Starting phenix.real_space_refine on Sat Nov 18 14:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcz_6630/11_2023/3jcz_6630.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 14724 2.51 5 N 4074 2.21 5 O 4374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 23286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Time building chain proxies: 11.41, per 1000 atoms: 0.49 Number of scatterers: 23286 At special positions: 0 Unit cell: (112.207, 115.395, 162.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4374 8.00 N 4074 7.00 C 14724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.27 Conformation dependent library (CDL) restraints added in 4.3 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 55.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.191A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.199A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.830A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY A 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.517A pdb=" N HIS A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.796A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 Processing helix chain 'A' and resid 434 through 442 removed outlier: 3.799A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR B 190 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.286A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.526A pdb=" N GLY B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.796A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 4.191A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY C 206 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP C 357 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 391 removed outlier: 3.687A pdb=" N TRP C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 421 removed outlier: 3.704A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 466 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'D' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 115 removed outlier: 4.199A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.830A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.284A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY D 206 " --> pdb=" O ILE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 425 Processing helix chain 'D' and resid 434 through 442 removed outlier: 3.799A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.617A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'E' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 182 " --> pdb=" O TRP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.141A pdb=" N TYR E 190 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.526A pdb=" N GLY E 206 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP E 357 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN E 463 " --> pdb=" O ARG E 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 466 " --> pdb=" O ARG E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.664A pdb=" N LYS F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 182 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR F 190 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.286A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY F 206 " --> pdb=" O ILE F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.517A pdb=" N HIS F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP F 357 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 440 " --> pdb=" O PHE F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 463 " --> pdb=" O ARG F 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 466 " --> pdb=" O ARG F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id= C, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 275 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 63 through 66 Processing sheet with id= F, first strand: chain 'B' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 275 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 63 through 66 Processing sheet with id= I, first strand: chain 'C' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 275 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 63 through 66 Processing sheet with id= L, first strand: chain 'D' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 275 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 63 through 66 Processing sheet with id= O, first strand: chain 'E' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 275 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 63 through 66 Processing sheet with id= R, first strand: chain 'F' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 275 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7529 1.33 - 1.45: 3147 1.45 - 1.57: 12916 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 23784 Sorted by residual: bond pdb=" CB PRO D 88 " pdb=" CG PRO D 88 " ideal model delta sigma weight residual 1.506 1.442 0.064 3.90e-02 6.57e+02 2.66e+00 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO E 88 " pdb=" CG PRO E 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO B 88 " pdb=" CG PRO B 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO C 88 " pdb=" CG PRO C 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.59e+00 ... (remaining 23779 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.52: 675 106.52 - 113.38: 13135 113.38 - 120.25: 8968 120.25 - 127.11: 9100 127.11 - 133.97: 240 Bond angle restraints: 32118 Sorted by residual: angle pdb=" CA PRO F 64 " pdb=" C PRO F 64 " pdb=" O PRO F 64 " ideal model delta sigma weight residual 123.16 119.66 3.50 1.49e+00 4.50e-01 5.53e+00 angle pdb=" CA PRO C 64 " pdb=" C PRO C 64 " pdb=" O PRO C 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.44e+00 angle pdb=" CA PRO E 64 " pdb=" C PRO E 64 " pdb=" O PRO E 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.41e+00 angle pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" O PRO B 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.41e+00 angle pdb=" CA PRO D 64 " pdb=" C PRO D 64 " pdb=" O PRO D 64 " ideal model delta sigma weight residual 123.16 119.70 3.46 1.49e+00 4.50e-01 5.38e+00 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.71: 13680 12.71 - 25.42: 488 25.42 - 38.13: 58 38.13 - 50.85: 18 50.85 - 63.56: 6 Dihedral angle restraints: 14250 sinusoidal: 5772 harmonic: 8478 Sorted by residual: dihedral pdb=" CA ALA D 375 " pdb=" C ALA D 375 " pdb=" N GLY D 376 " pdb=" CA GLY D 376 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ALA B 375 " pdb=" C ALA B 375 " pdb=" N GLY B 376 " pdb=" CA GLY B 376 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ALA A 375 " pdb=" C ALA A 375 " pdb=" N GLY A 376 " pdb=" CA GLY A 376 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 14247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1689 0.033 - 0.065: 1231 0.065 - 0.098: 405 0.098 - 0.131: 149 0.131 - 0.164: 18 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA PRO F 121 " pdb=" N PRO F 121 " pdb=" C PRO F 121 " pdb=" CB PRO F 121 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA PRO A 121 " pdb=" N PRO A 121 " pdb=" C PRO A 121 " pdb=" CB PRO A 121 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA PRO C 121 " pdb=" N PRO C 121 " pdb=" C PRO C 121 " pdb=" CB PRO C 121 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 3489 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 336 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO E 337 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 336 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO D 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 336 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO A 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.030 5.00e-02 4.00e+02 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5569 2.78 - 3.31: 22873 3.31 - 3.84: 37423 3.84 - 4.37: 48784 4.37 - 4.90: 80831 Nonbonded interactions: 195480 Sorted by model distance: nonbonded pdb=" OG SER F 83 " pdb=" ND1 HIS F 85 " model vdw 2.244 2.520 nonbonded pdb=" OG SER A 83 " pdb=" ND1 HIS A 85 " model vdw 2.245 2.520 nonbonded pdb=" OG SER D 83 " pdb=" ND1 HIS D 85 " model vdw 2.245 2.520 nonbonded pdb=" OG SER C 83 " pdb=" ND1 HIS C 85 " model vdw 2.245 2.520 nonbonded pdb=" OG SER B 83 " pdb=" ND1 HIS B 85 " model vdw 2.245 2.520 ... (remaining 195475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.010 Extract box with map and model: 5.000 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 57.260 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.008 0.064 23784 Z= 0.500 Angle : 0.692 6.537 32118 Z= 0.377 Chirality : 0.049 0.164 3492 Planarity : 0.005 0.054 4188 Dihedral : 7.317 63.557 8850 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.42 (0.13), residues: 2964 helix: -3.40 (0.09), residues: 1374 sheet: -3.08 (0.23), residues: 402 loop : -1.96 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 0.3823 time to fit residues: 336.7141 Evaluate side-chains 322 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 40.0000 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 HIS B 135 ASN B 391 HIS B 463 GLN C 205 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN E 391 HIS E 463 GLN F 205 GLN F 414 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23784 Z= 0.229 Angle : 0.573 5.371 32118 Z= 0.305 Chirality : 0.043 0.157 3492 Planarity : 0.005 0.041 4188 Dihedral : 5.565 61.061 3258 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.34 % Rotamer: Outliers : 2.80 % Allowed : 6.01 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.54 (0.14), residues: 2964 helix: -1.51 (0.12), residues: 1458 sheet: -2.56 (0.23), residues: 384 loop : -1.27 (0.18), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 409 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 46 residues processed: 435 average time/residue: 0.3664 time to fit residues: 247.0487 Evaluate side-chains 340 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2233 time to fit residues: 23.2434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 20.0000 chunk 82 optimal weight: 0.0270 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 0.0040 chunk 238 optimal weight: 9.9990 chunk 265 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.5854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 81 GLN B 463 GLN C 81 GLN C 135 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN F 81 GLN F 135 ASN F 205 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23784 Z= 0.166 Angle : 0.529 5.703 32118 Z= 0.278 Chirality : 0.042 0.150 3492 Planarity : 0.004 0.043 4188 Dihedral : 5.144 58.335 3258 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.68 % Allowed : 8.85 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.53 (0.15), residues: 2964 helix: -0.66 (0.13), residues: 1494 sheet: -2.10 (0.23), residues: 396 loop : -0.79 (0.20), residues: 1074 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 386 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 392 average time/residue: 0.3337 time to fit residues: 209.2971 Evaluate side-chains 320 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 310 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2047 time to fit residues: 7.5086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.0980 chunk 201 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 179 optimal weight: 0.0870 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 254 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23784 Z= 0.233 Angle : 0.554 6.739 32118 Z= 0.288 Chirality : 0.043 0.165 3492 Planarity : 0.004 0.048 4188 Dihedral : 5.028 57.135 3258 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.00 % Allowed : 10.22 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.18 (0.15), residues: 2964 helix: -0.35 (0.13), residues: 1536 sheet: -1.91 (0.24), residues: 396 loop : -0.68 (0.20), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 323 time to evaluate : 2.822 Fit side-chains outliers start: 50 outliers final: 40 residues processed: 337 average time/residue: 0.3354 time to fit residues: 183.3849 Evaluate side-chains 348 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 308 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2173 time to fit residues: 19.8811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN D 81 GLN E 205 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23784 Z= 0.318 Angle : 0.586 8.710 32118 Z= 0.305 Chirality : 0.045 0.160 3492 Planarity : 0.004 0.052 4188 Dihedral : 5.084 56.359 3258 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.52 % Allowed : 10.14 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.14 (0.15), residues: 2964 helix: -0.27 (0.13), residues: 1530 sheet: -1.79 (0.24), residues: 396 loop : -0.78 (0.20), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 314 time to evaluate : 2.856 Fit side-chains outliers start: 38 outliers final: 22 residues processed: 330 average time/residue: 0.3360 time to fit residues: 178.3530 Evaluate side-chains 326 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 304 time to evaluate : 2.640 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2267 time to fit residues: 12.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23784 Z= 0.289 Angle : 0.568 8.883 32118 Z= 0.295 Chirality : 0.045 0.158 3492 Planarity : 0.004 0.052 4188 Dihedral : 5.004 55.016 3258 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.84 % Allowed : 10.34 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.03 (0.15), residues: 2964 helix: -0.15 (0.13), residues: 1536 sheet: -1.67 (0.25), residues: 396 loop : -0.83 (0.20), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 303 time to evaluate : 2.561 Fit side-chains outliers start: 46 outliers final: 29 residues processed: 320 average time/residue: 0.3629 time to fit residues: 186.2795 Evaluate side-chains 313 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 284 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2223 time to fit residues: 16.5315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 162 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23784 Z= 0.269 Angle : 0.565 8.702 32118 Z= 0.293 Chirality : 0.044 0.156 3492 Planarity : 0.004 0.051 4188 Dihedral : 4.900 52.836 3258 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.88 % Allowed : 11.14 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.91 (0.15), residues: 2964 helix: -0.01 (0.13), residues: 1530 sheet: -1.58 (0.25), residues: 396 loop : -0.85 (0.20), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 311 time to evaluate : 2.910 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 318 average time/residue: 0.3419 time to fit residues: 176.0496 Evaluate side-chains 309 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 295 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2306 time to fit residues: 9.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23784 Z= 0.191 Angle : 0.527 7.927 32118 Z= 0.274 Chirality : 0.043 0.150 3492 Planarity : 0.004 0.048 4188 Dihedral : 4.709 50.712 3258 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.48 % Allowed : 11.82 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.69 (0.16), residues: 2964 helix: 0.18 (0.13), residues: 1548 sheet: -1.48 (0.26), residues: 396 loop : -0.79 (0.20), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 325 time to evaluate : 2.721 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 329 average time/residue: 0.3551 time to fit residues: 186.2022 Evaluate side-chains 312 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 302 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2069 time to fit residues: 7.7655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 238 optimal weight: 7.9990 chunk 249 optimal weight: 0.2980 chunk 263 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23784 Z= 0.138 Angle : 0.504 6.817 32118 Z= 0.262 Chirality : 0.041 0.141 3492 Planarity : 0.004 0.045 4188 Dihedral : 4.469 49.615 3258 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.44 % Allowed : 11.82 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.39 (0.16), residues: 2964 helix: 0.46 (0.13), residues: 1542 sheet: -1.32 (0.26), residues: 396 loop : -0.73 (0.20), residues: 1026 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 361 time to evaluate : 2.916 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 369 average time/residue: 0.3296 time to fit residues: 197.7988 Evaluate side-chains 323 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 317 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2145 time to fit residues: 6.3959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 30.0000 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23784 Z= 0.268 Angle : 0.565 10.797 32118 Z= 0.292 Chirality : 0.044 0.160 3492 Planarity : 0.004 0.053 4188 Dihedral : 4.582 47.584 3258 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.16 % Allowed : 12.94 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.50 (0.16), residues: 2964 helix: 0.36 (0.13), residues: 1536 sheet: -1.39 (0.26), residues: 396 loop : -0.72 (0.20), residues: 1032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 318 time to evaluate : 2.807 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 320 average time/residue: 0.3402 time to fit residues: 174.8552 Evaluate side-chains 310 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2022 time to fit residues: 3.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095619 restraints weight = 40050.127| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.13 r_work: 0.3148 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23784 Z= 0.156 Angle : 0.510 6.306 32118 Z= 0.267 Chirality : 0.042 0.143 3492 Planarity : 0.004 0.054 4188 Dihedral : 4.439 47.904 3258 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.20 % Allowed : 12.94 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.28 (0.16), residues: 2964 helix: 0.54 (0.13), residues: 1548 sheet: -1.29 (0.27), residues: 396 loop : -0.65 (0.20), residues: 1020 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5306.99 seconds wall clock time: 97 minutes 34.32 seconds (5854.32 seconds total)