Starting phenix.real_space_refine on Thu Sep 26 20:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/09_2024/6plo_20370.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 100 5.16 5 C 9230 2.51 5 N 2275 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, F, I, H, J Time building chain proxies: 6.45, per 1000 atoms: 0.46 Number of scatterers: 14165 At special positions: 0 Unit cell: (104.48, 105.786, 134.518, 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 100 16.00 O 2560 8.00 N 2275 7.00 C 9230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 36.7% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.656A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.579A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.573A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.691A pdb=" N GLY A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 304 through 324 removed outlier: 3.513A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.976A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 428 removed outlier: 3.566A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.199A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.656A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.580A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.573A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 266 through 285 removed outlier: 3.692A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 304 through 324 removed outlier: 3.513A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.975A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 428 removed outlier: 3.566A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.199A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.657A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.580A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 243 through 255 removed outlier: 3.573A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 Processing helix chain 'C' and resid 266 through 285 removed outlier: 3.691A pdb=" N GLY C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 304 through 324 removed outlier: 3.513A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.975A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 428 removed outlier: 3.566A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.198A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.657A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.580A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 238 through 243 Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.573A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 266 through 285 removed outlier: 3.691A pdb=" N GLY D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 304 through 324 removed outlier: 3.513A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.975A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 428 removed outlier: 3.566A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.198A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.657A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.580A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 243 through 255 removed outlier: 3.572A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'E' and resid 266 through 285 removed outlier: 3.691A pdb=" N GLY E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 304 through 324 removed outlier: 3.512A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 401 removed outlier: 3.975A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 428 removed outlier: 3.567A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.198A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 100 removed outlier: 6.327A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.327A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.327A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.327A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 100 removed outlier: 6.327A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 6.327A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 100 removed outlier: 6.326A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.326A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100 removed outlier: 6.327A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 6.327A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 632 hydrogen bonds defined for protein. 1806 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: 4.18 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4247 1.34 - 1.46: 3535 1.46 - 1.58: 6558 1.58 - 1.70: 0 1.70 - 1.83: 170 Bond restraints: 14510 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 18941 2.40 - 4.81: 601 4.81 - 7.21: 93 7.21 - 9.62: 35 9.62 - 12.02: 10 Bond angle restraints: 19680 Sorted by residual: angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.23 -10.69 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N VAL E 37 " pdb=" CA VAL E 37 " pdb=" C VAL E 37 " ideal model delta sigma weight residual 113.53 108.06 5.47 9.80e-01 1.04e+00 3.12e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 8613 21.71 - 43.42: 173 43.42 - 65.13: 10 65.13 - 86.85: 35 86.85 - 108.56: 20 Dihedral angle restraints: 8851 sinusoidal: 3736 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN D 261 " pdb=" C ASN D 261 " pdb=" N MET D 262 " pdb=" CA MET D 262 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN E 261 " pdb=" C ASN E 261 " pdb=" N MET E 262 " pdb=" CA MET E 262 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN B 261 " pdb=" C ASN B 261 " pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 8848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1574 0.055 - 0.110: 563 0.110 - 0.165: 93 0.165 - 0.220: 25 0.220 - 0.276: 5 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 411 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO C 411 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 411 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.036 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 163 2.61 - 3.18: 11171 3.18 - 3.75: 21403 3.75 - 4.33: 30620 4.33 - 4.90: 49789 Nonbonded interactions: 113146 Sorted by model distance: nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " model vdw 2.036 3.760 ... (remaining 113141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.010 Normalize map: mean=0, sd=1: 9.010 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: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.710 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.007 0.051 14510 Z= 0.478 Angle : 1.063 12.024 19680 Z= 0.542 Chirality : 0.058 0.276 2260 Planarity : 0.007 0.064 2435 Dihedral : 12.903 108.558 5525 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -5.29 (0.14), residues: 1710 helix: -4.71 (0.08), residues: 530 sheet: -2.76 (0.23), residues: 345 loop : -2.92 (0.17), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 302 HIS 0.004 0.002 HIS E 231 PHE 0.025 0.003 PHE C 115 TYR 0.024 0.003 TYR D 425 ARG 0.007 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.364 Fit side-chains REVERT: A 156 MET cc_start: 0.8587 (mmm) cc_final: 0.8137 (mmm) REVERT: A 426 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6313 (mptt) REVERT: B 63 SER cc_start: 0.8825 (t) cc_final: 0.8590 (m) REVERT: B 113 ASP cc_start: 0.9085 (p0) cc_final: 0.8795 (p0) REVERT: B 156 MET cc_start: 0.8611 (mmm) cc_final: 0.8081 (mmm) REVERT: B 426 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6306 (mmtm) REVERT: C 156 MET cc_start: 0.8607 (mmm) cc_final: 0.8149 (mmm) REVERT: C 173 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 426 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6227 (mptt) REVERT: D 43 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8801 (mtm180) REVERT: D 63 SER cc_start: 0.8777 (t) cc_final: 0.8575 (m) REVERT: D 156 MET cc_start: 0.8622 (mmm) cc_final: 0.8219 (mmm) REVERT: D 426 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6244 (mmtm) REVERT: E 156 MET cc_start: 0.8592 (mmm) cc_final: 0.8237 (mmm) REVERT: E 426 LYS cc_start: 0.7024 (ttmt) cc_final: 0.6205 (mmtt) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2740 time to fit residues: 171.8097 Evaluate side-chains 288 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 0.0970 chunk 99 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 141 ASN A 231 HIS A 235 GLN A 242 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 139 ASN B 141 ASN B 231 HIS B 235 GLN B 242 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 139 ASN C 141 ASN C 231 HIS C 235 GLN C 242 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 139 ASN D 141 ASN D 231 HIS D 235 GLN D 242 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 139 ASN E 141 ASN E 231 HIS E 235 GLN E 242 GLN ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14510 Z= 0.324 Angle : 0.766 6.061 19680 Z= 0.401 Chirality : 0.048 0.160 2260 Planarity : 0.006 0.041 2435 Dihedral : 11.708 74.677 2195 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.66 % Allowed : 10.20 % Favored : 86.14 % 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: -4.12 (0.16), residues: 1710 helix: -3.48 (0.14), residues: 560 sheet: -2.14 (0.24), residues: 350 loop : -2.32 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 84 HIS 0.004 0.001 HIS E 231 PHE 0.016 0.002 PHE D 322 TYR 0.013 0.002 TYR A 317 ARG 0.005 0.001 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 318 time to evaluate : 1.527 Fit side-chains REVERT: A 314 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7640 (tt) REVERT: A 317 TYR cc_start: 0.8754 (t80) cc_final: 0.8509 (t80) REVERT: A 415 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 416 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8432 (pt) REVERT: A 420 PHE cc_start: 0.7631 (t80) cc_final: 0.7148 (m-80) REVERT: A 426 LYS cc_start: 0.7144 (ttmt) cc_final: 0.6153 (mmtm) REVERT: B 63 SER cc_start: 0.8797 (t) cc_final: 0.8535 (m) REVERT: B 204 ILE cc_start: 0.9013 (pt) cc_final: 0.8796 (pt) REVERT: B 314 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7610 (tt) REVERT: B 415 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7633 (tt) REVERT: B 416 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8398 (pt) REVERT: B 420 PHE cc_start: 0.7716 (t80) cc_final: 0.7403 (t80) REVERT: B 426 LYS cc_start: 0.7248 (ttmt) cc_final: 0.6307 (mmtm) REVERT: C 179 MET cc_start: 0.8486 (mpp) cc_final: 0.8221 (mmm) REVERT: C 317 TYR cc_start: 0.8751 (t80) cc_final: 0.8489 (t80) REVERT: C 415 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7587 (tt) REVERT: C 426 LYS cc_start: 0.7121 (ttmt) cc_final: 0.6131 (mmtm) REVERT: D 415 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7708 (tt) REVERT: D 416 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (pt) REVERT: D 426 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6272 (mmtm) REVERT: E 301 ILE cc_start: 0.8860 (pt) cc_final: 0.8506 (mt) REVERT: E 415 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7655 (tt) REVERT: E 426 LYS cc_start: 0.7150 (ttmt) cc_final: 0.6161 (mmtm) outliers start: 56 outliers final: 18 residues processed: 349 average time/residue: 0.2106 time to fit residues: 106.9169 Evaluate side-chains 327 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 299 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 0.0040 chunk 153 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 62 ASN B 261 ASN C 62 ASN C 242 GLN C 261 ASN D 62 ASN D 242 GLN D 261 ASN E 62 ASN E 242 GLN E 261 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14510 Z= 0.161 Angle : 0.666 8.461 19680 Z= 0.340 Chirality : 0.046 0.144 2260 Planarity : 0.004 0.033 2435 Dihedral : 8.778 51.135 2195 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.55 % Allowed : 13.73 % Favored : 83.73 % 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: -3.35 (0.17), residues: 1710 helix: -2.53 (0.18), residues: 555 sheet: -1.55 (0.25), residues: 350 loop : -2.21 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.002 0.001 HIS E 217 PHE 0.016 0.001 PHE E 322 TYR 0.015 0.001 TYR B 317 ARG 0.004 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 1.627 Fit side-chains REVERT: A 229 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8333 (mtt-85) REVERT: A 301 ILE cc_start: 0.8628 (pt) cc_final: 0.8346 (mt) REVERT: A 416 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8410 (pt) REVERT: A 420 PHE cc_start: 0.7609 (t80) cc_final: 0.7176 (m-80) REVERT: A 426 LYS cc_start: 0.7092 (ttmt) cc_final: 0.6090 (mmtm) REVERT: B 63 SER cc_start: 0.8777 (t) cc_final: 0.8539 (m) REVERT: B 229 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8240 (mtt-85) REVERT: B 301 ILE cc_start: 0.8625 (pt) cc_final: 0.8319 (mt) REVERT: B 416 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8359 (pt) REVERT: B 426 LYS cc_start: 0.7201 (ttmt) cc_final: 0.6246 (mmtm) REVERT: C 301 ILE cc_start: 0.8549 (pt) cc_final: 0.8295 (mt) REVERT: C 426 LYS cc_start: 0.7055 (ttmt) cc_final: 0.6111 (mmtm) REVERT: D 229 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8200 (mtt-85) REVERT: D 301 ILE cc_start: 0.8607 (pt) cc_final: 0.8322 (mt) REVERT: D 416 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8305 (pt) REVERT: D 426 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6159 (mmtm) REVERT: E 229 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8186 (mtt-85) REVERT: E 301 ILE cc_start: 0.8728 (pt) cc_final: 0.8468 (mt) REVERT: E 426 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6127 (mmtm) outliers start: 39 outliers final: 22 residues processed: 335 average time/residue: 0.2733 time to fit residues: 130.9867 Evaluate side-chains 319 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 294 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 316 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN D 242 GLN E 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14510 Z= 0.359 Angle : 0.727 6.259 19680 Z= 0.368 Chirality : 0.048 0.150 2260 Planarity : 0.005 0.033 2435 Dihedral : 7.237 33.418 2195 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.31 % Allowed : 13.66 % Favored : 82.03 % 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: -2.92 (0.18), residues: 1710 helix: -2.04 (0.19), residues: 555 sheet: -1.22 (0.26), residues: 350 loop : -2.11 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 422 HIS 0.003 0.001 HIS A 125 PHE 0.021 0.002 PHE A 322 TYR 0.018 0.002 TYR B 175 ARG 0.008 0.001 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 290 time to evaluate : 1.626 Fit side-chains REVERT: A 204 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8798 (tt) REVERT: A 301 ILE cc_start: 0.8698 (pt) cc_final: 0.8405 (mt) REVERT: A 314 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 416 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8434 (pt) REVERT: A 426 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6197 (mmtm) REVERT: B 63 SER cc_start: 0.8822 (t) cc_final: 0.8567 (m) REVERT: B 229 ARG cc_start: 0.8652 (mmt90) cc_final: 0.8446 (mtt-85) REVERT: B 301 ILE cc_start: 0.8672 (pt) cc_final: 0.8348 (mt) REVERT: B 314 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 416 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8373 (pt) REVERT: B 426 LYS cc_start: 0.7228 (ttmt) cc_final: 0.6232 (mmtm) REVERT: C 204 ILE cc_start: 0.9028 (pt) cc_final: 0.8796 (tt) REVERT: C 229 ARG cc_start: 0.8630 (mmt90) cc_final: 0.8410 (mtt-85) REVERT: C 301 ILE cc_start: 0.8689 (pt) cc_final: 0.8426 (mt) REVERT: C 314 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7552 (tt) REVERT: C 426 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6234 (mmtm) REVERT: D 229 ARG cc_start: 0.8617 (mmt90) cc_final: 0.8377 (mtt-85) REVERT: D 301 ILE cc_start: 0.8626 (pt) cc_final: 0.8345 (mt) REVERT: D 416 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8339 (pt) REVERT: D 426 LYS cc_start: 0.7233 (ttmt) cc_final: 0.6163 (mmtm) REVERT: E 229 ARG cc_start: 0.8641 (mmt90) cc_final: 0.8361 (mtt-85) REVERT: E 301 ILE cc_start: 0.8758 (pt) cc_final: 0.8510 (mt) REVERT: E 426 LYS cc_start: 0.7223 (ttmt) cc_final: 0.6022 (mmtt) outliers start: 66 outliers final: 43 residues processed: 327 average time/residue: 0.2625 time to fit residues: 123.3020 Evaluate side-chains 325 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN C 242 GLN D 62 ASN D 242 GLN E 62 ASN E 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14510 Z= 0.357 Angle : 0.703 6.209 19680 Z= 0.358 Chirality : 0.047 0.144 2260 Planarity : 0.004 0.030 2435 Dihedral : 6.580 32.344 2195 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.51 % Allowed : 15.42 % Favored : 80.07 % 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: -2.59 (0.19), residues: 1710 helix: -1.73 (0.19), residues: 555 sheet: -0.92 (0.27), residues: 350 loop : -2.00 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 84 HIS 0.002 0.001 HIS C 231 PHE 0.036 0.002 PHE E 414 TYR 0.014 0.002 TYR C 175 ARG 0.005 0.001 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 288 time to evaluate : 1.632 Fit side-chains REVERT: A 204 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 301 ILE cc_start: 0.8692 (pt) cc_final: 0.8439 (mt) REVERT: A 314 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7481 (tt) REVERT: A 414 PHE cc_start: 0.8662 (t80) cc_final: 0.8388 (t80) REVERT: A 416 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8422 (pt) REVERT: A 426 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6185 (mmtm) REVERT: B 63 SER cc_start: 0.8838 (t) cc_final: 0.8571 (m) REVERT: B 301 ILE cc_start: 0.8698 (pt) cc_final: 0.8418 (mt) REVERT: B 314 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7451 (tt) REVERT: B 416 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8362 (pt) REVERT: B 426 LYS cc_start: 0.7249 (ttmt) cc_final: 0.6239 (mmtm) REVERT: C 204 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8777 (tt) REVERT: C 229 ARG cc_start: 0.8651 (mmt90) cc_final: 0.8388 (mtt-85) REVERT: C 301 ILE cc_start: 0.8704 (pt) cc_final: 0.8434 (mt) REVERT: C 426 LYS cc_start: 0.7172 (ttmt) cc_final: 0.6219 (mmtm) REVERT: D 229 ARG cc_start: 0.8646 (mmt90) cc_final: 0.8423 (mtt-85) REVERT: D 301 ILE cc_start: 0.8656 (pt) cc_final: 0.8394 (mt) REVERT: D 416 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8307 (pt) REVERT: D 426 LYS cc_start: 0.7243 (ttmt) cc_final: 0.6169 (mmtm) REVERT: E 204 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8805 (tt) REVERT: E 301 ILE cc_start: 0.8764 (pt) cc_final: 0.8540 (mt) REVERT: E 426 LYS cc_start: 0.7236 (ttmt) cc_final: 0.6019 (mmtt) outliers start: 69 outliers final: 43 residues processed: 325 average time/residue: 0.2634 time to fit residues: 123.1466 Evaluate side-chains 321 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 0.0370 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN C 242 GLN E 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14510 Z= 0.153 Angle : 0.643 9.206 19680 Z= 0.320 Chirality : 0.044 0.136 2260 Planarity : 0.004 0.029 2435 Dihedral : 5.594 30.345 2195 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.25 % Allowed : 15.88 % Favored : 79.87 % 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: -2.26 (0.19), residues: 1710 helix: -1.37 (0.20), residues: 555 sheet: -0.65 (0.27), residues: 350 loop : -1.92 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.001 0.001 HIS A 231 PHE 0.030 0.002 PHE B 414 TYR 0.012 0.001 TYR D 317 ARG 0.006 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 312 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8954 (pt) cc_final: 0.8728 (tt) REVERT: A 314 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7470 (tt) REVERT: A 414 PHE cc_start: 0.8504 (t80) cc_final: 0.8262 (t80) REVERT: A 416 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8413 (pt) REVERT: A 426 LYS cc_start: 0.7081 (ttmt) cc_final: 0.6102 (mmtm) REVERT: B 63 SER cc_start: 0.8814 (t) cc_final: 0.8578 (m) REVERT: B 301 ILE cc_start: 0.8572 (pt) cc_final: 0.8347 (mt) REVERT: B 314 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7401 (tt) REVERT: B 416 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (pt) REVERT: B 426 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6148 (mmtm) REVERT: C 149 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8438 (m) REVERT: C 204 ILE cc_start: 0.8955 (pt) cc_final: 0.8732 (tt) REVERT: C 229 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8356 (mtt-85) REVERT: C 301 ILE cc_start: 0.8588 (pt) cc_final: 0.8376 (mt) REVERT: C 314 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7484 (tt) REVERT: C 426 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6112 (mmtm) REVERT: D 159 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7497 (mmtt) REVERT: D 301 ILE cc_start: 0.8554 (pt) cc_final: 0.8346 (mt) REVERT: D 416 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8309 (pt) REVERT: D 426 LYS cc_start: 0.7128 (ttmt) cc_final: 0.6044 (mmtm) REVERT: E 159 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7567 (mmtt) REVERT: E 204 ILE cc_start: 0.8968 (pt) cc_final: 0.8728 (tt) REVERT: E 262 MET cc_start: 0.4247 (mpp) cc_final: 0.4013 (mpp) REVERT: E 426 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6054 (mmtm) outliers start: 65 outliers final: 42 residues processed: 341 average time/residue: 0.2750 time to fit residues: 133.0963 Evaluate side-chains 327 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 277 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 0.0060 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14510 Z= 0.161 Angle : 0.632 8.029 19680 Z= 0.315 Chirality : 0.044 0.141 2260 Planarity : 0.004 0.028 2435 Dihedral : 5.250 27.498 2195 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.58 % Allowed : 15.88 % Favored : 79.54 % 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: -1.97 (0.19), residues: 1710 helix: -1.10 (0.21), residues: 555 sheet: -0.40 (0.28), residues: 350 loop : -1.83 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.003 0.001 HIS B 125 PHE 0.024 0.002 PHE B 414 TYR 0.013 0.001 TYR B 317 ARG 0.008 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 282 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 204 ILE cc_start: 0.8954 (pt) cc_final: 0.8732 (tt) REVERT: A 314 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7471 (tt) REVERT: A 416 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8419 (pt) REVERT: A 426 LYS cc_start: 0.6996 (ttmt) cc_final: 0.6076 (mmtm) REVERT: B 32 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: B 63 SER cc_start: 0.8840 (t) cc_final: 0.8597 (m) REVERT: B 159 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7518 (mmtt) REVERT: B 301 ILE cc_start: 0.8550 (pt) cc_final: 0.8316 (mt) REVERT: B 314 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7417 (tt) REVERT: B 398 ARG cc_start: 0.6136 (mmt90) cc_final: 0.5448 (mmt180) REVERT: B 416 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8385 (pt) REVERT: B 426 LYS cc_start: 0.7081 (ttmt) cc_final: 0.6037 (mmtm) REVERT: C 149 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8466 (m) REVERT: C 204 ILE cc_start: 0.8935 (pt) cc_final: 0.8725 (tt) REVERT: C 301 ILE cc_start: 0.8583 (pt) cc_final: 0.8368 (mt) REVERT: C 314 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7467 (tt) REVERT: C 426 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6047 (mmtm) REVERT: D 159 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7474 (mmtt) REVERT: D 301 ILE cc_start: 0.8540 (pt) cc_final: 0.8327 (mt) REVERT: D 416 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (pt) REVERT: D 426 LYS cc_start: 0.7061 (ttmt) cc_final: 0.5984 (mmtm) REVERT: E 159 LYS cc_start: 0.7738 (mtpt) cc_final: 0.7536 (mmtt) REVERT: E 204 ILE cc_start: 0.8963 (pt) cc_final: 0.8725 (tt) REVERT: E 262 MET cc_start: 0.4329 (mpp) cc_final: 0.4120 (mpp) REVERT: E 426 LYS cc_start: 0.7068 (ttmt) cc_final: 0.6002 (mmtm) outliers start: 70 outliers final: 50 residues processed: 316 average time/residue: 0.2647 time to fit residues: 120.4021 Evaluate side-chains 331 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 272 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 0.0020 chunk 31 optimal weight: 0.0270 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN B 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14510 Z= 0.137 Angle : 0.621 7.986 19680 Z= 0.308 Chirality : 0.043 0.141 2260 Planarity : 0.003 0.027 2435 Dihedral : 4.896 24.220 2195 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.73 % Allowed : 16.99 % Favored : 79.28 % 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: -1.68 (0.19), residues: 1710 helix: -0.75 (0.21), residues: 555 sheet: -0.23 (0.28), residues: 350 loop : -1.75 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.002 0.001 HIS A 125 PHE 0.022 0.001 PHE B 414 TYR 0.012 0.001 TYR D 317 ARG 0.008 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 279 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 204 ILE cc_start: 0.8947 (pt) cc_final: 0.8713 (tt) REVERT: A 249 LEU cc_start: 0.7707 (mt) cc_final: 0.7426 (mp) REVERT: A 314 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 416 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8446 (pt) REVERT: A 426 LYS cc_start: 0.6930 (ttmt) cc_final: 0.6029 (mmtm) REVERT: B 63 SER cc_start: 0.8856 (t) cc_final: 0.8628 (m) REVERT: B 314 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7352 (tt) REVERT: B 398 ARG cc_start: 0.6005 (mmt90) cc_final: 0.5409 (mmt180) REVERT: B 426 LYS cc_start: 0.6983 (ttmt) cc_final: 0.6078 (mmtm) REVERT: C 149 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8422 (m) REVERT: C 204 ILE cc_start: 0.8925 (pt) cc_final: 0.8702 (tt) REVERT: C 314 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7385 (tt) REVERT: C 426 LYS cc_start: 0.7025 (ttmt) cc_final: 0.5984 (mmtm) REVERT: D 262 MET cc_start: 0.4472 (mpp) cc_final: 0.4271 (mpp) REVERT: D 314 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7494 (tt) REVERT: D 416 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (pt) REVERT: D 426 LYS cc_start: 0.7003 (ttmt) cc_final: 0.6035 (mmtm) REVERT: E 204 ILE cc_start: 0.8947 (pt) cc_final: 0.8721 (tt) REVERT: E 426 LYS cc_start: 0.7024 (ttmt) cc_final: 0.5981 (mmtm) outliers start: 57 outliers final: 39 residues processed: 311 average time/residue: 0.2610 time to fit residues: 117.6183 Evaluate side-chains 302 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 255 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.0010 chunk 144 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14510 Z= 0.141 Angle : 0.626 8.598 19680 Z= 0.306 Chirality : 0.043 0.142 2260 Planarity : 0.003 0.032 2435 Dihedral : 4.748 22.270 2195 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.46 % Allowed : 16.86 % Favored : 79.67 % 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: -1.49 (0.19), residues: 1710 helix: -0.52 (0.21), residues: 555 sheet: -0.14 (0.29), residues: 350 loop : -1.69 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 84 HIS 0.002 0.001 HIS E 125 PHE 0.034 0.002 PHE D 414 TYR 0.013 0.001 TYR B 317 ARG 0.008 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 266 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8506 (tt) REVERT: A 204 ILE cc_start: 0.8942 (pt) cc_final: 0.8719 (tt) REVERT: A 249 LEU cc_start: 0.7659 (mt) cc_final: 0.7416 (mp) REVERT: A 314 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 416 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 426 LYS cc_start: 0.6912 (ttmt) cc_final: 0.5986 (mmtm) REVERT: B 63 SER cc_start: 0.8862 (t) cc_final: 0.8627 (m) REVERT: B 243 MET cc_start: 0.8116 (mtt) cc_final: 0.7875 (mtt) REVERT: B 314 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7342 (tt) REVERT: B 398 ARG cc_start: 0.5965 (mmt90) cc_final: 0.5444 (mmt180) REVERT: B 426 LYS cc_start: 0.6983 (ttmt) cc_final: 0.6061 (mmtm) REVERT: C 149 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8405 (m) REVERT: C 204 ILE cc_start: 0.8921 (pt) cc_final: 0.8704 (tt) REVERT: C 314 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7376 (tt) REVERT: C 426 LYS cc_start: 0.6932 (ttmt) cc_final: 0.5917 (mmtm) REVERT: D 262 MET cc_start: 0.4400 (mpp) cc_final: 0.4194 (mpp) REVERT: D 314 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7454 (tt) REVERT: D 426 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6017 (mmtm) REVERT: E 204 ILE cc_start: 0.8941 (pt) cc_final: 0.8721 (tt) REVERT: E 314 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7538 (tt) REVERT: E 426 LYS cc_start: 0.6977 (ttmt) cc_final: 0.5952 (mmtm) outliers start: 53 outliers final: 34 residues processed: 300 average time/residue: 0.2556 time to fit residues: 111.6244 Evaluate side-chains 293 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 251 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN C 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14510 Z= 0.167 Angle : 0.642 7.917 19680 Z= 0.313 Chirality : 0.044 0.146 2260 Planarity : 0.004 0.034 2435 Dihedral : 4.751 22.324 2195 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.88 % Allowed : 17.25 % Favored : 79.87 % 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: -1.38 (0.20), residues: 1710 helix: -0.39 (0.22), residues: 555 sheet: -0.06 (0.29), residues: 350 loop : -1.66 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 84 HIS 0.002 0.001 HIS B 125 PHE 0.033 0.002 PHE A 414 TYR 0.012 0.001 TYR A 144 ARG 0.008 0.000 ARG A 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8471 (tt) REVERT: A 204 ILE cc_start: 0.8939 (pt) cc_final: 0.8725 (tt) REVERT: A 249 LEU cc_start: 0.7682 (mt) cc_final: 0.7456 (mp) REVERT: A 314 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7479 (tt) REVERT: A 426 LYS cc_start: 0.6922 (ttmt) cc_final: 0.5993 (mmtm) REVERT: B 63 SER cc_start: 0.8843 (t) cc_final: 0.8617 (m) REVERT: B 314 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (tt) REVERT: B 398 ARG cc_start: 0.5940 (mmt90) cc_final: 0.5445 (mmt180) REVERT: B 426 LYS cc_start: 0.6964 (ttmt) cc_final: 0.6036 (mmtm) REVERT: C 149 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8423 (m) REVERT: C 204 ILE cc_start: 0.8926 (pt) cc_final: 0.8725 (tt) REVERT: C 314 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7379 (tt) REVERT: C 426 LYS cc_start: 0.6965 (ttmt) cc_final: 0.5948 (mmtm) REVERT: D 262 MET cc_start: 0.4662 (mpp) cc_final: 0.4455 (mpp) REVERT: D 314 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7466 (tt) REVERT: D 426 LYS cc_start: 0.6989 (ttmt) cc_final: 0.5999 (mmtm) REVERT: E 204 ILE cc_start: 0.8939 (pt) cc_final: 0.8733 (tt) REVERT: E 314 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7569 (tt) REVERT: E 426 LYS cc_start: 0.6983 (ttmt) cc_final: 0.5952 (mmtm) outliers start: 44 outliers final: 34 residues processed: 289 average time/residue: 0.2908 time to fit residues: 122.8648 Evaluate side-chains 298 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 0.0870 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131018 restraints weight = 17462.413| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.29 r_work: 0.3281 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14510 Z= 0.138 Angle : 0.634 8.248 19680 Z= 0.307 Chirality : 0.043 0.143 2260 Planarity : 0.003 0.033 2435 Dihedral : 4.620 22.701 2195 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.94 % Allowed : 17.19 % Favored : 79.87 % 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 (0.20), residues: 1710 helix: -0.24 (0.22), residues: 555 sheet: -0.05 (0.28), residues: 350 loop : -1.63 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 84 HIS 0.001 0.001 HIS C 125 PHE 0.034 0.002 PHE D 414 TYR 0.011 0.001 TYR B 317 ARG 0.010 0.000 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.73 seconds wall clock time: 65 minutes 20.70 seconds (3920.70 seconds total)