.7399 (m-40) cc_final: 0.7069 (m-40) REVERT: Q 153 PHE cc_start: 0.8279 (t80) cc_final: 0.7967 (t80) REVERT: Q 166 ASN cc_start: 0.8402 (t0) cc_final: 0.7941 (t0) REVERT: Q 222 MET cc_start: 0.8642 (mtp) cc_final: 0.8111 (tpp) REVERT: R 2 HIS cc_start: 0.7412 (p-80) cc_final: 0.7192 (p-80) REVERT: R 23 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7596 (mmtt) REVERT: T 24 ARG cc_start: 0.8066 (ttm110) cc_final: 0.7095 (tpt170) REVERT: U 27 LEU cc_start: 0.7867 (tp) cc_final: 0.7576 (mt) REVERT: V 70 LEU cc_start: 0.9060 (tp) cc_final: 0.8665 (tp) REVERT: W 25 VAL cc_start: 0.8732 (t) cc_final: 0.8504 (p) REVERT: A 48 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 195 MET cc_start: 0.7885 (mtp) cc_final: 0.7479 (ttm) REVERT: B 146 ILE cc_start: 0.8860 (mm) cc_final: 0.8519 (tp) REVERT: B 261 SER cc_start: 0.8003 (t) cc_final: 0.7701 (p) REVERT: C 58 ASP cc_start: 0.8363 (t70) cc_final: 0.8122 (t70) REVERT: C 96 MET cc_start: 0.7994 (mmt) cc_final: 0.7592 (mmm) REVERT: C 172 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8370 (tttp) REVERT: C 240 MET cc_start: 0.8725 (mmp) cc_final: 0.8149 (mmt) REVERT: C 303 LEU cc_start: 0.8826 (tp) cc_final: 0.8487 (tt) REVERT: C 311 LYS cc_start: 0.9192 (mttm) cc_final: 0.8765 (mtpp) REVERT: E 23 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7472 (mmtt) REVERT: J 16 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7260 (tpt170) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.8666 time to fit residues: 782.8745 Evaluate side-chains 424 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 chunk 305 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 193 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 418 GLN Q 200 HIS R 53 ASN A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 31772 Z= 0.290 Angle : 0.602 11.552 43226 Z= 0.307 Chirality : 0.045 1.457 4750 Planarity : 0.005 0.094 5514 Dihedral : 6.894 88.870 4322 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3850 helix: -0.01 (0.12), residues: 1902 sheet: -2.21 (0.28), residues: 328 loop : -1.68 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 379 HIS 0.006 0.001 HIS Q 198 PHE 0.016 0.001 PHE A 64 TYR 0.028 0.002 TYR J 59 ARG 0.008 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7993 (mt-10) REVERT: N 195 MET cc_start: 0.7936 (mtp) cc_final: 0.7579 (ttm) REVERT: O 146 ILE cc_start: 0.8533 (mt) cc_final: 0.8181 (tp) REVERT: P 96 MET cc_start: 0.8017 (mmt) cc_final: 0.7548 (mmm) REVERT: P 122 THR cc_start: 0.9390 (t) cc_final: 0.9169 (m) REVERT: P 139 SER cc_start: 0.9159 (m) cc_final: 0.8958 (m) REVERT: P 172 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8312 (tttp) REVERT: P 240 MET cc_start: 0.8717 (mmp) cc_final: 0.8123 (mmt) REVERT: P 287 LYS cc_start: 0.8530 (tttt) cc_final: 0.8273 (tptm) REVERT: P 311 LYS cc_start: 0.9222 (mttm) cc_final: 0.9007 (mtpp) REVERT: P 315 MET cc_start: 0.8595 (mmt) cc_final: 0.8371 (mmt) REVERT: Q 43 MET cc_start: 0.8392 (tpp) cc_final: 0.8191 (tpp) REVERT: Q 75 ASN cc_start: 0.7356 (m-40) cc_final: 0.7087 (m-40) REVERT: Q 153 PHE cc_start: 0.8266 (t80) cc_final: 0.7973 (t80) REVERT: Q 166 ASN cc_start: 0.8402 (t0) cc_final: 0.8013 (t0) REVERT: Q 222 MET cc_start: 0.8782 (mtp) cc_final: 0.7741 (tpp) REVERT: R 23 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7531 (mmtt) REVERT: T 18 LEU cc_start: 0.8920 (tp) cc_final: 0.8719 (tp) REVERT: T 38 LEU cc_start: 0.9006 (mt) cc_final: 0.8776 (tp) REVERT: U 27 LEU cc_start: 0.7911 (tp) cc_final: 0.7530 (mt) REVERT: V 70 LEU cc_start: 0.9044 (tp) cc_final: 0.8667 (tp) REVERT: W 40 ASP cc_start: 0.7119 (m-30) cc_final: 0.6883 (m-30) REVERT: A 195 MET cc_start: 0.7938 (mtp) cc_final: 0.7501 (ttm) REVERT: B 146 ILE cc_start: 0.8833 (mm) cc_final: 0.8500 (tp) REVERT: B 261 SER cc_start: 0.7948 (t) cc_final: 0.7641 (p) REVERT: C 58 ASP cc_start: 0.8413 (t70) cc_final: 0.8117 (t70) REVERT: C 96 MET cc_start: 0.8046 (mmt) cc_final: 0.7577 (mmm) REVERT: C 172 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8354 (tttp) REVERT: C 240 MET cc_start: 0.8616 (mmp) cc_final: 0.7985 (mmt) REVERT: C 303 LEU cc_start: 0.8861 (tp) cc_final: 0.8509 (tt) REVERT: C 311 LYS cc_start: 0.9237 (mttm) cc_final: 0.8759 (mtpp) REVERT: G 18 LEU cc_start: 0.8849 (tp) cc_final: 0.8602 (tp) REVERT: J 16 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7247 (tpt170) REVERT: J 18 SER cc_start: 0.8496 (p) cc_final: 0.8192 (p) outliers start: 0 outliers final: 0 residues processed: 546 average time/residue: 0.7757 time to fit residues: 689.7635 Evaluate side-chains 426 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN N 215 HIS ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN Q 200 HIS R 57 GLN R 161 HIS A 126 GLN A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 31772 Z= 0.299 Angle : 0.603 11.507 43226 Z= 0.307 Chirality : 0.045 1.458 4750 Planarity : 0.004 0.052 5514 Dihedral : 6.844 89.074 4322 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3850 helix: 0.11 (0.12), residues: 1904 sheet: -2.23 (0.27), residues: 352 loop : -1.64 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 379 HIS 0.007 0.001 HIS D 41 PHE 0.025 0.002 PHE P 183 TYR 0.025 0.002 TYR J 59 ARG 0.006 0.001 ARG R 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 558 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8076 (mt-10) REVERT: N 195 MET cc_start: 0.7925 (mtp) cc_final: 0.7568 (ttm) REVERT: O 146 ILE cc_start: 0.8557 (mt) cc_final: 0.8244 (tp) REVERT: P 96 MET cc_start: 0.8068 (mmt) cc_final: 0.7590 (mmm) REVERT: P 172 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8280 (tttp) REVERT: P 287 LYS cc_start: 0.8508 (tttt) cc_final: 0.8251 (tptm) REVERT: P 311 LYS cc_start: 0.9231 (mttm) cc_final: 0.9006 (mtpp) REVERT: Q 43 MET cc_start: 0.8665 (tpp) cc_final: 0.8318 (tpp) REVERT: Q 75 ASN cc_start: 0.7510 (m-40) cc_final: 0.7221 (m-40) REVERT: Q 153 PHE cc_start: 0.8252 (t80) cc_final: 0.7988 (t80) REVERT: Q 166 ASN cc_start: 0.8402 (t0) cc_final: 0.7985 (t0) REVERT: Q 222 MET cc_start: 0.8801 (mtp) cc_final: 0.7801 (tpp) REVERT: R 23 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7652 (mmtt) REVERT: T 38 LEU cc_start: 0.9010 (mt) cc_final: 0.8790 (tp) REVERT: U 27 LEU cc_start: 0.7951 (tp) cc_final: 0.7534 (mt) REVERT: U 56 GLU cc_start: 0.7587 (tt0) cc_final: 0.7334 (mt-10) REVERT: V 70 LEU cc_start: 0.9070 (tp) cc_final: 0.8697 (tp) REVERT: W 40 ASP cc_start: 0.6661 (m-30) cc_final: 0.5475 (t0) REVERT: W 44 GLU cc_start: 0.7513 (mp0) cc_final: 0.7023 (mp0) REVERT: A 195 MET cc_start: 0.7871 (mtp) cc_final: 0.7463 (ttm) REVERT: B 143 GLN cc_start: 0.8656 (tp40) cc_final: 0.8297 (tp-100) REVERT: B 261 SER cc_start: 0.8080 (t) cc_final: 0.7763 (p) REVERT: C 58 ASP cc_start: 0.8388 (t70) cc_final: 0.8031 (m-30) REVERT: C 96 MET cc_start: 0.8045 (mmt) cc_final: 0.7554 (mmm) REVERT: C 139 SER cc_start: 0.9209 (m) cc_final: 0.8964 (m) REVERT: C 171 ASP cc_start: 0.9073 (t70) cc_final: 0.8759 (t70) REVERT: C 172 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8756 (tttt) REVERT: C 240 MET cc_start: 0.8770 (mmp) cc_final: 0.8064 (mmt) REVERT: C 303 LEU cc_start: 0.8878 (tp) cc_final: 0.8581 (tt) REVERT: C 311 LYS cc_start: 0.9217 (mttm) cc_final: 0.8790 (mtpp) REVERT: D 43 MET cc_start: 0.8743 (tpp) cc_final: 0.8414 (tpp) REVERT: G 18 LEU cc_start: 0.8964 (tp) cc_final: 0.8671 (tp) REVERT: J 16 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7299 (tpt170) REVERT: J 18 SER cc_start: 0.8545 (p) cc_final: 0.8226 (p) REVERT: J 40 ASP cc_start: 0.6827 (m-30) cc_final: 0.6515 (t70) outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.7962 time to fit residues: 719.2929 Evaluate side-chains 430 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 HIS R 53 ASN A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN C 312 GLN D 75 ASN E 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 31772 Z= 0.379 Angle : 0.652 11.521 43226 Z= 0.334 Chirality : 0.046 1.445 4750 Planarity : 0.005 0.064 5514 Dihedral : 6.968 89.589 4322 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.13), residues: 3850 helix: 0.00 (0.12), residues: 1920 sheet: -2.19 (0.28), residues: 328 loop : -1.85 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 379 HIS 0.008 0.001 HIS D 198 PHE 0.016 0.002 PHE P 18 TYR 0.027 0.002 TYR N 386 ARG 0.008 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 554 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8228 (mt-10) REVERT: N 195 MET cc_start: 0.8004 (mtp) cc_final: 0.7680 (ttm) REVERT: O 146 ILE cc_start: 0.8670 (mt) cc_final: 0.8394 (tp) REVERT: O 204 MET cc_start: 0.8934 (mtp) cc_final: 0.8682 (mtt) REVERT: P 96 MET cc_start: 0.8061 (mmt) cc_final: 0.7579 (mmm) REVERT: P 172 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8376 (tttp) REVERT: P 287 LYS cc_start: 0.8515 (tttt) cc_final: 0.8305 (tptm) REVERT: Q 43 MET cc_start: 0.8778 (tpp) cc_final: 0.8433 (tpp) REVERT: Q 75 ASN cc_start: 0.7508 (m-40) cc_final: 0.7222 (m-40) REVERT: Q 166 ASN cc_start: 0.8467 (t0) cc_final: 0.8077 (t0) REVERT: R 30 GLU cc_start: 0.8802 (mp0) cc_final: 0.8592 (mp0) REVERT: U 27 LEU cc_start: 0.7916 (tp) cc_final: 0.7550 (mt) REVERT: V 70 LEU cc_start: 0.9158 (tp) cc_final: 0.8763 (tp) REVERT: A 48 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8125 (mt-10) REVERT: B 261 SER cc_start: 0.8089 (t) cc_final: 0.7817 (p) REVERT: C 58 ASP cc_start: 0.8388 (t70) cc_final: 0.7943 (m-30) REVERT: C 96 MET cc_start: 0.8045 (mmt) cc_final: 0.7562 (mmm) REVERT: C 139 SER cc_start: 0.9072 (m) cc_final: 0.8820 (m) REVERT: C 171 ASP cc_start: 0.9096 (t70) cc_final: 0.8757 (t70) REVERT: C 172 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8716 (tttt) REVERT: C 315 MET cc_start: 0.8454 (mmt) cc_final: 0.8121 (mmm) REVERT: C 318 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8566 (mtp-110) REVERT: D 43 MET cc_start: 0.8763 (tpp) cc_final: 0.8392 (tpp) REVERT: G 18 LEU cc_start: 0.9026 (tp) cc_final: 0.8808 (tp) REVERT: J 16 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7269 (tpt170) REVERT: J 18 SER cc_start: 0.8547 (p) cc_final: 0.8272 (p) outliers start: 0 outliers final: 0 residues processed: 554 average time/residue: 0.7636 time to fit residues: 686.1458 Evaluate side-chains 418 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 3.9990 chunk 350 optimal weight: 0.4980 chunk 320 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 340 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 126 GLN N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN A 215 HIS ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN C 312 GLN E 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31772 Z= 0.196 Angle : 0.557 11.505 43226 Z= 0.281 Chirality : 0.045 1.491 4750 Planarity : 0.004 0.059 5514 Dihedral : 6.690 88.731 4322 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3850 helix: 0.41 (0.12), residues: 1912 sheet: -2.00 (0.28), residues: 326 loop : -1.44 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 379 HIS 0.005 0.001 HIS E 141 PHE 0.019 0.001 PHE P 183 TYR 0.025 0.001 TYR P 155 ARG 0.006 0.000 ARG P 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 567 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 566 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8061 (mt-10) REVERT: O 146 ILE cc_start: 0.8605 (mt) cc_final: 0.8321 (tp) REVERT: O 204 MET cc_start: 0.8879 (mtp) cc_final: 0.8647 (mtt) REVERT: O 344 VAL cc_start: 0.8416 (t) cc_final: 0.8168 (p) REVERT: P 96 MET cc_start: 0.7770 (mmt) cc_final: 0.7273 (mmm) REVERT: P 139 SER cc_start: 0.9036 (m) cc_final: 0.8764 (m) REVERT: P 240 MET cc_start: 0.8545 (mmp) cc_final: 0.8299 (mmm) REVERT: P 287 LYS cc_start: 0.8490 (tttt) cc_final: 0.8261 (tptm) REVERT: Q 43 MET cc_start: 0.8692 (tpp) cc_final: 0.8304 (tpp) REVERT: Q 75 ASN cc_start: 0.7393 (m-40) cc_final: 0.7145 (m-40) REVERT: Q 166 ASN cc_start: 0.8419 (t0) cc_final: 0.8018 (t0) REVERT: R 30 GLU cc_start: 0.8703 (mp0) cc_final: 0.8446 (mp0) REVERT: T 18 LEU cc_start: 0.8983 (tp) cc_final: 0.8758 (tp) REVERT: U 27 LEU cc_start: 0.7908 (tp) cc_final: 0.7528 (mt) REVERT: U 56 GLU cc_start: 0.7681 (tt0) cc_final: 0.7299 (mt-10) REVERT: V 70 LEU cc_start: 0.9074 (tp) cc_final: 0.8673 (tp) REVERT: W 40 ASP cc_start: 0.7280 (m-30) cc_final: 0.6814 (t0) REVERT: A 48 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 195 MET cc_start: 0.7951 (mtp) cc_final: 0.7740 (ttm) REVERT: B 261 SER cc_start: 0.8090 (t) cc_final: 0.7742 (p) REVERT: C 18 PHE cc_start: 0.8647 (m-10) cc_final: 0.7108 (t80) REVERT: C 96 MET cc_start: 0.7827 (mmt) cc_final: 0.7340 (mmm) REVERT: C 139 SER cc_start: 0.8990 (m) cc_final: 0.8720 (m) REVERT: C 171 ASP cc_start: 0.9021 (t70) cc_final: 0.8682 (t70) REVERT: C 172 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8333 (tttp) REVERT: C 311 LYS cc_start: 0.9304 (mtpt) cc_final: 0.9007 (mtpp) REVERT: C 315 MET cc_start: 0.8255 (mmt) cc_final: 0.8030 (mmt) REVERT: D 19 SER cc_start: 0.9111 (m) cc_final: 0.8002 (p) REVERT: D 43 MET cc_start: 0.8724 (tpp) cc_final: 0.8229 (tpp) REVERT: E 53 ASN cc_start: 0.8361 (m-40) cc_final: 0.7642 (t0) REVERT: G 18 LEU cc_start: 0.9005 (tp) cc_final: 0.8686 (tp) REVERT: G 38 LEU cc_start: 0.8946 (mt) cc_final: 0.8721 (tp) REVERT: J 16 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7247 (tpt170) REVERT: J 18 SER cc_start: 0.8500 (p) cc_final: 0.8175 (p) REVERT: J 40 ASP cc_start: 0.6757 (m-30) cc_final: 0.6543 (t70) outliers start: 1 outliers final: 0 residues processed: 567 average time/residue: 0.8109 time to fit residues: 753.9869 Evaluate side-chains 435 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 10.0000 chunk 360 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 378 optimal weight: 9.9990 chunk 348 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN D 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 31772 Z= 0.313 Angle : 0.611 11.458 43226 Z= 0.310 Chirality : 0.046 1.451 4750 Planarity : 0.004 0.050 5514 Dihedral : 6.745 89.979 4322 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.14), residues: 3850 helix: 0.34 (0.12), residues: 1916 sheet: -2.16 (0.28), residues: 310 loop : -1.49 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP P 379 HIS 0.006 0.001 HIS D 41 PHE 0.015 0.002 PHE P 183 TYR 0.026 0.002 TYR P 155 ARG 0.007 0.001 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 538 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 48 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8146 (mt-10) REVERT: O 146 ILE cc_start: 0.8683 (mt) cc_final: 0.8425 (tp) REVERT: O 204 MET cc_start: 0.8961 (mtp) cc_final: 0.8717 (mtt) REVERT: P 96 MET cc_start: 0.7852 (mmt) cc_final: 0.7384 (mmm) REVERT: P 139 SER cc_start: 0.9091 (m) cc_final: 0.8850 (m) REVERT: P 172 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8203 (tttp) REVERT: P 287 LYS cc_start: 0.8530 (tttt) cc_final: 0.8273 (tptm) REVERT: P 315 MET cc_start: 0.8369 (mmt) cc_final: 0.8160 (mmt) REVERT: Q 43 MET cc_start: 0.8790 (tpp) cc_final: 0.8433 (tpp) REVERT: Q 75 ASN cc_start: 0.7428 (m-40) cc_final: 0.7143 (m-40) REVERT: Q 166 ASN cc_start: 0.8462 (t0) cc_final: 0.8077 (t0) REVERT: T 18 LEU cc_start: 0.8978 (tp) cc_final: 0.8772 (tp) REVERT: U 27 LEU cc_start: 0.7836 (tp) cc_final: 0.7446 (mt) REVERT: V 70 LEU cc_start: 0.9177 (tp) cc_final: 0.8738 (tp) REVERT: W 40 ASP cc_start: 0.7372 (m-30) cc_final: 0.6438 (t0) REVERT: W 44 GLU cc_start: 0.7549 (mp0) cc_final: 0.7117 (mp0) REVERT: A 48 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 195 MET cc_start: 0.8015 (mtp) cc_final: 0.7723 (ttm) REVERT: B 261 SER cc_start: 0.8064 (t) cc_final: 0.7838 (p) REVERT: C 96 MET cc_start: 0.7882 (mmt) cc_final: 0.7388 (mmm) REVERT: C 139 SER cc_start: 0.9057 (m) cc_final: 0.8799 (m) REVERT: C 171 ASP cc_start: 0.9075 (t70) cc_final: 0.8747 (t70) REVERT: C 172 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8429 (tttm) REVERT: D 19 SER cc_start: 0.9167 (m) cc_final: 0.8115 (p) REVERT: D 43 MET cc_start: 0.8685 (tpp) cc_final: 0.8303 (tpp) REVERT: J 16 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7267 (tpt170) REVERT: J 18 SER cc_start: 0.8521 (p) cc_final: 0.8232 (p) REVERT: J 40 ASP cc_start: 0.6873 (m-30) cc_final: 0.6635 (t70) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.8158 time to fit residues: 721.9569 Evaluate side-chains 421 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 8.9990 chunk 321 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094510 restraints weight = 180523.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.097858 restraints weight = 77743.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099871 restraints weight = 41494.704| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31772 Z= 0.192 Angle : 0.554 11.513 43226 Z= 0.278 Chirality : 0.045 1.500 4750 Planarity : 0.004 0.056 5514 Dihedral : 6.557 88.452 4322 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3850 helix: 0.57 (0.12), residues: 1904 sheet: -2.06 (0.28), residues: 310 loop : -1.24 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP P 379 HIS 0.004 0.001 HIS E 141 PHE 0.020 0.001 PHE P 183 TYR 0.029 0.001 TYR C 155 ARG 0.008 0.000 ARG P 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12935.39 seconds wall clock time: 221 minutes 31.08 seconds (13291.08 seconds total)