Starting phenix.real_space_refine on Tue Aug 26 10:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk6_19262/08_2025/8rk6_19262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk6_19262/08_2025/8rk6_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_19262/08_2025/8rk6_19262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk6_19262/08_2025/8rk6_19262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rk6_19262/08_2025/8rk6_19262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk6_19262/08_2025/8rk6_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, E, B, F, D, G Time building chain proxies: 7.54, per 1000 atoms: 0.21 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.56 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: 10.92 Time building geometry restraints manager: 3.96 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: 0.09 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: 14.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.900 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 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 aren 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 covalent geometry : bond 0.00199 (36666) covalent geometry : angle 0.45490 (50004) hydrogen bonds : bond 0.24019 ( 801) hydrogen bonds : angle 9.69238 ( 2097) Misc. bond : bond 0.78051 ( 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 : 0.904 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: 0.7050 (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: 0.2206 time to fit residues: 339.1259 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 : 1.314 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 98 HIS E 159 ASN 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 = 0.4022 r_free = 0.4022 target = 0.162653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140273 restraints weight = 71142.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141876 restraints weight = 43393.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142651 restraints weight = 29988.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143191 restraints weight = 22070.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143313 restraints weight = 18722.292| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 36717 Z= 0.222 Angle : 0.776 20.518 50004 Z= 0.406 Chirality : 0.049 0.241 5610 Planarity : 0.014 0.385 6576 Dihedral : 4.716 61.145 5142 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 2.41 % Allowed : 10.23 % Favored : 87.36 % 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 aren not related in a simple way. whole: -0.66 (0.12), residues: 4641 helix: 0.86 (0.24), residues: 477 sheet: 0.06 (0.15), residues: 1308 loop : -0.92 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 466 TYR 0.020 0.002 TYR I 194 PHE 0.074 0.003 PHE E 208 TRP 0.038 0.002 TRP G 12 HIS 0.009 0.001 HIS F 446 Details of bonding type rmsd covalent geometry : bond 0.00481 (36666) covalent geometry : angle 0.77561 (50004) hydrogen bonds : bond 0.05283 ( 801) hydrogen bonds : angle 7.35573 ( 2097) Misc. bond : bond 0.01372 ( 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 639 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 548 time to evaluate : 1.371 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: I 35 ARG cc_start: 0.5879 (ptp-170) cc_final: 0.4803 (ttp80) REVERT: C 83 MET cc_start: 0.3990 (mpp) cc_final: 0.3003 (ttp) REVERT: C 223 TYR cc_start: 0.7290 (m-80) cc_final: 0.7080 (m-80) REVERT: C 438 GLN cc_start: 0.7811 (tt0) cc_final: 0.7586 (tt0) REVERT: C 502 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6772 (pm20) REVERT: C 563 ARG cc_start: 0.5947 (tpt170) cc_final: 0.5223 (mtm-85) REVERT: M 105 TYR cc_start: 0.8155 (t80) cc_final: 0.7656 (t80) REVERT: M 118 LYS cc_start: 0.3511 (tttt) cc_final: 0.2901 (tttm) REVERT: M 170 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7160 (tp) REVERT: M 198 TRP cc_start: 0.6055 (t-100) cc_final: 0.4144 (p-90) REVERT: M 627 SER cc_start: 0.7396 (t) cc_final: 0.6898 (p) REVERT: A 45 ARG cc_start: 0.5575 (mmt-90) cc_final: 0.5284 (mtm180) REVERT: A 99 TYR cc_start: 0.8188 (t80) cc_final: 0.7841 (t80) REVERT: A 135 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7289 (t0) REVERT: B 83 MET cc_start: 0.3110 (mpp) cc_final: 0.2115 (ttm) REVERT: B 472 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.5839 (mtt180) REVERT: B 502 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6540 (mt-10) REVERT: D 33 ARG cc_start: 0.6170 (ttp-110) cc_final: 0.5296 (ptt180) REVERT: D 79 ASP cc_start: 0.5727 (t70) cc_final: 0.5412 (t70) REVERT: D 118 LYS cc_start: 0.2967 (tttt) cc_final: 0.2538 (ttpp) REVERT: D 170 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7410 (tp) REVERT: D 489 PRO cc_start: 0.8030 (Cg_exo) cc_final: 0.7708 (Cg_endo) REVERT: F 223 TYR cc_start: 0.7557 (m-80) cc_final: 0.7266 (m-80) REVERT: F 419 MET cc_start: 0.7378 (mtt) cc_final: 0.6719 (mtt) REVERT: F 472 ARG cc_start: 0.7126 (ttp-170) cc_final: 0.6187 (mtt180) REVERT: G 33 ARG cc_start: 0.6053 (ttp-110) cc_final: 0.5770 (ptt180) REVERT: G 46 SER cc_start: 0.7892 (p) cc_final: 0.7624 (t) REVERT: G 118 LYS cc_start: 0.4069 (tttt) cc_final: 0.3380 (mttm) REVERT: G 253 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6430 (pt0) REVERT: G 701 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7391 (ptm160) REVERT: G 714 ASP cc_start: 0.5741 (t0) cc_final: 0.5489 (t0) outliers start: 91 outliers final: 62 residues processed: 605 average time/residue: 0.2154 time to fit residues: 210.8785 Evaluate side-chains 507 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 441 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 253 GLU 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: 0.9990 chunk 428 optimal weight: 0.7980 chunk 427 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 337 optimal weight: 50.0000 chunk 303 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 437 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 ASN M 371 ASN M 661 GLN M 711 GLN A 14 GLN A 98 HIS A 154 HIS A 198 GLN B 124 GLN D 512 GLN D 711 GLN E 14 GLN E 159 ASN E 203 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137371 restraints weight = 70660.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139557 restraints weight = 41502.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139906 restraints weight = 26957.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.140607 restraints weight = 21895.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140948 restraints weight = 17720.152| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 36717 Z= 0.180 Angle : 0.688 19.132 50004 Z= 0.359 Chirality : 0.046 0.210 5610 Planarity : 0.013 0.358 6576 Dihedral : 5.032 133.676 5142 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 3.17 % Allowed : 11.71 % Favored : 85.12 % 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 aren not related in a simple way. whole: -0.84 (0.12), residues: 4641 helix: 0.58 (0.23), residues: 483 sheet: -0.00 (0.15), residues: 1272 loop : -1.03 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.001 ARG C 227 TYR 0.015 0.001 TYR G 618 PHE 0.062 0.002 PHE B 237 TRP 0.045 0.002 TRP G 12 HIS 0.013 0.001 HIS I 218 Details of bonding type rmsd covalent geometry : bond 0.00373 (36666) covalent geometry : angle 0.68824 (50004) hydrogen bonds : bond 0.04403 ( 801) hydrogen bonds : angle 6.66527 ( 2097) Misc. bond : bond 0.01237 ( 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 589 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 469 time to evaluate : 1.441 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 131 ASP cc_start: 0.6613 (t0) cc_final: 0.6320 (m-30) REVERT: C 83 MET cc_start: 0.4112 (mpp) cc_final: 0.3085 (ttp) REVERT: C 223 TYR cc_start: 0.7392 (m-80) cc_final: 0.7145 (m-80) REVERT: C 360 MET cc_start: 0.7030 (mmt) cc_final: 0.6750 (mmt) REVERT: C 499 THR cc_start: 0.7025 (OUTLIER) cc_final: 0.6653 (p) REVERT: C 502 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6629 (mt-10) REVERT: C 509 ARG cc_start: 0.5731 (ttp80) cc_final: 0.5241 (tmm160) REVERT: M 25 LYS cc_start: 0.7553 (mptt) cc_final: 0.7336 (mmtm) REVERT: M 105 TYR cc_start: 0.8221 (t80) cc_final: 0.7467 (t80) REVERT: M 118 LYS cc_start: 0.3629 (tttt) cc_final: 0.2915 (tttm) REVERT: M 127 ASN cc_start: 0.5940 (t0) cc_final: 0.5009 (t0) REVERT: M 170 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6776 (tp) REVERT: A 45 ARG cc_start: 0.5763 (mmt-90) cc_final: 0.5257 (mtm110) REVERT: A 99 TYR cc_start: 0.8163 (t80) cc_final: 0.7788 (t80) REVERT: A 122 SER cc_start: 0.7163 (p) cc_final: 0.6417 (t) REVERT: A 135 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7485 (t0) REVERT: B 83 MET cc_start: 0.3068 (mpp) cc_final: 0.2375 (ttm) REVERT: B 217 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: B 470 TYR cc_start: 0.7347 (t80) cc_final: 0.7097 (t80) REVERT: B 502 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6544 (mt-10) REVERT: D 33 ARG cc_start: 0.6457 (ttp-110) cc_final: 0.5240 (ptt180) REVERT: D 118 LYS cc_start: 0.2566 (tttt) cc_final: 0.1775 (ttmm) REVERT: D 165 ARG cc_start: 0.7013 (tpt90) cc_final: 0.6595 (tpt-90) REVERT: D 170 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7376 (tp) REVERT: E 195 VAL cc_start: 0.8509 (t) cc_final: 0.8260 (m) REVERT: F 419 MET cc_start: 0.7540 (mtt) cc_final: 0.6877 (mtt) REVERT: F 472 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.6296 (mtt180) REVERT: G 33 ARG cc_start: 0.6193 (ttp-110) cc_final: 0.5773 (ptt180) REVERT: G 118 LYS cc_start: 0.3877 (tttt) cc_final: 0.3533 (mtpt) REVERT: G 246 ASP cc_start: 0.6054 (t0) cc_final: 0.5735 (t70) outliers start: 120 outliers final: 81 residues processed: 548 average time/residue: 0.2284 time to fit residues: 203.7730 Evaluate side-chains 496 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 410 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 126 THR 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 227 ARG 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 660 LEU 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 217 GLU 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 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 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 553 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 18 LEU 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 166 THR 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 200 SER Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 302 SER Chi-restraints excluded: chain F residue 314 TRP Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 449 ASP Chi-restraints excluded: chain F residue 456 VAL 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 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 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: 0.0970 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 50.0000 chunk 159 optimal weight: 2.9990 chunk 340 optimal weight: 50.0000 chunk 315 optimal weight: 3.9990 chunk 318 optimal weight: 0.2980 chunk 198 optimal weight: 0.0010 chunk 335 optimal weight: 50.0000 chunk 170 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 ASN M 289 ASN M 661 GLN D 512 GLN F 124 GLN G 288 ASN G 289 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137298 restraints weight = 70034.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138868 restraints weight = 42035.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139299 restraints weight = 29099.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139937 restraints weight = 22959.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.139988 restraints weight = 19183.269| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 36717 Z= 0.151 Angle : 0.635 16.534 50004 Z= 0.330 Chirality : 0.045 0.216 5610 Planarity : 0.012 0.400 6576 Dihedral : 5.138 155.350 5142 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 3.07 % Allowed : 14.51 % Favored : 82.42 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.87 (0.12), residues: 4641 helix: 0.73 (0.24), residues: 483 sheet: -0.06 (0.14), residues: 1290 loop : -1.08 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.001 ARG C 227 TYR 0.012 0.001 TYR F 102 PHE 0.074 0.002 PHE F 237 TRP 0.030 0.001 TRP M 402 HIS 0.007 0.001 HIS I 218 Details of bonding type rmsd covalent geometry : bond 0.00308 (36666) covalent geometry : angle 0.63489 (50004) hydrogen bonds : bond 0.03795 ( 801) hydrogen bonds : angle 6.28039 ( 2097) Misc. bond : bond 0.01185 ( 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 563 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 447 time to evaluate : 1.893 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 122 SER cc_start: 0.7072 (p) cc_final: 0.6700 (t) REVERT: I 251 ASN cc_start: 0.8644 (t0) cc_final: 0.8425 (t0) REVERT: C 83 MET cc_start: 0.3933 (mpp) cc_final: 0.3081 (ttp) REVERT: C 360 MET cc_start: 0.7067 (mmt) cc_final: 0.6766 (mmt) REVERT: C 470 TYR cc_start: 0.7133 (t80) cc_final: 0.6698 (t80) REVERT: C 489 ASP cc_start: 0.5966 (p0) cc_final: 0.5702 (p0) REVERT: C 499 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6786 (p) REVERT: C 509 ARG cc_start: 0.5745 (ttp80) cc_final: 0.5322 (tmm160) REVERT: C 563 ARG cc_start: 0.6116 (tpt170) cc_final: 0.5720 (mtm180) REVERT: M 105 TYR cc_start: 0.8222 (t80) cc_final: 0.7409 (t80) REVERT: M 118 LYS cc_start: 0.3604 (tttt) cc_final: 0.2883 (ptmt) REVERT: M 295 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5559 (tp40) REVERT: M 661 GLN cc_start: 0.4569 (OUTLIER) cc_final: 0.4014 (mm-40) REVERT: A 45 ARG cc_start: 0.5796 (mmt-90) cc_final: 0.5434 (mtm110) REVERT: A 99 TYR cc_start: 0.8198 (t80) cc_final: 0.7787 (t80) REVERT: A 122 SER cc_start: 0.7215 (p) cc_final: 0.6591 (t) REVERT: A 135 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 247 ASP cc_start: 0.6476 (m-30) cc_final: 0.6058 (m-30) REVERT: B 83 MET cc_start: 0.3002 (mpp) cc_final: 0.2429 (ttm) REVERT: B 217 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5822 (mp0) REVERT: B 502 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6520 (mt-10) REVERT: D 33 ARG cc_start: 0.6649 (ttp-110) cc_final: 0.5373 (ptt180) REVERT: D 118 LYS cc_start: 0.2959 (tttt) cc_final: 0.2375 (ttmm) REVERT: F 472 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6237 (mtt180) REVERT: G 33 ARG cc_start: 0.6265 (ttp-110) cc_final: 0.5718 (ptt180) REVERT: G 90 LEU cc_start: 0.5772 (mp) cc_final: 0.5549 (mt) REVERT: G 118 LYS cc_start: 0.3734 (tttt) cc_final: 0.3097 (mttm) outliers start: 116 outliers final: 87 residues processed: 531 average time/residue: 0.2269 time to fit residues: 197.4997 Evaluate side-chains 486 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 395 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 146 THR Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 227 ARG 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 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 262 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 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 51 ILE Chi-restraints excluded: chain A residue 126 THR 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 217 GLU 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 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 199 THR 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 477 ASP Chi-restraints excluded: chain D residue 553 VAL Chi-restraints excluded: chain D residue 566 VAL 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 166 THR 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 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 396 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 501 THR 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 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 434 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 643 ILE Chi-restraints excluded: chain G residue 701 ARG 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: 0.0070 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 371 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 GLN C 124 GLN ** M 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN D 288 ASN D 501 ASN E 159 ASN G 713 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136978 restraints weight = 70924.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138960 restraints weight = 39981.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139653 restraints weight = 25632.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139664 restraints weight = 18422.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139664 restraints weight = 18320.012| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 36717 Z= 0.155 Angle : 0.631 18.125 50004 Z= 0.327 Chirality : 0.045 0.230 5610 Planarity : 0.010 0.313 6576 Dihedral : 5.013 154.234 5142 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.61 % Rotamer: Outliers : 3.99 % Allowed : 14.91 % Favored : 81.10 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -0.92 (0.12), residues: 4641 helix: 0.77 (0.25), residues: 465 sheet: -0.12 (0.14), residues: 1296 loop : -1.10 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG F 227 TYR 0.023 0.001 TYR B 385 PHE 0.063 0.002 PHE F 237 TRP 0.031 0.001 TRP D 402 HIS 0.006 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00322 (36666) covalent geometry : angle 0.63146 (50004) hydrogen bonds : bond 0.03662 ( 801) hydrogen bonds : angle 6.09694 ( 2097) Misc. bond : bond 0.01162 ( 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 579 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 428 time to evaluate : 1.412 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 122 SER cc_start: 0.7259 (p) cc_final: 0.6892 (t) REVERT: I 131 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6019 (m-30) REVERT: C 83 MET cc_start: 0.3942 (mpp) cc_final: 0.2852 (ttp) REVERT: C 291 TYR cc_start: 0.7825 (p90) cc_final: 0.7489 (p90) REVERT: C 470 TYR cc_start: 0.6944 (t80) cc_final: 0.6391 (t80) REVERT: C 489 ASP cc_start: 0.6003 (p0) cc_final: 0.5727 (p0) REVERT: C 499 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6883 (p) REVERT: C 509 ARG cc_start: 0.5740 (ttp80) cc_final: 0.5305 (tmm160) REVERT: C 563 ARG cc_start: 0.6163 (tpt170) cc_final: 0.5796 (mtm180) REVERT: M 89 MET cc_start: 0.5216 (mmt) cc_final: 0.3258 (ppp) REVERT: M 105 TYR cc_start: 0.8277 (t80) cc_final: 0.7352 (t80) REVERT: M 118 LYS cc_start: 0.3580 (tttt) cc_final: 0.3046 (ptpp) REVERT: M 295 GLN cc_start: 0.6518 (mm-40) cc_final: 0.5941 (tp40) REVERT: M 661 GLN cc_start: 0.4474 (mp10) cc_final: 0.3613 (mm-40) REVERT: A 45 ARG cc_start: 0.5925 (mmt-90) cc_final: 0.5482 (mtm180) REVERT: A 99 TYR cc_start: 0.8288 (t80) cc_final: 0.7762 (t80) REVERT: A 122 SER cc_start: 0.7373 (p) cc_final: 0.6642 (t) REVERT: A 135 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7520 (t0) REVERT: A 136 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: A 247 ASP cc_start: 0.6636 (m-30) cc_final: 0.6425 (m-30) REVERT: B 83 MET cc_start: 0.2970 (mpp) cc_final: 0.2488 (ttm) REVERT: B 217 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6177 (mt-10) REVERT: D 33 ARG cc_start: 0.6877 (ttp-110) cc_final: 0.5296 (ptt180) REVERT: D 118 LYS cc_start: 0.3049 (tttt) cc_final: 0.1968 (ttmm) REVERT: D 165 ARG cc_start: 0.6830 (tpt90) cc_final: 0.6425 (tpt-90) REVERT: D 253 GLU cc_start: 0.6774 (tp30) cc_final: 0.6503 (tp30) REVERT: D 302 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6150 (pp20) REVERT: F 472 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.6129 (mtt180) REVERT: G 33 ARG cc_start: 0.6277 (ttp-110) cc_final: 0.5646 (ptt180) REVERT: G 118 LYS cc_start: 0.3673 (tttt) cc_final: 0.3014 (mttm) outliers start: 151 outliers final: 102 residues processed: 544 average time/residue: 0.2341 time to fit residues: 208.6881 Evaluate side-chains 490 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 383 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 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 480 ARG 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 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 262 THR Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 337 ASP Chi-restraints excluded: chain M residue 373 LEU 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 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 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 217 GLU 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 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 109 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 247 GLU 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 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 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 220 LEU 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 407 MET Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 501 THR 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 218 GLU 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 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 509 THR Chi-restraints excluded: chain G residue 516 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 286 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 417 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 213 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 442 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 161 optimal weight: 0.0270 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN M 256 GLN M 288 ASN ** M 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN B 152 ASN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 438 GLN D 288 ASN ** F 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 GLN G 713 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129546 restraints weight = 70804.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131545 restraints weight = 41533.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132210 restraints weight = 25853.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132628 restraints weight = 19841.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132870 restraints weight = 17871.729| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 36717 Z= 0.262 Angle : 0.810 19.155 50004 Z= 0.422 Chirality : 0.051 0.251 5610 Planarity : 0.012 0.344 6576 Dihedral : 6.807 175.473 5142 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.02 % Rotamer: Outliers : 4.73 % Allowed : 15.78 % Favored : 79.49 % Cbeta Deviations : 0.00 % 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 aren not related in a simple way. whole: -1.45 (0.12), residues: 4641 helix: -0.02 (0.23), residues: 483 sheet: -0.36 (0.14), residues: 1314 loop : -1.48 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.002 ARG F 227 TYR 0.025 0.002 TYR D 136 PHE 0.061 0.003 PHE B 237 TRP 0.035 0.003 TRP D 198 HIS 0.018 0.002 HIS I 218 Details of bonding type rmsd covalent geometry : bond 0.00600 (36666) covalent geometry : angle 0.81030 (50004) hydrogen bonds : bond 0.04940 ( 801) hydrogen bonds : angle 6.50184 ( 2097) Misc. bond : bond 0.01239 ( 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 576 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 397 time to evaluate : 1.452 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: 0.7248 (tt0) cc_final: 0.6640 (pp30) REVERT: I 131 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: I 153 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 83 MET cc_start: 0.4287 (mpp) cc_final: 0.4062 (mtp) REVERT: C 489 ASP cc_start: 0.6125 (p0) cc_final: 0.5818 (p0) REVERT: C 499 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 563 ARG cc_start: 0.6264 (tpt170) cc_final: 0.5918 (mtp180) REVERT: M 89 MET cc_start: 0.5459 (mmt) cc_final: 0.4170 (ppp) REVERT: M 105 TYR cc_start: 0.8349 (t80) cc_final: 0.7312 (t80) REVERT: M 118 LYS cc_start: 0.3519 (tttt) cc_final: 0.2960 (ptpp) REVERT: M 253 GLU cc_start: 0.6817 (mp0) cc_final: 0.6272 (pm20) REVERT: M 295 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6190 (tp40) REVERT: M 661 GLN cc_start: 0.4668 (mp10) cc_final: 0.4271 (tp40) REVERT: M 671 THR cc_start: 0.4167 (OUTLIER) cc_final: 0.3739 (t) REVERT: A 45 ARG cc_start: 0.6681 (mmt-90) cc_final: 0.5979 (mtm180) REVERT: A 145 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6986 (mpt180) REVERT: B 83 MET cc_start: 0.2932 (mpp) cc_final: 0.2211 (mtt) REVERT: B 217 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: B 277 ASP cc_start: 0.7496 (m-30) cc_final: 0.6884 (m-30) REVERT: D 33 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.5897 (ptt-90) REVERT: D 89 MET cc_start: 0.5201 (tpt) cc_final: 0.3644 (ppp) REVERT: D 253 GLU cc_start: 0.6887 (tp30) cc_final: 0.6671 (tp30) REVERT: D 302 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6314 (pp20) REVERT: F 83 MET cc_start: 0.4134 (ptm) cc_final: 0.3359 (pmm) REVERT: F 417 ILE cc_start: 0.7970 (mm) cc_final: 0.7680 (mm) REVERT: F 472 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6097 (mtt180) REVERT: G 33 ARG cc_start: 0.6377 (ttp-110) cc_final: 0.5682 (ptt-90) REVERT: G 118 LYS cc_start: 0.3429 (tttt) cc_final: 0.2634 (mttm) REVERT: G 168 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.4772 (mmm160) REVERT: G 297 ARG cc_start: 0.4933 (mtp180) cc_final: 0.4609 (mtp85) REVERT: G 313 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8077 (tt) outliers start: 179 outliers final: 133 residues processed: 528 average time/residue: 0.2339 time to fit residues: 201.9751 Evaluate side-chains 490 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 349 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 261 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 287 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 480 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 262 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 509 THR Chi-restraints excluded: chain M residue 515 VAL Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 660 LEU Chi-restraints excluded: chain M residue 671 THR 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 142 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain B residue 217 GLU 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 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 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 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 393 THR Chi-restraints excluded: chain D residue 402 TRP 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 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 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 246 ASP Chi-restraints excluded: chain F residue 174 ILE 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 407 MET 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 G residue 17 ASP Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 72 ASP 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 453 SER 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 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: 6.9990 chunk 30 optimal weight: 50.0000 chunk 184 optimal weight: 50.0000 chunk 375 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 430 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 136 GLN I 231 GLN M 288 ASN M 512 GLN B 257 GLN F 230 GLN ** G 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128905 restraints weight = 70103.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130047 restraints weight = 46032.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131164 restraints weight = 30296.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131871 restraints weight = 21714.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132308 restraints weight = 16743.057| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 36717 Z= 0.203 Angle : 0.731 22.935 50004 Z= 0.380 Chirality : 0.047 0.281 5610 Planarity : 0.012 0.391 6576 Dihedral : 7.238 179.032 5142 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 4.26 % Allowed : 17.23 % Favored : 78.51 % 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 aren not related in a simple way. whole: -1.45 (0.12), residues: 4641 helix: 0.06 (0.23), residues: 483 sheet: -0.32 (0.14), residues: 1263 loop : -1.50 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.001 ARG C 227 TYR 0.019 0.002 TYR F 385 PHE 0.044 0.002 PHE F 237 TRP 0.025 0.002 TRP D 198 HIS 0.007 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00448 (36666) covalent geometry : angle 0.73143 (50004) hydrogen bonds : bond 0.04227 ( 801) hydrogen bonds : angle 6.32853 ( 2097) Misc. bond : bond 0.01266 ( 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 549 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 388 time to evaluate : 1.441 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: I 63 GLN cc_start: 0.7276 (tt0) cc_final: 0.6687 (pp30) REVERT: I 131 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: I 153 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: I 264 LYS cc_start: 0.5829 (tmtt) cc_final: 0.5157 (pttm) REVERT: C 287 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5480 (p0) REVERT: C 496 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6732 (tpt-90) REVERT: C 499 THR cc_start: 0.7244 (OUTLIER) cc_final: 0.6980 (p) REVERT: C 509 ARG cc_start: 0.6144 (ttp80) cc_final: 0.5284 (tmm160) REVERT: C 563 ARG cc_start: 0.6270 (tpt170) cc_final: 0.5957 (mtm180) REVERT: M 89 MET cc_start: 0.5317 (mmt) cc_final: 0.4331 (ppp) REVERT: M 118 LYS cc_start: 0.3447 (tttt) cc_final: 0.2756 (ptpp) REVERT: M 253 GLU cc_start: 0.6710 (mp0) cc_final: 0.6201 (pm20) REVERT: M 402 TRP cc_start: 0.4814 (OUTLIER) cc_final: 0.4354 (t-100) REVERT: M 661 GLN cc_start: 0.4830 (mp10) cc_final: 0.4488 (tp40) REVERT: M 701 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6931 (ptm-80) REVERT: A 45 ARG cc_start: 0.6703 (mmt-90) cc_final: 0.5912 (mtm180) REVERT: A 119 THR cc_start: 0.7481 (p) cc_final: 0.7209 (p) REVERT: A 145 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6864 (mpt180) REVERT: B 83 MET cc_start: 0.3132 (mpp) cc_final: 0.2350 (mtt) REVERT: B 217 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: B 277 ASP cc_start: 0.7439 (m-30) cc_final: 0.6788 (m-30) REVERT: B 470 TYR cc_start: 0.7434 (t80) cc_final: 0.7210 (t80) REVERT: B 506 ASP cc_start: 0.7058 (t70) cc_final: 0.6576 (t70) REVERT: D 33 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.5887 (ptt-90) REVERT: D 89 MET cc_start: 0.5262 (tpt) cc_final: 0.3736 (ppp) REVERT: D 253 GLU cc_start: 0.6854 (tp30) cc_final: 0.6526 (tp30) REVERT: D 302 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6169 (pp20) REVERT: F 83 MET cc_start: 0.4227 (ptm) cc_final: 0.3460 (pmm) REVERT: F 417 ILE cc_start: 0.7927 (mm) cc_final: 0.7672 (mm) REVERT: F 472 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6176 (mtt180) REVERT: F 498 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.7007 (tt) REVERT: G 33 ARG cc_start: 0.6474 (ttp-110) cc_final: 0.5561 (ptt-90) REVERT: G 118 LYS cc_start: 0.3469 (tttt) cc_final: 0.2688 (mttm) REVERT: G 168 ARG cc_start: 0.5242 (OUTLIER) cc_final: 0.4716 (mmm160) outliers start: 161 outliers final: 121 residues processed: 503 average time/residue: 0.2363 time to fit residues: 193.8450 Evaluate side-chains 485 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 353 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 135 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 261 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 287 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 496 ARG 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 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 257 GLU Chi-restraints excluded: chain M residue 288 ASN 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 509 THR Chi-restraints excluded: chain M residue 516 VAL 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 85 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 ARG 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 217 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 343 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 485 ILE 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 D residue 109 VAL Chi-restraints excluded: chain D residue 170 LEU 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 297 ARG Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 402 TRP 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 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 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 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 221 ASN 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 407 MET 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 498 LEU Chi-restraints excluded: chain F residue 501 THR 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 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 270 ILE Chi-restraints excluded: chain G residue 306 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 444 LEU Chi-restraints excluded: chain G residue 453 SER Chi-restraints excluded: chain G residue 477 ASP 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 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: 0.8980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 354 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 chunk 258 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 154 HIS M 127 ASN B 152 ASN B 230 GLN B 257 GLN D 711 GLN ** F 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN G 288 ASN G 295 GLN ** G 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128810 restraints weight = 70683.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130762 restraints weight = 40165.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131428 restraints weight = 26279.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132022 restraints weight = 19691.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132074 restraints weight = 16802.432| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 36717 Z= 0.222 Angle : 0.772 26.485 50004 Z= 0.400 Chirality : 0.048 0.379 5610 Planarity : 0.015 0.502 6576 Dihedral : 7.179 179.107 5142 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 4.34 % Allowed : 17.50 % Favored : 78.17 % 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 aren not related in a simple way. whole: -1.58 (0.12), residues: 4641 helix: -0.02 (0.23), residues: 480 sheet: -0.46 (0.14), residues: 1254 loop : -1.56 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.002 ARG F 227 TYR 0.018 0.002 TYR M 567 PHE 0.049 0.002 PHE F 237 TRP 0.030 0.002 TRP D 12 HIS 0.007 0.001 HIS I 218 Details of bonding type rmsd covalent geometry : bond 0.00489 (36666) covalent geometry : angle 0.77163 (50004) hydrogen bonds : bond 0.04304 ( 801) hydrogen bonds : angle 6.36711 ( 2097) Misc. bond : bond 0.01542 ( 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 532 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 368 time to evaluate : 1.413 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: 0.7211 (tt0) cc_final: 0.6781 (pp30) REVERT: I 131 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6036 (m-30) REVERT: I 153 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: I 264 LYS cc_start: 0.5950 (tmtt) cc_final: 0.5282 (pttm) REVERT: C 139 TRP cc_start: -0.0628 (OUTLIER) cc_final: -0.1004 (m-90) REVERT: C 287 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5666 (p0) REVERT: C 386 GLN cc_start: 0.6599 (mt0) cc_final: 0.6395 (mt0) REVERT: C 496 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6780 (tpt-90) REVERT: C 499 THR cc_start: 0.7260 (OUTLIER) cc_final: 0.7009 (p) REVERT: C 509 ARG cc_start: 0.6254 (ttp80) cc_final: 0.5363 (tmm160) REVERT: C 563 ARG cc_start: 0.6294 (tpt170) cc_final: 0.5873 (mtm180) REVERT: M 89 MET cc_start: 0.5517 (mmt) cc_final: 0.4429 (ppp) REVERT: M 118 LYS cc_start: 0.3543 (tttt) cc_final: 0.2774 (ptpp) REVERT: M 253 GLU cc_start: 0.6778 (mp0) cc_final: 0.6191 (pm20) REVERT: M 313 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7817 (tt) REVERT: M 402 TRP cc_start: 0.4868 (OUTLIER) cc_final: 0.4315 (t-100) REVERT: M 671 THR cc_start: 0.4358 (OUTLIER) cc_final: 0.3662 (p) REVERT: M 701 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6865 (ptm-80) REVERT: A 45 ARG cc_start: 0.6737 (mmt-90) cc_final: 0.5965 (mtm180) REVERT: A 119 THR cc_start: 0.7502 (p) cc_final: 0.7251 (p) REVERT: A 145 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6896 (mpt180) REVERT: B 83 MET cc_start: 0.2922 (mpp) cc_final: 0.2635 (mtt) REVERT: B 152 ASN cc_start: 0.6016 (t0) cc_final: 0.5814 (t0) REVERT: B 217 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: B 277 ASP cc_start: 0.7429 (m-30) cc_final: 0.6733 (m-30) REVERT: B 470 TYR cc_start: 0.7460 (t80) cc_final: 0.7208 (t80) REVERT: D 33 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.5897 (ptt-90) REVERT: D 253 GLU cc_start: 0.6912 (tp30) cc_final: 0.6604 (tp30) REVERT: D 302 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6289 (pp20) REVERT: D 433 ASN cc_start: 0.7083 (t0) cc_final: 0.6701 (m110) REVERT: F 78 LEU cc_start: 0.0880 (OUTLIER) cc_final: 0.0581 (tt) REVERT: F 83 MET cc_start: 0.4322 (ptm) cc_final: 0.3511 (pmm) REVERT: F 417 ILE cc_start: 0.7922 (mm) cc_final: 0.7684 (mm) REVERT: F 498 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7014 (tt) REVERT: G 33 ARG cc_start: 0.6590 (ttp-110) cc_final: 0.5591 (ptt-90) REVERT: G 72 ASP cc_start: 0.7342 (t0) cc_final: 0.6969 (t70) REVERT: G 118 LYS cc_start: 0.3477 (tttt) cc_final: 0.2698 (mttm) REVERT: G 168 ARG cc_start: 0.5239 (OUTLIER) cc_final: 0.4657 (mmm160) REVERT: G 313 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7910 (tt) outliers start: 164 outliers final: 130 residues processed: 483 average time/residue: 0.1974 time to fit residues: 157.2243 Evaluate side-chains 494 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 348 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 261 MET Chi-restraints excluded: chain C residue 139 TRP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 287 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 496 ARG 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 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 257 GLU 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 644 ASP Chi-restraints excluded: chain M residue 671 THR 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 85 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 ARG 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 217 GLU 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 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 504 ASP 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 D residue 109 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 257 GLU 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 393 THR Chi-restraints excluded: chain D residue 402 TRP 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 532 THR 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 261 MET Chi-restraints excluded: chain F residue 78 LEU 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 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 407 MET 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 480 ARG Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 501 THR 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 170 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 461 optimal weight: 2.9990 chunk 305 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 295 GLN M 661 GLN B 257 GLN G 295 GLN ** G 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130099 restraints weight = 70564.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132114 restraints weight = 40771.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132681 restraints weight = 26320.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134138 restraints weight = 20351.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133626 restraints weight = 14552.196| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5464 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= 0.176 Angle : 0.737 25.374 50004 Z= 0.380 Chirality : 0.047 0.367 5610 Planarity : 0.013 0.359 6576 Dihedral : 7.092 178.367 5142 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.70 % Favored : 93.15 % Rotamer: Outliers : 3.65 % Allowed : 18.48 % Favored : 77.87 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: -1.56 (0.12), residues: 4641 helix: 0.16 (0.24), residues: 480 sheet: -0.50 (0.14), residues: 1287 loop : -1.55 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.002 ARG F 227 TYR 0.018 0.001 TYR M 567 PHE 0.055 0.002 PHE F 237 TRP 0.022 0.002 TRP G 12 HIS 0.005 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00370 (36666) covalent geometry : angle 0.73679 (50004) hydrogen bonds : bond 0.03836 ( 801) hydrogen bonds : angle 6.19935 ( 2097) Misc. bond : bond 0.01452 ( 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 509 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 371 time to evaluate : 1.363 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 63 GLN cc_start: 0.7169 (tt0) cc_final: 0.6731 (pp30) REVERT: I 95 TYR cc_start: 0.8460 (m-80) cc_final: 0.8224 (m-80) REVERT: I 131 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: I 153 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: I 264 LYS cc_start: 0.5981 (tmtt) cc_final: 0.5295 (pttm) REVERT: C 287 ASP cc_start: 0.5885 (OUTLIER) cc_final: 0.5579 (p0) REVERT: C 386 GLN cc_start: 0.6404 (mt0) cc_final: 0.6193 (mt0) REVERT: C 470 TYR cc_start: 0.7125 (t80) cc_final: 0.6897 (t80) REVERT: C 496 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6667 (tpt-90) REVERT: C 499 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6957 (p) REVERT: C 509 ARG cc_start: 0.6236 (ttp80) cc_final: 0.5369 (tmm160) REVERT: C 563 ARG cc_start: 0.6203 (tpt170) cc_final: 0.5852 (mtm180) REVERT: M 89 MET cc_start: 0.5520 (mmt) cc_final: 0.4453 (ppp) REVERT: M 118 LYS cc_start: 0.3489 (tttt) cc_final: 0.2763 (ptpp) REVERT: M 253 GLU cc_start: 0.6697 (mp0) cc_final: 0.6127 (pm20) REVERT: M 402 TRP cc_start: 0.4973 (OUTLIER) cc_final: 0.4539 (t-100) REVERT: M 661 GLN cc_start: 0.5564 (OUTLIER) cc_final: 0.4928 (tp40) REVERT: A 45 ARG cc_start: 0.6623 (mmt-90) cc_final: 0.5811 (mtm180) REVERT: A 145 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6857 (mpt180) REVERT: B 217 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6364 (mt-10) REVERT: B 277 ASP cc_start: 0.7389 (m-30) cc_final: 0.6715 (m-30) REVERT: D 33 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.5893 (ptt-90) REVERT: D 253 GLU cc_start: 0.6865 (tp30) cc_final: 0.6536 (tp30) REVERT: D 302 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6199 (pp20) REVERT: D 433 ASN cc_start: 0.6935 (t0) cc_final: 0.6502 (m110) REVERT: F 83 MET cc_start: 0.4430 (ptm) cc_final: 0.3624 (pmm) REVERT: F 417 ILE cc_start: 0.7889 (mm) cc_final: 0.7674 (mm) REVERT: G 33 ARG cc_start: 0.6597 (ttp-110) cc_final: 0.5588 (ptt-90) REVERT: G 72 ASP cc_start: 0.7313 (t0) cc_final: 0.6857 (t70) REVERT: G 118 LYS cc_start: 0.3348 (tttt) cc_final: 0.2560 (mttm) REVERT: G 313 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7799 (tt) outliers start: 138 outliers final: 109 residues processed: 469 average time/residue: 0.2121 time to fit residues: 162.8605 Evaluate side-chains 475 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 356 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 261 MET Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 287 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 456 VAL Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG 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 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 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 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 644 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 85 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 217 GLU 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 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 498 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR 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 402 TRP 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 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 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 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 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 416 TRP 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 523 THR Chi-restraints excluded: chain G residue 70 THR 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 481 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 594 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 311 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 446 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 95 optimal weight: 0.0060 chunk 148 optimal weight: 0.0040 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: 0.5980 overall best weight: 0.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN D 295 GLN D 580 ASN ** D 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN F 394 ASN ** G 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127899 restraints weight = 70757.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129497 restraints weight = 40861.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130386 restraints weight = 28206.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131219 restraints weight = 20563.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131569 restraints weight = 15715.434| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.331 36717 Z= 0.396 Angle : 1.065 59.200 50004 Z= 0.572 Chirality : 0.052 0.802 5610 Planarity : 0.015 0.515 6576 Dihedral : 7.731 178.194 5142 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.70 % Favored : 93.13 % Rotamer: Outliers : 3.46 % Allowed : 18.61 % Favored : 77.93 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.55 (0.12), residues: 4641 helix: 0.19 (0.24), residues: 480 sheet: -0.50 (0.14), residues: 1287 loop : -1.55 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.143 0.002 ARG B 227 TYR 0.013 0.001 TYR I 95 PHE 0.053 0.002 PHE F 237 TRP 0.022 0.001 TRP G 12 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00626 (36666) covalent geometry : angle 1.06466 (50004) hydrogen bonds : bond 0.03927 ( 801) hydrogen bonds : angle 6.23712 ( 2097) Misc. bond : bond 0.04310 ( 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 489 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 358 time to evaluate : 1.189 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: I 63 GLN cc_start: 0.7184 (tt0) cc_final: 0.6770 (pp30) REVERT: I 95 TYR cc_start: 0.8452 (m-80) cc_final: 0.8218 (m-80) REVERT: I 131 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6144 (m-30) REVERT: I 134 MET cc_start: 0.6401 (mmm) cc_final: 0.6112 (mmm) REVERT: I 153 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: I 264 LYS cc_start: 0.5934 (tmtt) cc_final: 0.5269 (pttm) REVERT: C 287 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5612 (p0) REVERT: C 496 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6669 (tpt-90) REVERT: C 499 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6949 (p) REVERT: C 509 ARG cc_start: 0.6236 (ttp80) cc_final: 0.5362 (tmm160) REVERT: C 563 ARG cc_start: 0.6177 (tpt170) cc_final: 0.5825 (mtm180) REVERT: M 89 MET cc_start: 0.5536 (mmt) cc_final: 0.4453 (ppp) REVERT: M 118 LYS cc_start: 0.3536 (tttt) cc_final: 0.2787 (ptpp) REVERT: M 253 GLU cc_start: 0.6688 (mp0) cc_final: 0.6124 (pm20) REVERT: M 402 TRP cc_start: 0.4953 (OUTLIER) cc_final: 0.4521 (t-100) REVERT: A 45 ARG cc_start: 0.6621 (mmt-90) cc_final: 0.5824 (mtm180) REVERT: A 145 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6837 (mpt180) REVERT: B 217 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: B 277 ASP cc_start: 0.7388 (m-30) cc_final: 0.6734 (m-30) REVERT: D 33 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.5881 (ptt-90) REVERT: D 253 GLU cc_start: 0.6894 (tp30) cc_final: 0.6541 (tp30) REVERT: D 302 GLU cc_start: 0.6431 (mm-30) cc_final: 0.6183 (pp20) REVERT: D 433 ASN cc_start: 0.6925 (t0) cc_final: 0.6525 (m110) REVERT: F 78 LEU cc_start: 0.0859 (OUTLIER) cc_final: 0.0647 (mp) REVERT: F 83 MET cc_start: 0.4427 (ptm) cc_final: 0.3675 (pmm) REVERT: F 417 ILE cc_start: 0.7892 (mm) cc_final: 0.7675 (mm) REVERT: G 33 ARG cc_start: 0.6589 (ttp-110) cc_final: 0.5586 (ptt-90) REVERT: G 72 ASP cc_start: 0.7304 (t0) cc_final: 0.6834 (t70) REVERT: G 118 LYS cc_start: 0.3351 (tttt) cc_final: 0.2564 (mttm) REVERT: G 313 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7803 (tt) outliers start: 131 outliers final: 114 residues processed: 454 average time/residue: 0.1977 time to fit residues: 148.5566 Evaluate side-chains 471 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 347 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 261 MET Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 287 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 401 VAL Chi-restraints excluded: chain C residue 416 TRP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 496 ARG 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 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 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 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 644 ASP Chi-restraints excluded: chain M residue 678 SER Chi-restraints excluded: chain A residue 12 ASP 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 142 THR Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 217 GLU 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 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 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 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 402 TRP 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 516 VAL Chi-restraints excluded: chain D residue 532 THR 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 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 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 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 416 TRP 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 523 THR Chi-restraints excluded: chain F residue 557 LEU 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 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 509 THR Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 594 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 343 optimal weight: 0.0970 chunk 122 optimal weight: 0.0970 chunk 380 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN D 580 ASN ** D 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN F 394 ASN ** G 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129986 restraints weight = 70136.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131437 restraints weight = 41132.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132017 restraints weight = 28570.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132586 restraints weight = 21886.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132919 restraints weight = 17520.910| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 36717 Z= 0.274 Angle : 0.961 59.199 50004 Z= 0.506 Chirality : 0.050 0.649 5610 Planarity : 0.015 0.466 6576 Dihedral : 7.452 177.702 5142 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.79 % Favored : 93.06 % Rotamer: Outliers : 3.62 % Allowed : 18.48 % Favored : 77.90 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.56 (0.12), residues: 4641 helix: 0.14 (0.24), residues: 480 sheet: -0.50 (0.14), residues: 1287 loop : -1.55 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.002 ARG C 466 TYR 0.014 0.001 TYR M 567 PHE 0.051 0.002 PHE F 237 TRP 0.022 0.002 TRP G 12 HIS 0.005 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00535 (36666) covalent geometry : angle 0.96057 (50004) hydrogen bonds : bond 0.04026 ( 801) hydrogen bonds : angle 6.23556 ( 2097) Misc. bond : bond 0.03017 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8060.63 seconds wall clock time: 139 minutes 11.21 seconds (8351.21 seconds total)