Starting phenix.real_space_refine on Mon Jul 6 13:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk6_19262/07_2026/8rk6_19262.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 105 5.16 5 C 22554 2.51 5 N 6324 2.21 5 O 6891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2099 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4278 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 30, 'TRANS': 523} Chain: "M" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5581 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 40, 'TRANS': 686} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Restraints were copied for chains: A, E, B, F, D, G Time building chain proxies: 8.53, per 1000 atoms: 0.24 Number of scatterers: 35877 At special positions: 0 Unit cell: (207.566, 211.734, 200.898, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 3 26.01 S 105 16.00 O 6891 8.00 N 6324 7.00 C 22554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=51, symmetry=0 Number of additional bonds: simple=51, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8472 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 57 sheets defined 15.3% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 75 through 80 removed outlier: 3.860A pdb=" N LEU I 80 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 83 No H-bonds generated for 'chain 'I' and resid 81 through 83' Processing helix chain 'I' and resid 129 through 135 removed outlier: 3.541A pdb=" N ASP I 135 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 241 through 250 Processing helix chain 'I' and resid 251 through 255 Processing helix chain 'C' and resid 20 through 27 removed outlier: 3.646A pdb=" N ILE C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 4.128A pdb=" N ALA C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'C' and resid 420 through 435 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.614A pdb=" N VAL C 525 " --> pdb=" O PRO C 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 63 removed outlier: 3.535A pdb=" N LYS M 62 " --> pdb=" O GLY M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 91 Processing helix chain 'M' and resid 136 through 139 Processing helix chain 'M' and resid 153 through 164 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.567A pdb=" N MET M 175 " --> pdb=" O ARG M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 191 Processing helix chain 'M' and resid 203 through 216 removed outlier: 3.653A pdb=" N PHE M 207 " --> pdb=" O SER M 203 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 295 removed outlier: 3.547A pdb=" N SER M 294 " --> pdb=" O ALA M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 327 Processing helix chain 'M' and resid 338 through 341 Processing helix chain 'M' and resid 421 through 429 removed outlier: 3.758A pdb=" N LEU M 425 " --> pdb=" O PRO M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 436 removed outlier: 4.002A pdb=" N LEU M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 504 through 508 Processing helix chain 'M' and resid 587 through 591 Processing helix chain 'M' and resid 634 through 639 Processing helix chain 'M' and resid 683 through 691 removed outlier: 3.811A pdb=" N ASP M 687 " --> pdb=" O PRO M 683 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET M 688 " --> pdb=" O LEU M 684 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA M 689 " --> pdb=" O ALA M 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.860A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.540A pdb=" N ASP A 135 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.646A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 4.128A pdb=" N ALA B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'B' and resid 420 through 435 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.613A pdb=" N VAL B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.535A pdb=" N LYS D 62 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 136 through 139 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.567A pdb=" N MET D 175 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 191 Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.654A pdb=" N PHE D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.547A pdb=" N SER D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 327 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 421 through 429 removed outlier: 3.758A pdb=" N LEU D 425 " --> pdb=" O PRO D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 436 removed outlier: 4.002A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 587 through 591 Processing helix chain 'D' and resid 634 through 639 Processing helix chain 'D' and resid 683 through 691 removed outlier: 3.812A pdb=" N ASP D 687 " --> pdb=" O PRO D 683 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET D 688 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 75 through 80 removed outlier: 3.860A pdb=" N LEU E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 129 through 135 removed outlier: 3.541A pdb=" N ASP E 135 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 241 through 250 Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'F' and resid 20 through 27 removed outlier: 3.646A pdb=" N ILE F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP F 25 " --> pdb=" O THR F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 removed outlier: 4.129A pdb=" N ALA F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 239 Processing helix chain 'F' and resid 249 through 252 Processing helix chain 'F' and resid 420 through 435 Processing helix chain 'F' and resid 469 through 474 Processing helix chain 'F' and resid 521 through 525 removed outlier: 3.614A pdb=" N VAL F 525 " --> pdb=" O PRO F 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.535A pdb=" N LYS G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 91 Processing helix chain 'G' and resid 136 through 139 Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.568A pdb=" N MET G 175 " --> pdb=" O ARG G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 191 Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.654A pdb=" N PHE G 207 " --> pdb=" O SER G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 295 removed outlier: 3.547A pdb=" N SER G 294 " --> pdb=" O ALA G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 327 Processing helix chain 'G' and resid 338 through 341 Processing helix chain 'G' and resid 421 through 429 removed outlier: 3.757A pdb=" N LEU G 425 " --> pdb=" O PRO G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 436 removed outlier: 4.002A pdb=" N LEU G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 508 Processing helix chain 'G' and resid 587 through 591 Processing helix chain 'G' and resid 634 through 639 Processing helix chain 'G' and resid 683 through 691 removed outlier: 3.811A pdb=" N ASP G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET G 688 " --> pdb=" O LEU G 684 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA G 689 " --> pdb=" O ALA G 685 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'I' and resid 37 through 39 removed outlier: 3.525A pdb=" N ILE I 37 " --> pdb=" O PHE I 44 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ILE I 43 " --> pdb=" O ARG I 27 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER I 29 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP I 108 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP I 96 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL I 106 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS I 98 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA I 104 " --> pdb=" O HIS I 98 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE I 112 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL I 128 " --> pdb=" O ILE I 112 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER I 122 " --> pdb=" O PRO I 118 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'I' and resid 56 through 58 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 58 current: chain 'M' and resid 331 through 336 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 331 through 336 current: chain 'M' and resid 358 through 370 removed outlier: 5.775A pdb=" N THR M 381 " --> pdb=" O GLY M 366 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE M 368 " --> pdb=" O THR M 379 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR M 379 " --> pdb=" O ILE M 368 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'I' and resid 165 through 167 removed outlier: 7.231A pdb=" N ASN I 203 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN I 211 " --> pdb=" O HIS I 218 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 83 through 88 removed outlier: 7.263A pdb=" N GLU C 84 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR C 170 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY C 86 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 165 " --> pdb=" O TRP C 157 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 92 through 100 removed outlier: 3.910A pdb=" N GLU C 135 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 120 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 175 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 175 through 176 current: chain 'C' and resid 215 through 222 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 215 through 222 current: chain 'C' and resid 291 through 299 removed outlier: 6.795A pdb=" N ASP C 305 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL C 299 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 303 through 306 current: chain 'C' and resid 341 through 350 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 341 through 350 current: chain 'C' and resid 409 through 417 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 409 through 417 current: chain 'C' and resid 533 through 536 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 533 through 536 current: chain 'C' and resid 553 through 561 Processing sheet with id=7, first strand: chain 'C' and resid 195 through 199 removed outlier: 4.346A pdb=" N ASN C 196 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 208 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 198 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 206 " --> pdb=" O LEU C 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=9, first strand: chain 'C' and resid 482 through 484 Processing sheet with id=10, first strand: chain 'M' and resid 13 through 24 removed outlier: 7.568A pdb=" N TYR M 14 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE M 16 " --> pdb=" O GLY M 107 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY M 107 " --> pdb=" O PHE M 16 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR M 101 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR M 110 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY M 66 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY M 65 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU M 56 " --> pdb=" O GLY M 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE M 52 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 48 " --> pdb=" O VAL M 73 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'M' and resid 37 through 44 removed outlier: 5.280A pdb=" N THR M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA M 34 " --> pdb=" O THR M 38 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS M 30 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE M 44 " --> pdb=" O GLU M 28 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU M 28 " --> pdb=" O ILE M 44 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL M 29 " --> pdb=" O ARG M 124 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG M 124 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA M 31 " --> pdb=" O LEU M 122 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'M' and resid 141 through 144 Processing sheet with id=13, first strand: chain 'M' and resid 217 through 221 Processing sheet with id=14, first strand: chain 'M' and resid 281 through 287 removed outlier: 7.222A pdb=" N GLN M 268 " --> pdb=" O GLU M 301 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE M 303 " --> pdb=" O GLN M 268 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE M 270 " --> pdb=" O ILE M 303 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'M' and resid 415 through 419 removed outlier: 7.184A pdb=" N SER M 442 " --> pdb=" O THR M 565 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR M 565 " --> pdb=" O SER M 442 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU M 444 " --> pdb=" O ASP M 563 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'M' and resid 457 through 464 removed outlier: 4.035A pdb=" N GLY M 474 " --> pdb=" O LEU M 460 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP M 462 " --> pdb=" O ASP M 472 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASP M 472 " --> pdb=" O ASP M 462 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 471 through 476 current: chain 'M' and resid 584 through 585 Processing sheet with id=17, first strand: chain 'M' and resid 481 through 484 removed outlier: 6.931A pdb=" N THR M 481 " --> pdb=" O ALA M 502 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA M 502 " --> pdb=" O THR M 481 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY M 493 " --> pdb=" O ARG M 537 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG M 537 " --> pdb=" O GLY M 493 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR M 532 " --> pdb=" O VAL M 526 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL M 526 " --> pdb=" O THR M 532 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR M 534 " --> pdb=" O ASP M 524 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'M' and resid 616 through 617 Processing sheet with id=19, first strand: chain 'M' and resid 622 through 623 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 622 through 623 current: chain 'M' and resid 668 through 675 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 668 through 675 current: chain 'M' and resid 707 through 708 No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.525A pdb=" N ILE A 37 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ILE A 43 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N SER A 29 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP A 108 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP A 96 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL A 106 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS A 98 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA A 104 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A 112 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 128 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'A' and resid 56 through 58 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 58 current: chain 'D' and resid 331 through 336 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 331 through 336 current: chain 'D' and resid 358 through 370 removed outlier: 5.775A pdb=" N THR D 381 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE D 368 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR D 379 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'A' and resid 165 through 167 removed outlier: 7.231A pdb=" N ASN A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 211 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'B' and resid 83 through 88 removed outlier: 7.263A pdb=" N GLU B 84 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR B 170 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY B 86 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 165 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'B' and resid 92 through 100 removed outlier: 3.910A pdb=" N GLU B 135 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 120 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'B' and resid 175 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 175 through 176 current: chain 'B' and resid 215 through 222 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 215 through 222 current: chain 'B' and resid 291 through 299 removed outlier: 6.795A pdb=" N ASP B 305 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL B 299 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 303 through 306 current: chain 'B' and resid 341 through 350 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 341 through 350 current: chain 'B' and resid 409 through 417 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 409 through 417 current: chain 'B' and resid 533 through 536 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 533 through 536 current: chain 'B' and resid 553 through 561 Processing sheet with id=26, first strand: chain 'B' and resid 195 through 199 removed outlier: 4.345A pdb=" N ASN B 196 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 208 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 198 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 206 " --> pdb=" O LEU B 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=26 Processing sheet with id=27, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=28, first strand: chain 'B' and resid 482 through 484 Processing sheet with id=29, first strand: chain 'D' and resid 13 through 24 removed outlier: 7.569A pdb=" N TYR D 14 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 16 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D 107 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR D 101 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR D 110 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N GLY D 66 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 65 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU D 56 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 52 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 48 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 37 through 44 removed outlier: 5.281A pdb=" N THR D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA D 34 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS D 30 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE D 44 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU D 28 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL D 29 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG D 124 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 31 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'D' and resid 141 through 144 Processing sheet with id=32, first strand: chain 'D' and resid 217 through 221 Processing sheet with id=33, first strand: chain 'D' and resid 281 through 287 removed outlier: 7.222A pdb=" N GLN D 268 " --> pdb=" O GLU D 301 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE D 303 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 270 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'D' and resid 415 through 419 removed outlier: 7.184A pdb=" N SER D 442 " --> pdb=" O THR D 565 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR D 565 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU D 444 " --> pdb=" O ASP D 563 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'D' and resid 457 through 464 removed outlier: 4.035A pdb=" N GLY D 474 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP D 462 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASP D 472 " --> pdb=" O ASP D 462 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 471 through 476 current: chain 'D' and resid 584 through 585 Processing sheet with id=36, first strand: chain 'D' and resid 481 through 484 removed outlier: 6.931A pdb=" N THR D 481 " --> pdb=" O ALA D 502 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA D 502 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY D 493 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 537 " --> pdb=" O GLY D 493 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 532 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL D 526 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR D 534 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'D' and resid 616 through 617 Processing sheet with id=38, first strand: chain 'D' and resid 622 through 623 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 622 through 623 current: chain 'D' and resid 668 through 675 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 668 through 675 current: chain 'D' and resid 707 through 708 No H-bonds generated for sheet with id=38 Processing sheet with id=39, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.525A pdb=" N ILE E 37 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N ILE E 43 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N SER E 29 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP E 108 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP E 96 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL E 106 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N HIS E 98 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA E 104 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE E 112 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL E 128 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'E' and resid 56 through 58 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 58 current: chain 'G' and resid 331 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 331 through 336 current: chain 'G' and resid 358 through 370 removed outlier: 5.775A pdb=" N THR G 381 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE G 368 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR G 379 " --> pdb=" O ILE G 368 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'E' and resid 165 through 167 removed outlier: 7.231A pdb=" N ASN E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN E 211 " --> pdb=" O HIS E 218 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'F' and resid 83 through 88 removed outlier: 7.263A pdb=" N GLU F 84 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR F 170 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY F 86 " --> pdb=" O THR F 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 165 " --> pdb=" O TRP F 157 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'F' and resid 92 through 100 removed outlier: 3.910A pdb=" N GLU F 135 " --> pdb=" O ASN F 100 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR F 120 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'F' and resid 175 through 176 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 175 through 176 current: chain 'F' and resid 215 through 222 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 215 through 222 current: chain 'F' and resid 291 through 299 removed outlier: 6.795A pdb=" N ASP F 305 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL F 299 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY F 303 " --> pdb=" O VAL F 299 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 303 through 306 current: chain 'F' and resid 341 through 350 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 341 through 350 current: chain 'F' and resid 409 through 417 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 409 through 417 current: chain 'F' and resid 533 through 536 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 533 through 536 current: chain 'F' and resid 553 through 561 Processing sheet with id=45, first strand: chain 'F' and resid 195 through 199 removed outlier: 4.345A pdb=" N ASN F 196 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 208 " --> pdb=" O ASN F 196 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 198 " --> pdb=" O GLN F 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN F 206 " --> pdb=" O LEU F 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=45 Processing sheet with id=46, first strand: chain 'F' and resid 364 through 365 Processing sheet with id=47, first strand: chain 'F' and resid 482 through 484 Processing sheet with id=48, first strand: chain 'G' and resid 13 through 24 removed outlier: 7.569A pdb=" N TYR G 14 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE G 16 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 107 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR G 101 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR G 110 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY G 66 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY G 65 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU G 56 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE G 52 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 48 " --> pdb=" O VAL G 73 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'G' and resid 37 through 44 removed outlier: 5.280A pdb=" N THR G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA G 34 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS G 30 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 44 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU G 28 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL G 29 " --> pdb=" O ARG G 124 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG G 124 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA G 31 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'G' and resid 141 through 144 Processing sheet with id=51, first strand: chain 'G' and resid 217 through 221 Processing sheet with id=52, first strand: chain 'G' and resid 281 through 287 removed outlier: 7.222A pdb=" N GLN G 268 " --> pdb=" O GLU G 301 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE G 303 " --> pdb=" O GLN G 268 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 270 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'G' and resid 415 through 419 removed outlier: 7.184A pdb=" N SER G 442 " --> pdb=" O THR G 565 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR G 565 " --> pdb=" O SER G 442 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU G 444 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'G' and resid 457 through 464 removed outlier: 4.035A pdb=" N GLY G 474 " --> pdb=" O LEU G 460 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP G 462 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASP G 472 " --> pdb=" O ASP G 462 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 471 through 476 current: chain 'G' and resid 584 through 585 Processing sheet with id=55, first strand: chain 'G' and resid 481 through 484 removed outlier: 6.930A pdb=" N THR G 481 " --> pdb=" O ALA G 502 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA G 502 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY G 493 " --> pdb=" O ARG G 537 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG G 537 " --> pdb=" O GLY G 493 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR G 532 " --> pdb=" O VAL G 526 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL G 526 " --> pdb=" O THR G 532 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR G 534 " --> pdb=" O ASP G 524 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'G' and resid 616 through 617 Processing sheet with id=57, first strand: chain 'G' and resid 622 through 623 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 622 through 623 current: chain 'G' and resid 668 through 675 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 668 through 675 current: chain 'G' and resid 707 through 708 No H-bonds generated for sheet with id=57 801 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12213 1.34 - 1.46: 7805 1.46 - 1.58: 16489 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 36666 Sorted by residual: bond pdb=" C PRO G 399 " pdb=" N PRO G 400 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" C PRO M 399 " pdb=" N PRO M 400 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.65e+00 bond pdb=" C PRO D 399 " pdb=" N PRO D 400 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" N PRO C 52 " pdb=" CD PRO C 52 " ideal model delta sigma weight residual 1.473 1.489 -0.016 1.40e-02 5.10e+03 1.23e+00 bond pdb=" N PRO F 52 " pdb=" CD PRO F 52 " ideal model delta sigma weight residual 1.473 1.488 -0.015 1.40e-02 5.10e+03 1.12e+00 ... (remaining 36661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 48950 1.24 - 2.47: 760 2.47 - 3.71: 237 3.71 - 4.94: 42 4.94 - 6.18: 15 Bond angle restraints: 50004 Sorted by residual: angle pdb=" N GLY M 727 " pdb=" CA GLY M 727 " pdb=" C GLY M 727 " ideal model delta sigma weight residual 113.24 107.06 6.18 1.31e+00 5.83e-01 2.23e+01 angle pdb=" N GLY G 727 " pdb=" CA GLY G 727 " pdb=" C GLY G 727 " ideal model delta sigma weight residual 113.24 107.08 6.16 1.31e+00 5.83e-01 2.21e+01 angle pdb=" N GLY D 727 " pdb=" CA GLY D 727 " pdb=" C GLY D 727 " ideal model delta sigma weight residual 113.24 107.10 6.14 1.31e+00 5.83e-01 2.20e+01 angle pdb=" N ILE D 650 " pdb=" CA ILE D 650 " pdb=" C ILE D 650 " ideal model delta sigma weight residual 111.88 108.61 3.27 1.06e+00 8.90e-01 9.51e+00 angle pdb=" N ILE M 650 " pdb=" CA ILE M 650 " pdb=" C ILE M 650 " ideal model delta sigma weight residual 111.88 108.62 3.26 1.06e+00 8.90e-01 9.45e+00 ... (remaining 49999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19826 17.92 - 35.84: 1539 35.84 - 53.76: 271 53.76 - 71.67: 60 71.67 - 89.59: 24 Dihedral angle restraints: 21720 sinusoidal: 8448 harmonic: 13272 Sorted by residual: dihedral pdb=" CA ASN B 74 " pdb=" C ASN B 74 " pdb=" N ARG B 75 " pdb=" CA ARG B 75 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ASN F 74 " pdb=" C ASN F 74 " pdb=" N ARG F 75 " pdb=" CA ARG F 75 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ASN C 74 " pdb=" C ASN C 74 " pdb=" N ARG C 75 " pdb=" CA ARG C 75 " ideal model delta harmonic sigma weight residual 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 21717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5038 0.076 - 0.152: 569 0.152 - 0.228: 0 0.228 - 0.304: 0 0.304 - 0.381: 3 Chirality restraints: 5610 Sorted by residual: chirality pdb=" CA LEU G 726 " pdb=" N LEU G 726 " pdb=" C LEU G 726 " pdb=" CB LEU G 726 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU D 726 " pdb=" N LEU D 726 " pdb=" C LEU D 726 " pdb=" CB LEU D 726 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA LEU M 726 " pdb=" N LEU M 726 " pdb=" C LEU M 726 " pdb=" CB LEU M 726 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5607 not shown) Planarity restraints: 6576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 51 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO F 52 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 52 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 52 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 51 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 52 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 51 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO B 52 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.036 5.00e-02 4.00e+02 ... (remaining 6573 not shown) Histogram of nonbonded interaction distances: 0.28 - 1.20: 78 1.20 - 2.13: 405 2.13 - 3.05: 24508 3.05 - 3.98: 89385 3.98 - 4.90: 164461 Warning: very small nonbonded interaction distances. Nonbonded interactions: 278837 Sorted by model distance: nonbonded pdb=" C PRO I 48 " pdb=" CZ ARG B 400 " model vdw 0.278 3.500 nonbonded pdb=" CZ ARG C 400 " pdb=" C PRO E 48 " model vdw 0.278 3.500 nonbonded pdb=" C PRO A 48 " pdb=" CZ ARG F 400 " model vdw 0.278 3.500 nonbonded pdb=" CE2 TRP M 402 " pdb=" CE LYS E 264 " model vdw 0.370 3.660 nonbonded pdb=" CE LYS I 264 " pdb=" CE2 TRP D 402 " model vdw 0.370 3.660 ... (remaining 278832 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: 0.11 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.690 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: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.029 1.140 36717 Z= 2.911 Angle : 0.455 6.181 50004 Z= 0.245 Chirality : 0.043 0.381 5610 Planarity : 0.004 0.066 6576 Dihedral : 13.292 89.593 13248 Min Nonbonded Distance : 0.278 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4641 helix: 2.21 (0.26), residues: 447 sheet: 0.23 (0.15), residues: 1221 loop : -0.86 (0.12), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 415 TYR 0.010 0.001 TYR F 102 PHE 0.008 0.001 PHE G 724 TRP 0.006 0.001 TRP C 99 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (36666) covalent geometry : angle 0.45490 / 0.24 (50004) hydrogen bonds : bond 0.24019 / 16.50 ( 801) hydrogen bonds : angle 9.69238 / 6.86 ( 2097) Misc. bond : bond 0.78051 / 52.42 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 979 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 35 ARG cc_start: 0.6007 (ptp-170) cc_final: 0.4881 (ttp80) REVERT: C 83 MET cc_start: 0.3691 (mpp) cc_final: 0.2979 (ttp) REVERT: C 223 TYR cc_start: 0.7285 (m-80) cc_final: 0.7051 (m-80) REVERT: C 226 ASP cc_start: 0.5960 (p0) cc_final: 0.5437 (p0) REVERT: C 277 ASP cc_start: 0.6574 (m-30) cc_final: 0.6360 (m-30) REVERT: C 289 PHE cc_start: 0.4548 (m-80) cc_final: 0.2904 (m-80) REVERT: C 308 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6279 (mmt-90) REVERT: C 360 MET cc_start: 0.6742 (mmt) cc_final: 0.6536 (mmt) REVERT: C 419 MET cc_start: 0.6755 (mtt) cc_final: 0.6546 (mtt) REVERT: C 502 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6779 (pm20) REVERT: C 563 ARG cc_start: 0.5829 (tpt170) cc_final: 0.5176 (mtm180) REVERT: M 15 TYR cc_start: 0.7203 (m-10) cc_final: 0.6968 (m-10) REVERT: M 118 LYS cc_start: 0.3477 (tttt) cc_final: 0.3047 (tttm) REVERT: M 120 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5266 (mt-10) REVERT: M 134 PRO cc_start: 0.6853 (Cg_exo) cc_final: 0.6454 (Cg_endo) REVERT: M 198 TRP cc_start: 0.5562 (t-100) cc_final: 0.4008 (p-90) REVERT: M 418 ILE cc_start: 0.7826 (pt) cc_final: 0.7515 (tp) REVERT: A 37 ILE cc_start: 0.8250 (mp) cc_final: 0.8038 (mt) REVERT: A 45 ARG cc_start: 0.5323 (mmt-90) cc_final: 0.5017 (mtm180) REVERT: A 97 MET cc_start: 0.7479 (ptm) cc_final: 0.7226 (ptm) REVERT: A 99 TYR cc_start: 0.8092 (t80) cc_final: 0.7820 (t80) REVERT: A 204 TYR cc_start: 0.6447 (m-80) cc_final: 0.5714 (m-80) REVERT: B 83 MET cc_start: 0.2847 (mpp) cc_final: 0.2215 (ttm) REVERT: B 277 ASP cc_start: 0.7334 (m-30) cc_final: 0.7124 (m-30) REVERT: B 340 THR cc_start: 0.7397 (p) cc_final: 0.7105 (t) REVERT: B 389 LEU cc_start: 0.6762 (tp) cc_final: 0.6517 (mt) REVERT: B 419 MET cc_start: 0.6937 (mtt) cc_final: 0.6670 (mtp) REVERT: B 502 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6584 (mt-10) REVERT: D 118 LYS cc_start: 0.3534 (tttt) cc_final: 0.2450 (ttpp) REVERT: D 233 LEU cc_start: 0.7219 (mt) cc_final: 0.7001 (mt) REVERT: D 418 ILE cc_start: 0.7882 (pt) cc_final: 0.7473 (tt) REVERT: D 534 THR cc_start: 0.7891 (m) cc_final: 0.7593 (p) REVERT: E 95 TYR cc_start: 0.7808 (m-80) cc_final: 0.7537 (m-80) REVERT: E 154 HIS cc_start: 0.7785 (p90) cc_final: 0.7572 (p-80) REVERT: E 241 LEU cc_start: 0.7294 (mt) cc_final: 0.7060 (mp) REVERT: F 223 TYR cc_start: 0.7521 (m-80) cc_final: 0.7165 (m-80) REVERT: F 419 MET cc_start: 0.7296 (mtt) cc_final: 0.6966 (mtp) REVERT: G 33 ARG cc_start: 0.6062 (ttp-110) cc_final: 0.5459 (ptt180) REVERT: G 46 SER cc_start: 0.7971 (p) cc_final: 0.7671 (t) REVERT: G 118 LYS cc_start: 0.3947 (tttt) cc_final: 0.2657 (ttpp) REVERT: G 325 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6850 (ttmm) REVERT: G 414 VAL cc_start: 0.7585 (t) cc_final: 0.7219 (m) REVERT: G 418 ILE cc_start: 0.7864 (pt) cc_final: 0.7346 (tt) REVERT: G 627 SER cc_start: 0.6711 (t) cc_final: 0.6189 (p) REVERT: G 714 ASP cc_start: 0.5140 (t0) cc_final: 0.4716 (t0) outliers start: 0 outliers final: 0 residues processed: 979 average time/residue: 0.2166 time to fit residues: 335.7696 Evaluate side-chains 519 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.2980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 HIS I 203 ASN C 331 GLN M 8 GLN M 49 GLN M 256 GLN ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 HIS B 199 GLN B 438 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN E 98 HIS G 49 GLN G 256 GLN G 281 GLN G 371 ASN G 501 ASN G 580 ASN G 711 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.162585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140193 restraints weight = 71070.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141672 restraints weight = 43723.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142266 restraints weight = 30310.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142892 restraints weight = 24147.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143973 restraints weight = 19341.148| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 36717 Z= 0.225 Angle : 0.782 20.801 50004 Z= 0.410 Chirality : 0.049 0.230 5610 Planarity : 0.014 0.383 6576 Dihedral : 4.734 61.044 5142 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 2.41 % Allowed : 10.34 % Favored : 87.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4641 helix: 0.82 (0.24), residues: 477 sheet: 0.05 (0.15), residues: 1308 loop : -0.92 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.002 ARG F 227 TYR 0.021 0.002 TYR I 194 PHE 0.067 0.003 PHE E 208 TRP 0.033 0.002 TRP G 12 HIS 0.009 0.001 HIS F 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (36666) covalent geometry : angle 0.78175 / 0.41 (50004) hydrogen bonds : bond 0.05259 / 3.58 ( 801) hydrogen bonds : angle 7.33966 / 5.17 ( 2097) Misc. bond : bond 0.01436 / 0.96 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 551 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 35 ARG cc_start: 0.5887 (ptp-170) cc_final: 0.4798 (ttp80) REVERT: C 83 MET cc_start: 0.3970 (mpp) cc_final: 0.2964 (ttp) REVERT: C 223 TYR cc_start: 0.7293 (m-80) cc_final: 0.7075 (m-80) REVERT: C 438 GLN cc_start: 0.7813 (tt0) cc_final: 0.7579 (tt0) REVERT: C 502 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6752 (pm20) REVERT: C 563 ARG cc_start: 0.5938 (tpt170) cc_final: 0.5211 (mtm-85) REVERT: M 105 TYR cc_start: 0.8157 (t80) cc_final: 0.7655 (t80) REVERT: M 118 LYS cc_start: 0.3519 (tttt) cc_final: 0.2900 (tttm) REVERT: M 170 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7221 (tp) REVERT: M 198 TRP cc_start: 0.6067 (t-100) cc_final: 0.4167 (p-90) REVERT: M 627 SER cc_start: 0.7301 (t) cc_final: 0.6781 (p) REVERT: A 45 ARG cc_start: 0.5579 (mmt-90) cc_final: 0.5287 (mtm180) REVERT: A 99 TYR cc_start: 0.8193 (t80) cc_final: 0.7839 (t80) REVERT: A 135 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7288 (t0) REVERT: B 83 MET cc_start: 0.3099 (mpp) cc_final: 0.2119 (ttm) REVERT: B 472 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.5855 (mtt180) REVERT: B 502 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6532 (mt-10) REVERT: D 33 ARG cc_start: 0.6187 (ttp-110) cc_final: 0.5274 (ptt180) REVERT: D 79 ASP cc_start: 0.5731 (t70) cc_final: 0.5413 (t70) REVERT: D 118 LYS cc_start: 0.2978 (tttt) cc_final: 0.2560 (ttpp) REVERT: D 170 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7404 (tp) REVERT: D 489 PRO cc_start: 0.8111 (Cg_exo) cc_final: 0.7790 (Cg_endo) REVERT: E 114 ASP cc_start: 0.6444 (t0) cc_final: 0.6205 (t0) REVERT: F 223 TYR cc_start: 0.7565 (m-80) cc_final: 0.7274 (m-80) REVERT: F 419 MET cc_start: 0.7432 (mtt) cc_final: 0.6770 (mtt) REVERT: F 472 ARG cc_start: 0.7108 (ttp-170) cc_final: 0.6177 (mtt180) REVERT: G 33 ARG cc_start: 0.6051 (ttp-110) cc_final: 0.5757 (ptt180) REVERT: G 46 SER cc_start: 0.7891 (p) cc_final: 0.7620 (t) REVERT: G 118 LYS cc_start: 0.4096 (tttt) cc_final: 0.3402 (mttm) REVERT: G 253 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6431 (pt0) REVERT: G 701 ARG cc_start: 0.7602 (ptp-170) cc_final: 0.7363 (ptm160) REVERT: G 714 ASP cc_start: 0.5762 (t0) cc_final: 0.5505 (t0) outliers start: 91 outliers final: 61 residues processed: 606 average time/residue: 0.2096 time to fit residues: 205.5567 Evaluate side-chains 503 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 438 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 392 THR Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 253 GLU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 392 THR Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 643 ILE Chi-restraints excluded: chain G residue 678 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 428 optimal weight: 0.8980 chunk 427 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 337 optimal weight: 50.0000 chunk 303 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 chunk 437 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN M 289 ASN M 371 ASN M 661 GLN A 14 GLN A 20 GLN A 98 HIS A 154 HIS A 198 GLN B 124 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN E 14 GLN E 159 ASN E 203 ASN F 124 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134372 restraints weight = 70733.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136127 restraints weight = 41599.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136401 restraints weight = 27321.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137022 restraints weight = 22278.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137524 restraints weight = 18111.622| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 36717 Z= 0.212 Angle : 0.724 15.623 50004 Z= 0.379 Chirality : 0.048 0.254 5610 Planarity : 0.012 0.377 6576 Dihedral : 5.248 137.654 5142 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 3.30 % Allowed : 12.61 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.12), residues: 4641 helix: 0.34 (0.23), residues: 492 sheet: -0.14 (0.14), residues: 1293 loop : -1.15 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG A 206 TYR 0.026 0.002 TYR C 385 PHE 0.052 0.003 PHE B 237 TRP 0.044 0.002 TRP G 12 HIS 0.015 0.002 HIS I 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (36666) covalent geometry : angle 0.72426 / 0.38 (50004) hydrogen bonds : bond 0.04750 / 3.21 ( 801) hydrogen bonds : angle 6.65808 / 4.73 ( 2097) Misc. bond : bond 0.01240 / 0.80 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 473 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 MET cc_start: 0.4083 (mpp) cc_final: 0.3143 (ttp) REVERT: C 360 MET cc_start: 0.7066 (mmt) cc_final: 0.6768 (mmt) REVERT: C 489 ASP cc_start: 0.5965 (p0) cc_final: 0.5665 (p0) REVERT: C 502 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6667 (mt-10) REVERT: C 509 ARG cc_start: 0.5878 (ttp80) cc_final: 0.5289 (tmm160) REVERT: C 563 ARG cc_start: 0.6265 (tpt170) cc_final: 0.5802 (mtm180) REVERT: M 25 LYS cc_start: 0.7640 (mptt) cc_final: 0.7434 (mmtm) REVERT: M 105 TYR cc_start: 0.8272 (t80) cc_final: 0.7400 (t80) REVERT: M 118 LYS cc_start: 0.3629 (tttt) cc_final: 0.2911 (tttm) REVERT: M 170 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.6742 (tp) REVERT: A 45 ARG cc_start: 0.6001 (mmt-90) cc_final: 0.5422 (mtm110) REVERT: A 99 TYR cc_start: 0.8227 (t80) cc_final: 0.7804 (t80) REVERT: A 135 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 247 ASP cc_start: 0.6554 (m-30) cc_final: 0.6208 (m-30) REVERT: B 83 MET cc_start: 0.3058 (mpp) cc_final: 0.2429 (ttm) REVERT: B 351 MET cc_start: 0.8172 (mmm) cc_final: 0.7953 (mmm) REVERT: B 502 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6622 (mt-10) REVERT: D 33 ARG cc_start: 0.6666 (ttp-110) cc_final: 0.5271 (ptt180) REVERT: D 118 LYS cc_start: 0.2707 (tttt) cc_final: 0.1869 (ttmm) REVERT: E 195 VAL cc_start: 0.8542 (t) cc_final: 0.8226 (m) REVERT: F 472 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.6083 (mtt180) REVERT: G 33 ARG cc_start: 0.6302 (ttp-110) cc_final: 0.5639 (ptt180) REVERT: G 118 LYS cc_start: 0.3868 (tttt) cc_final: 0.3581 (mtpt) REVERT: G 246 ASP cc_start: 0.6207 (t0) cc_final: 0.5869 (t70) REVERT: G 289 ASN cc_start: 0.8272 (m-40) cc_final: 0.8056 (m110) REVERT: G 701 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.7442 (ptm160) REVERT: G 714 ASP cc_start: 0.5933 (t0) cc_final: 0.5722 (t70) outliers start: 125 outliers final: 88 residues processed: 558 average time/residue: 0.2087 time to fit residues: 190.2589 Evaluate side-chains 489 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 399 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 337 ASP Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 515 VAL Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 505 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 157 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 50.0000 chunk 159 optimal weight: 0.9990 chunk 340 optimal weight: 50.0000 chunk 315 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 198 optimal weight: 0.1980 chunk 335 optimal weight: 50.0000 chunk 170 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 14 GLN I 136 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN M 288 ASN M 289 ASN A 154 HIS ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN F 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132036 restraints weight = 70101.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133426 restraints weight = 40352.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133724 restraints weight = 28086.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134119 restraints weight = 22784.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134369 restraints weight = 20232.926| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 36717 Z= 0.189 Angle : 0.684 15.441 50004 Z= 0.356 Chirality : 0.046 0.225 5610 Planarity : 0.011 0.361 6576 Dihedral : 5.678 169.767 5142 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.75 % Favored : 94.12 % Rotamer: Outliers : 3.97 % Allowed : 14.59 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 4641 helix: 0.33 (0.23), residues: 483 sheet: -0.21 (0.14), residues: 1335 loop : -1.25 (0.11), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.001 ARG C 227 TYR 0.017 0.002 TYR C 385 PHE 0.078 0.002 PHE F 237 TRP 0.046 0.002 TRP G 12 HIS 0.011 0.001 HIS I 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (36666) covalent geometry : angle 0.68419 / 0.36 (50004) hydrogen bonds : bond 0.04232 / 2.87 ( 801) hydrogen bonds : angle 6.41103 / 4.57 ( 2097) Misc. bond : bond 0.01216 / 0.77 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 423 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 153 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: C 83 MET cc_start: 0.4025 (mpp) cc_final: 0.3126 (ttp) REVERT: C 489 ASP cc_start: 0.6051 (p0) cc_final: 0.5845 (p0) REVERT: C 499 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6799 (p) REVERT: C 502 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6655 (mt-10) REVERT: C 509 ARG cc_start: 0.5838 (ttp80) cc_final: 0.5309 (tmm160) REVERT: C 563 ARG cc_start: 0.6225 (tpt170) cc_final: 0.5792 (mtm180) REVERT: M 105 TYR cc_start: 0.8297 (t80) cc_final: 0.7375 (t80) REVERT: M 118 LYS cc_start: 0.3625 (tttt) cc_final: 0.3096 (ptpp) REVERT: M 258 LYS cc_start: 0.7570 (mmtm) cc_final: 0.7280 (tppt) REVERT: A 45 ARG cc_start: 0.6150 (mmt-90) cc_final: 0.5528 (mtm110) REVERT: A 99 TYR cc_start: 0.8277 (t80) cc_final: 0.7796 (t80) REVERT: A 135 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 247 ASP cc_start: 0.6705 (m-30) cc_final: 0.6480 (m-30) REVERT: B 83 MET cc_start: 0.2811 (mpp) cc_final: 0.2482 (ttm) REVERT: B 416 TRP cc_start: 0.6503 (OUTLIER) cc_final: 0.6290 (p-90) REVERT: D 33 ARG cc_start: 0.6897 (ttp-110) cc_final: 0.5305 (ptt180) REVERT: D 118 LYS cc_start: 0.2881 (tttt) cc_final: 0.2059 (ttmm) REVERT: D 165 ARG cc_start: 0.7162 (tpt90) cc_final: 0.6638 (tpt-90) REVERT: F 472 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6225 (mtt180) REVERT: G 33 ARG cc_start: 0.6333 (ttp-110) cc_final: 0.5666 (ptt180) REVERT: G 118 LYS cc_start: 0.3784 (tttt) cc_final: 0.3016 (mttm) REVERT: G 168 ARG cc_start: 0.5394 (OUTLIER) cc_final: 0.5168 (mmm160) REVERT: G 714 ASP cc_start: 0.6079 (t0) cc_final: 0.5838 (t0) outliers start: 150 outliers final: 108 residues processed: 533 average time/residue: 0.2016 time to fit residues: 177.0896 Evaluate side-chains 490 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 377 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 337 ASP Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 168 ARG Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 370 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 240 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 371 optimal weight: 0.9980 chunk 224 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 154 HIS ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 ASN ** M 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 661 GLN A 136 GLN A 154 HIS D 288 ASN E 159 ASN G 288 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132822 restraints weight = 70117.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134284 restraints weight = 40136.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134813 restraints weight = 26929.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135281 restraints weight = 20488.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135317 restraints weight = 18111.894| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 36717 Z= 0.149 Angle : 0.626 17.298 50004 Z= 0.327 Chirality : 0.045 0.215 5610 Planarity : 0.011 0.448 6576 Dihedral : 5.366 163.277 5142 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 3.75 % Allowed : 16.26 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.12), residues: 4641 helix: 0.50 (0.24), residues: 483 sheet: -0.25 (0.14), residues: 1347 loop : -1.23 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG F 227 TYR 0.012 0.001 TYR F 385 PHE 0.073 0.002 PHE F 237 TRP 0.036 0.001 TRP G 12 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (36666) covalent geometry : angle 0.62600 / 0.33 (50004) hydrogen bonds : bond 0.03636 / 2.49 ( 801) hydrogen bonds : angle 6.16577 / 4.39 ( 2097) Misc. bond : bond 0.01200 / 0.76 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 418 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 122 SER cc_start: 0.7345 (p) cc_final: 0.7004 (t) REVERT: I 131 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.5974 (m-30) REVERT: I 251 ASN cc_start: 0.8584 (t0) cc_final: 0.8348 (t0) REVERT: C 83 MET cc_start: 0.4085 (mpp) cc_final: 0.3071 (ttp) REVERT: C 291 TYR cc_start: 0.7862 (p90) cc_final: 0.7484 (p90) REVERT: C 360 MET cc_start: 0.7258 (mmt) cc_final: 0.6903 (mmt) REVERT: C 489 ASP cc_start: 0.6019 (p0) cc_final: 0.5780 (p0) REVERT: C 499 THR cc_start: 0.7125 (OUTLIER) cc_final: 0.6884 (p) REVERT: C 502 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6625 (mt-10) REVERT: C 509 ARG cc_start: 0.5839 (ttp80) cc_final: 0.5297 (tmm160) REVERT: C 563 ARG cc_start: 0.6224 (tpt170) cc_final: 0.5869 (mtm180) REVERT: M 105 TYR cc_start: 0.8218 (t80) cc_final: 0.7373 (t80) REVERT: M 118 LYS cc_start: 0.3586 (tttt) cc_final: 0.3074 (ptpp) REVERT: M 295 GLN cc_start: 0.6588 (mm-40) cc_final: 0.6068 (tp40) REVERT: A 45 ARG cc_start: 0.6188 (mmt-90) cc_final: 0.5483 (mtm180) REVERT: A 99 TYR cc_start: 0.8283 (t80) cc_final: 0.7828 (t80) REVERT: A 135 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7540 (t0) REVERT: A 136 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: A 247 ASP cc_start: 0.6719 (m-30) cc_final: 0.6350 (m-30) REVERT: B 470 TYR cc_start: 0.7389 (t80) cc_final: 0.7075 (t80) REVERT: D 33 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.5447 (ptt180) REVERT: D 118 LYS cc_start: 0.2891 (tttt) cc_final: 0.2265 (ttmm) REVERT: D 165 ARG cc_start: 0.7067 (tpt90) cc_final: 0.6522 (tpt-90) REVERT: D 170 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7302 (tp) REVERT: D 302 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6254 (pp20) REVERT: F 182 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (p0) REVERT: F 472 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.6048 (mtt180) REVERT: G 33 ARG cc_start: 0.6340 (ttp-110) cc_final: 0.5669 (ptt180) REVERT: G 118 LYS cc_start: 0.3660 (tttt) cc_final: 0.3058 (mttm) REVERT: G 297 ARG cc_start: 0.4917 (mtp180) cc_final: 0.4174 (mtp180) outliers start: 142 outliers final: 97 residues processed: 528 average time/residue: 0.2079 time to fit residues: 180.7630 Evaluate side-chains 485 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 382 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 135 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 288 ASN Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 337 ASP Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 661 GLN Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 286 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 417 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 213 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 442 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 288 ASN ** M 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 661 GLN B 152 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 438 GLN B 494 HIS D 288 ASN F 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127984 restraints weight = 70795.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129794 restraints weight = 40017.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.130517 restraints weight = 26080.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.130949 restraints weight = 20718.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131143 restraints weight = 18948.540| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 36717 Z= 0.263 Angle : 0.787 22.396 50004 Z= 0.410 Chirality : 0.051 0.246 5610 Planarity : 0.011 0.373 6576 Dihedral : 6.309 165.651 5142 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 5.13 % Allowed : 16.26 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.12), residues: 4641 helix: -0.07 (0.23), residues: 483 sheet: -0.46 (0.14), residues: 1284 loop : -1.50 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG B 227 TYR 0.030 0.002 TYR B 385 PHE 0.044 0.003 PHE F 237 TRP 0.036 0.003 TRP G 12 HIS 0.015 0.002 HIS I 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (36666) covalent geometry : angle 0.78691 / 0.41 (50004) hydrogen bonds : bond 0.04937 / 3.30 ( 801) hydrogen bonds : angle 6.51114 / 4.65 ( 2097) Misc. bond : bond 0.01145 / 0.73 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 393 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 GLN cc_start: 0.7238 (tt0) cc_final: 0.6567 (pp30) REVERT: I 131 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6020 (m-30) REVERT: I 153 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: I 251 ASN cc_start: 0.8868 (t0) cc_final: 0.8451 (t0) REVERT: C 83 MET cc_start: 0.4321 (mpp) cc_final: 0.4117 (mtp) REVERT: C 139 TRP cc_start: -0.0676 (OUTLIER) cc_final: -0.1076 (m-90) REVERT: C 211 ARG cc_start: 0.4918 (mmt-90) cc_final: 0.4444 (mtt90) REVERT: C 496 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6704 (tpt-90) REVERT: C 499 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 502 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6743 (mt-10) REVERT: C 563 ARG cc_start: 0.6340 (tpt170) cc_final: 0.5864 (mtm180) REVERT: M 89 MET cc_start: 0.5503 (mmt) cc_final: 0.4151 (ppp) REVERT: M 118 LYS cc_start: 0.3553 (tttt) cc_final: 0.2843 (ptpp) REVERT: M 253 GLU cc_start: 0.6757 (mp0) cc_final: 0.6138 (pm20) REVERT: M 295 GLN cc_start: 0.6828 (mm-40) cc_final: 0.6250 (tp40) REVERT: M 661 GLN cc_start: 0.5545 (OUTLIER) cc_final: 0.5123 (tp40) REVERT: M 701 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6020 (ptm160) REVERT: A 45 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.5931 (mtm180) REVERT: A 119 THR cc_start: 0.7495 (p) cc_final: 0.7285 (p) REVERT: B 83 MET cc_start: 0.4127 (OUTLIER) cc_final: 0.1644 (pmm) REVERT: B 277 ASP cc_start: 0.7514 (m-30) cc_final: 0.6866 (m-30) REVERT: D 33 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.5933 (ptt-90) REVERT: D 302 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6270 (pp20) REVERT: D 433 ASN cc_start: 0.7085 (t0) cc_final: 0.6755 (m110) REVERT: F 83 MET cc_start: 0.4256 (ptm) cc_final: 0.3413 (pmm) REVERT: F 417 ILE cc_start: 0.7894 (mm) cc_final: 0.7625 (mm) REVERT: F 472 ARG cc_start: 0.7432 (ttp-170) cc_final: 0.6103 (mtt180) REVERT: G 33 ARG cc_start: 0.6432 (ttp-110) cc_final: 0.5707 (ptt-90) REVERT: G 72 ASP cc_start: 0.7430 (t0) cc_final: 0.6993 (t70) REVERT: G 118 LYS cc_start: 0.3439 (tttt) cc_final: 0.2669 (mttm) REVERT: G 168 ARG cc_start: 0.5309 (OUTLIER) cc_final: 0.4738 (mmm160) REVERT: G 313 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8035 (tt) outliers start: 194 outliers final: 145 residues processed: 534 average time/residue: 0.1957 time to fit residues: 172.1765 Evaluate side-chains 505 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 350 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 508 VAL Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 515 VAL Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 661 GLN Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 168 ARG Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 262 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 371 ASN Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 ILE Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 135 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 184 optimal weight: 50.0000 chunk 375 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 413 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 430 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 231 GLN M 127 ASN M 288 ASN M 512 GLN M 661 GLN B 257 GLN B 494 HIS F 394 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.152567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129308 restraints weight = 71096.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131079 restraints weight = 40829.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132077 restraints weight = 27053.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131950 restraints weight = 20550.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132678 restraints weight = 18872.975| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 36717 Z= 0.199 Angle : 0.723 23.812 50004 Z= 0.375 Chirality : 0.047 0.336 5610 Planarity : 0.012 0.427 6576 Dihedral : 6.640 172.572 5142 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.55 % Favored : 93.32 % Rotamer: Outliers : 4.57 % Allowed : 17.63 % Favored : 77.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.12), residues: 4641 helix: -0.03 (0.23), residues: 483 sheet: -0.45 (0.14), residues: 1272 loop : -1.51 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.001 ARG B 227 TYR 0.016 0.002 TYR I 95 PHE 0.035 0.002 PHE E 208 TRP 0.037 0.002 TRP G 12 HIS 0.007 0.001 HIS I 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (36666) covalent geometry : angle 0.72323 / 0.37 (50004) hydrogen bonds : bond 0.04215 / 2.86 ( 801) hydrogen bonds : angle 6.39055 / 4.56 ( 2097) Misc. bond : bond 0.01351 / 0.82 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 379 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 GLN cc_start: 0.7183 (tt0) cc_final: 0.6681 (pp30) REVERT: I 114 ASP cc_start: 0.7422 (t0) cc_final: 0.7209 (t0) REVERT: I 131 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6066 (m-30) REVERT: I 153 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6753 (m-30) REVERT: I 176 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8348 (m) REVERT: I 251 ASN cc_start: 0.8793 (t0) cc_final: 0.8406 (t0) REVERT: C 83 MET cc_start: 0.4244 (mpp) cc_final: 0.4033 (mtp) REVERT: C 211 ARG cc_start: 0.4763 (mmt-90) cc_final: 0.4545 (mtm-85) REVERT: C 496 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6928 (tpt-90) REVERT: C 499 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6949 (p) REVERT: C 502 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6799 (mt-10) REVERT: C 509 ARG cc_start: 0.6202 (ttp80) cc_final: 0.5461 (tmm160) REVERT: C 563 ARG cc_start: 0.6370 (tpt170) cc_final: 0.5975 (mtm180) REVERT: M 89 MET cc_start: 0.5372 (mmt) cc_final: 0.4354 (ppp) REVERT: M 118 LYS cc_start: 0.3653 (tttt) cc_final: 0.2917 (ptpp) REVERT: M 253 GLU cc_start: 0.6747 (mp0) cc_final: 0.6096 (pm20) REVERT: M 295 GLN cc_start: 0.6656 (mm-40) cc_final: 0.5905 (tp40) REVERT: M 313 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7794 (tt) REVERT: M 402 TRP cc_start: 0.4998 (OUTLIER) cc_final: 0.4072 (t-100) REVERT: M 701 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7035 (ptm-80) REVERT: A 45 ARG cc_start: 0.6756 (mmt-90) cc_final: 0.5887 (mtm180) REVERT: A 135 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7876 (t0) REVERT: B 83 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.1763 (pmm) REVERT: B 277 ASP cc_start: 0.7469 (m-30) cc_final: 0.6823 (m-30) REVERT: B 396 SER cc_start: 0.4552 (OUTLIER) cc_final: 0.3019 (t) REVERT: B 470 TYR cc_start: 0.7383 (t80) cc_final: 0.7182 (t80) REVERT: B 491 THR cc_start: 0.6095 (m) cc_final: 0.5879 (m) REVERT: B 506 ASP cc_start: 0.7129 (t70) cc_final: 0.6652 (t70) REVERT: D 253 GLU cc_start: 0.6939 (tp30) cc_final: 0.6696 (tp30) REVERT: D 302 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6206 (pp20) REVERT: D 433 ASN cc_start: 0.7093 (t0) cc_final: 0.6729 (m110) REVERT: F 78 LEU cc_start: 0.0862 (OUTLIER) cc_final: 0.0540 (tt) REVERT: F 83 MET cc_start: 0.4374 (ptm) cc_final: 0.3529 (pmm) REVERT: F 417 ILE cc_start: 0.7887 (mm) cc_final: 0.7639 (mm) REVERT: G 33 ARG cc_start: 0.6510 (ttp-110) cc_final: 0.5568 (ptt-90) REVERT: G 118 LYS cc_start: 0.3562 (tttt) cc_final: 0.2781 (mttm) REVERT: G 168 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.4794 (mmm160) REVERT: G 313 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7889 (tt) outliers start: 173 outliers final: 132 residues processed: 505 average time/residue: 0.1993 time to fit residues: 166.2397 Evaluate side-chains 497 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 351 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 288 ASN Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 507 ASP Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 515 VAL Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 416 TRP Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 480 ARG Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 168 ARG Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 371 ASN Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 ILE Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 352 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.0040 chunk 132 optimal weight: 0.7980 chunk 309 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 50.0000 chunk 258 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 263 optimal weight: 0.2980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 8 GLN M 127 ASN M 288 ASN B 230 GLN B 257 GLN B 494 HIS ** F 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130245 restraints weight = 70225.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132310 restraints weight = 40911.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132801 restraints weight = 25938.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133631 restraints weight = 19077.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133863 restraints weight = 15360.780| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 36717 Z= 0.162 Angle : 0.693 24.825 50004 Z= 0.360 Chirality : 0.046 0.318 5610 Planarity : 0.014 0.482 6576 Dihedral : 6.383 168.288 5142 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 4.02 % Allowed : 18.19 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.12), residues: 4641 helix: 0.14 (0.24), residues: 483 sheet: -0.39 (0.14), residues: 1266 loop : -1.49 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.001 ARG F 227 TYR 0.013 0.001 TYR I 95 PHE 0.035 0.002 PHE A 208 TRP 0.034 0.001 TRP G 12 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (36666) covalent geometry : angle 0.69328 / 0.36 (50004) hydrogen bonds : bond 0.03783 / 2.60 ( 801) hydrogen bonds : angle 6.16101 / 4.37 ( 2097) Misc. bond : bond 0.01309 / 0.81 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 383 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 GLN cc_start: 0.7103 (tt0) cc_final: 0.6650 (pp30) REVERT: I 95 TYR cc_start: 0.8419 (m-80) cc_final: 0.8207 (m-80) REVERT: I 131 ASP cc_start: 0.6496 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: I 153 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: I 176 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8356 (m) REVERT: I 251 ASN cc_start: 0.8756 (t0) cc_final: 0.8312 (t0) REVERT: C 211 ARG cc_start: 0.4739 (mmt-90) cc_final: 0.4487 (mtm-85) REVERT: C 496 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6901 (tpt-90) REVERT: C 499 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6919 (p) REVERT: C 502 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6791 (mt-10) REVERT: C 509 ARG cc_start: 0.6187 (ttp80) cc_final: 0.5416 (tmm160) REVERT: C 563 ARG cc_start: 0.6240 (tpt170) cc_final: 0.5867 (mtm180) REVERT: M 89 MET cc_start: 0.5396 (mmt) cc_final: 0.4363 (ppp) REVERT: M 118 LYS cc_start: 0.3607 (tttt) cc_final: 0.2887 (ptpp) REVERT: M 253 GLU cc_start: 0.6705 (mp0) cc_final: 0.6047 (pm20) REVERT: M 295 GLN cc_start: 0.6660 (mm-40) cc_final: 0.6436 (tt0) REVERT: M 313 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (tt) REVERT: M 402 TRP cc_start: 0.4995 (OUTLIER) cc_final: 0.4680 (t-100) REVERT: M 701 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6954 (ptm-80) REVERT: A 45 ARG cc_start: 0.6693 (mmt-90) cc_final: 0.5809 (mtm180) REVERT: A 135 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7885 (t0) REVERT: B 83 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.2016 (pmm) REVERT: B 277 ASP cc_start: 0.7396 (m-30) cc_final: 0.6727 (m-30) REVERT: B 396 SER cc_start: 0.4552 (OUTLIER) cc_final: 0.2938 (t) REVERT: B 470 TYR cc_start: 0.7285 (t80) cc_final: 0.7058 (t80) REVERT: B 491 THR cc_start: 0.6206 (m) cc_final: 0.5990 (m) REVERT: D 33 ARG cc_start: 0.7259 (ttp-110) cc_final: 0.6006 (ptt-90) REVERT: D 165 ARG cc_start: 0.7148 (tpt90) cc_final: 0.6502 (tpt-90) REVERT: D 302 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6209 (pp20) REVERT: D 433 ASN cc_start: 0.7008 (t0) cc_final: 0.6580 (m-40) REVERT: D 661 GLN cc_start: 0.5349 (mp10) cc_final: 0.4997 (tp40) REVERT: F 83 MET cc_start: 0.4430 (ptm) cc_final: 0.3696 (pmm) REVERT: G 33 ARG cc_start: 0.6495 (ttp-110) cc_final: 0.5560 (ptt-90) REVERT: G 72 ASP cc_start: 0.7304 (t0) cc_final: 0.6927 (t70) REVERT: G 118 LYS cc_start: 0.3366 (tttt) cc_final: 0.2571 (mttm) REVERT: G 313 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7816 (tt) outliers start: 152 outliers final: 115 residues processed: 495 average time/residue: 0.1964 time to fit residues: 160.9581 Evaluate side-chains 482 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 355 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 288 ASN Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 480 ARG Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 371 ASN Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 170 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 210 optimal weight: 0.0070 chunk 171 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 461 optimal weight: 0.1980 chunk 305 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 386 GLN M 610 GLN B 257 GLN B 494 HIS D 580 ASN F 230 GLN F 386 GLN F 394 ASN G 295 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131338 restraints weight = 70161.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132685 restraints weight = 42378.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133385 restraints weight = 29247.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134102 restraints weight = 20854.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134299 restraints weight = 17019.725| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 36717 Z= 0.160 Angle : 0.686 21.867 50004 Z= 0.357 Chirality : 0.046 0.330 5610 Planarity : 0.011 0.370 6576 Dihedral : 6.260 167.896 5142 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 3.65 % Allowed : 18.85 % Favored : 77.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4641 helix: 0.16 (0.24), residues: 483 sheet: -0.42 (0.14), residues: 1287 loop : -1.50 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.001 ARG A 206 TYR 0.018 0.001 TYR M 567 PHE 0.033 0.002 PHE I 208 TRP 0.041 0.002 TRP G 402 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (36666) covalent geometry : angle 0.68559 / 0.36 (50004) hydrogen bonds : bond 0.03642 / 2.50 ( 801) hydrogen bonds : angle 6.09503 / 4.32 ( 2097) Misc. bond : bond 0.01284 / 0.78 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 375 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 GLN cc_start: 0.7148 (tt0) cc_final: 0.6691 (pp30) REVERT: I 131 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: I 153 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: C 139 TRP cc_start: -0.0578 (OUTLIER) cc_final: -0.0959 (m-90) REVERT: C 496 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7002 (tpt-90) REVERT: C 499 THR cc_start: 0.7255 (OUTLIER) cc_final: 0.6959 (p) REVERT: C 509 ARG cc_start: 0.6184 (ttp80) cc_final: 0.5434 (tmm160) REVERT: C 563 ARG cc_start: 0.6154 (tpt170) cc_final: 0.5852 (mtm180) REVERT: M 89 MET cc_start: 0.5480 (mmt) cc_final: 0.4494 (ppp) REVERT: M 118 LYS cc_start: 0.3617 (tttt) cc_final: 0.2942 (ptpp) REVERT: M 253 GLU cc_start: 0.6727 (mp0) cc_final: 0.6087 (pm20) REVERT: M 402 TRP cc_start: 0.4904 (OUTLIER) cc_final: 0.4637 (t-100) REVERT: M 701 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7082 (ptm-80) REVERT: A 45 ARG cc_start: 0.6672 (mmt-90) cc_final: 0.5847 (mtm180) REVERT: A 135 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7808 (t0) REVERT: B 277 ASP cc_start: 0.7376 (m-30) cc_final: 0.6766 (m-30) REVERT: B 396 SER cc_start: 0.4663 (OUTLIER) cc_final: 0.3204 (t) REVERT: B 415 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6557 (mtp85) REVERT: B 470 TYR cc_start: 0.7292 (t80) cc_final: 0.7061 (t80) REVERT: D 33 ARG cc_start: 0.7248 (ttp-110) cc_final: 0.6070 (ptt-90) REVERT: D 165 ARG cc_start: 0.7156 (tpt90) cc_final: 0.6555 (tpt-90) REVERT: D 433 ASN cc_start: 0.6967 (t0) cc_final: 0.6542 (m-40) REVERT: D 661 GLN cc_start: 0.5411 (mp10) cc_final: 0.5050 (tp40) REVERT: F 83 MET cc_start: 0.4462 (ptm) cc_final: 0.3578 (pmm) REVERT: F 417 ILE cc_start: 0.7958 (mm) cc_final: 0.7611 (mm) REVERT: G 33 ARG cc_start: 0.6486 (ttp-110) cc_final: 0.5592 (ptt-90) REVERT: G 72 ASP cc_start: 0.7281 (t0) cc_final: 0.6902 (t70) REVERT: G 118 LYS cc_start: 0.3399 (tttt) cc_final: 0.2616 (mttm) REVERT: G 269 LEU cc_start: 0.8031 (tp) cc_final: 0.7818 (tp) REVERT: G 313 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7803 (tt) outliers start: 138 outliers final: 113 residues processed: 477 average time/residue: 0.2029 time to fit residues: 159.6579 Evaluate side-chains 474 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 351 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 444 LEU Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 480 ARG Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 202 ASP Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 371 ASN Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 311 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 446 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 148 optimal weight: 0.0370 chunk 32 optimal weight: 50.0000 chunk 405 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 354 optimal weight: 3.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN M 288 ASN B 257 GLN B 494 HIS D 610 GLN E 159 ASN G 288 ASN G 295 GLN G 433 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127788 restraints weight = 70971.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129338 restraints weight = 42517.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130001 restraints weight = 28246.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130658 restraints weight = 19811.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130822 restraints weight = 16252.700| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 36717 Z= 0.222 Angle : 0.801 28.648 50004 Z= 0.414 Chirality : 0.049 0.451 5610 Planarity : 0.012 0.426 6576 Dihedral : 7.324 177.266 5142 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.80 % Favored : 92.03 % Rotamer: Outliers : 3.75 % Allowed : 18.66 % Favored : 77.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.12), residues: 4641 helix: -0.03 (0.23), residues: 480 sheet: -0.49 (0.14), residues: 1278 loop : -1.63 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.001 ARG F 227 TYR 0.019 0.002 TYR C 385 PHE 0.042 0.002 PHE F 237 TRP 0.069 0.002 TRP D 12 HIS 0.006 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (36666) covalent geometry : angle 0.80126 / 0.41 (50004) hydrogen bonds : bond 0.04252 / 2.88 ( 801) hydrogen bonds : angle 6.27845 / 4.44 ( 2097) Misc. bond : bond 0.01311 / 0.79 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 346 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 GLN cc_start: 0.7246 (tt0) cc_final: 0.6718 (pp30) REVERT: I 131 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.6086 (m-30) REVERT: I 153 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: I 251 ASN cc_start: 0.8792 (t0) cc_final: 0.8531 (t0) REVERT: C 139 TRP cc_start: -0.0400 (OUTLIER) cc_final: -0.0722 (m-90) REVERT: C 496 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6958 (tpt-90) REVERT: C 499 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6883 (p) REVERT: C 563 ARG cc_start: 0.6218 (tpt170) cc_final: 0.5835 (mtm180) REVERT: M 89 MET cc_start: 0.5465 (mmt) cc_final: 0.4343 (ppp) REVERT: M 118 LYS cc_start: 0.3521 (tttt) cc_final: 0.2844 (ptpp) REVERT: M 253 GLU cc_start: 0.6798 (mp0) cc_final: 0.6194 (pm20) REVERT: M 402 TRP cc_start: 0.5121 (OUTLIER) cc_final: 0.4707 (t-100) REVERT: M 701 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7018 (ptm-80) REVERT: A 45 ARG cc_start: 0.6886 (mmt-90) cc_final: 0.5962 (mtm180) REVERT: A 135 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7806 (t0) REVERT: B 277 ASP cc_start: 0.7429 (m-30) cc_final: 0.6769 (m-30) REVERT: B 470 TYR cc_start: 0.7422 (t80) cc_final: 0.7194 (t80) REVERT: D 33 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6125 (ptt-90) REVERT: D 165 ARG cc_start: 0.7152 (tpt90) cc_final: 0.6556 (tpt-90) REVERT: D 433 ASN cc_start: 0.7057 (t0) cc_final: 0.6639 (m110) REVERT: D 661 GLN cc_start: 0.5587 (mp10) cc_final: 0.5151 (tp40) REVERT: F 78 LEU cc_start: 0.0931 (OUTLIER) cc_final: 0.0575 (tt) REVERT: F 83 MET cc_start: 0.4652 (ptm) cc_final: 0.3615 (pmm) REVERT: F 417 ILE cc_start: 0.8066 (mm) cc_final: 0.7656 (mm) REVERT: G 33 ARG cc_start: 0.6596 (ttp-110) cc_final: 0.5668 (ptt-90) REVERT: G 118 LYS cc_start: 0.3486 (tttt) cc_final: 0.2694 (mttm) REVERT: G 313 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7919 (tt) outliers start: 142 outliers final: 120 residues processed: 452 average time/residue: 0.1968 time to fit residues: 148.3233 Evaluate side-chains 458 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 328 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 136 GLN Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ARG Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 554 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 402 TRP Chi-restraints excluded: chain M residue 456 GLN Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 500 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 594 ASP Chi-restraints excluded: chain M residue 643 ILE Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain M residue 701 ARG Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 456 GLN Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 501 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 354 THR Chi-restraints excluded: chain G residue 371 ASN Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain G residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 343 optimal weight: 0.9980 chunk 122 optimal weight: 0.0020 chunk 380 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 303 optimal weight: 6.9990 chunk 423 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 136 GLN C 386 GLN M 288 ASN B 257 GLN F 386 GLN F 394 ASN G 295 GLN G 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129771 restraints weight = 70062.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131468 restraints weight = 40282.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132075 restraints weight = 26304.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132832 restraints weight = 18921.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133030 restraints weight = 15144.805| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 36717 Z= 0.164 Angle : 0.724 24.023 50004 Z= 0.378 Chirality : 0.046 0.351 5610 Planarity : 0.011 0.425 6576 Dihedral : 7.476 178.449 5142 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.36 % Favored : 93.49 % Rotamer: Outliers : 3.38 % Allowed : 19.19 % Favored : 77.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4641 helix: 0.19 (0.24), residues: 480 sheet: -0.51 (0.14), residues: 1287 loop : -1.57 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.001 ARG A 206 TYR 0.012 0.001 TYR C 385 PHE 0.045 0.002 PHE F 237 TRP 0.054 0.002 TRP D 12 HIS 0.004 0.001 HIS I 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (36666) covalent geometry : angle 0.72423 / 0.38 (50004) hydrogen bonds : bond 0.03700 / 2.52 ( 801) hydrogen bonds : angle 6.15573 / 4.36 ( 2097) Misc. bond : bond 0.01274 / 0.80 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7371.00 seconds wall clock time: 126 minutes 58.92 seconds (7618.92 seconds total)