Starting phenix.real_space_refine on Mon Jul 6 13:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk7_19263/07_2026/8rk7_19263.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 3 7.16 5 S 105 5.16 5 C 22554 2.51 5 N 6324 2.21 5 O 6891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2099 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4278 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 30, 'TRANS': 523} Chain: "M" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5581 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 40, 'TRANS': 686} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Restraints were copied for chains: A, E, B, F, D, G Time building chain proxies: 9.63, per 1000 atoms: 0.27 Number of scatterers: 35877 At special positions: 0 Unit cell: (209.234, 210.067, 201.731, 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=57, symmetry=0 Number of additional bonds: simple=57, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8472 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 57 sheets defined 15.3% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 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: 3.540A 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: 3.647A 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: 3.759A pdb=" N LEU M 425 " --> pdb=" O PRO M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 430 through 436 removed outlier: 4.001A 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: 3.812A 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: 3.647A 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: 3.615A pdb=" N VAL B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.534A 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: 3.652A 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: 4.001A 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: 3.811A 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: 4.209A 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: 3.861A 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: 3.540A 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: 3.647A pdb=" N ILE F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 25 " --> pdb=" O THR F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 removed outlier: 4.128A 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: 3.567A 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: 3.653A 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: 3.758A pdb=" N LEU G 425 " --> pdb=" O PRO G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 436 removed outlier: 4.001A 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: 3.812A 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: 4.209A 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: 5.615A 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: 5.237A 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: 5.774A pdb=" N THR M 381 " --> pdb=" O GLY M 366 " (cutoff:3.500A) removed outlier: 5.148A 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: 7.232A 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: 6.794A 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: 3.513A 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: 7.569A pdb=" N TYR M 14 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.576A 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: 6.812A 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: 6.683A pdb=" N GLY M 65 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.524A 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: 3.550A 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: 5.281A 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: 4.448A pdb=" N CYS M 30 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE M 44 " --> pdb=" O GLU M 28 " (cutoff:3.500A) removed outlier: 4.658A 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: 3.771A 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: 6.329A 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: 7.185A 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: 4.034A pdb=" N GLY M 474 " --> pdb=" O LEU M 460 " (cutoff:3.500A) removed outlier: 6.989A 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: 4.634A 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: 3.663A pdb=" N ARG M 537 " --> pdb=" O GLY M 493 " (cutoff:3.500A) removed outlier: 6.626A 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: 5.482A 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: 5.615A 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: 5.237A pdb=" N ILE A 112 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 128 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 7.068A 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: 5.774A pdb=" N THR D 381 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE D 368 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 7.382A 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: 7.232A 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: 4.877A pdb=" N GLY B 86 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.593A 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: 6.794A 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: 4.346A 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: 3.540A pdb=" N LEU B 198 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.576A pdb=" N PHE D 16 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 107 " --> pdb=" O PHE D 16 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 101 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 110 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 5.548A 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: 3.550A 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: 5.280A 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: 3.771A 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: 7.223A pdb=" N GLN D 268 " --> pdb=" O GLU D 301 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE D 303 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 6.329A 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: 4.676A 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: 4.034A 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: 6.930A 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: 4.425A pdb=" N GLY D 493 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 3.663A 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: 5.482A pdb=" N SER E 29 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 3.679A 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: 5.615A 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: 5.407A pdb=" N VAL E 128 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 7.068A 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: 5.774A pdb=" N THR G 381 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 5.148A 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: 7.262A 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: 4.876A pdb=" N GLY F 86 " --> pdb=" O THR F 170 " (cutoff:3.500A) removed outlier: 3.527A 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: 6.794A 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: 4.346A 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: 3.718A 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: 5.547A 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: 3.588A 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: 6.869A 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: 3.771A 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: 7.185A 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: 6.931A 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: 4.425A 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: 6.626A 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: 6.312A 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: 7.52 Time building geometry restraints manager: 3.62 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: 7773 1.46 - 1.58: 16521 1.58 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 36666 Sorted by residual: bond pdb=" C PRO D 399 " pdb=" N PRO D 400 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+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 1.69e+00 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 1.64e+00 bond pdb=" N PRO F 52 " pdb=" CD PRO F 52 " ideal model delta sigma weight residual 1.473 1.489 -0.016 1.40e-02 5.10e+03 1.32e+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 1.30e+00 ... (remaining 36661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 48950 1.24 - 2.47: 761 2.47 - 3.71: 235 3.71 - 4.94: 43 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 2.22e+01 angle pdb=" N GLY G 727 " pdb=" CA GLY G 727 " pdb=" C GLY G 727 " ideal model delta sigma weight residual 113.24 107.07 6.17 1.31e+00 5.83e-01 2.22e+01 angle pdb=" N GLY D 727 " pdb=" CA GLY D 727 " pdb=" C GLY D 727 " ideal model delta sigma weight residual 113.24 107.08 6.16 1.31e+00 5.83e-01 2.21e+01 angle pdb=" N ILE G 650 " pdb=" CA ILE G 650 " pdb=" C ILE G 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 9.46e+00 ... (remaining 49999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 19828 17.90 - 35.81: 1536 35.81 - 53.71: 272 53.71 - 71.62: 60 71.62 - 89.52: 24 Dihedral angle restraints: 21720 sinusoidal: 8448 harmonic: 13272 Sorted by residual: 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 180.00 152.37 27.63 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 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 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 180.00 152.41 27.59 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 21717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5038 0.075 - 0.151: 569 0.151 - 0.226: 0 0.226 - 0.302: 0 0.302 - 0.377: 3 Chirality restraints: 5610 Sorted by residual: 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 3.56e+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 3.56e+00 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 3.53e+00 ... (remaining 5607 not shown) Planarity restraints: 6576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 51 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 52 " 0.115 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 delta sigma weight rms_deltas residual plane pdb=" C GLN F 51 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO F 52 " 0.115 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 6.61e-02 7.00e+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 ... (remaining 6573 not shown) Histogram of nonbonded interaction distances: 0.45 - 1.34: 153 1.34 - 2.23: 780 2.23 - 3.12: 29503 3.12 - 4.01: 89717 4.01 - 4.90: 163201 Warning: very small nonbonded interaction distances. Nonbonded interactions: 283354 Sorted by model distance: nonbonded pdb=" N PRO I 48 " pdb=" NH1 ARG B 400 " model vdw 0.452 3.200 nonbonded pdb=" NH1 ARG C 400 " pdb=" N PRO E 48 " model vdw 0.452 3.200 nonbonded pdb=" N PRO A 48 " pdb=" NH1 ARG F 400 " model vdw 0.452 3.200 nonbonded pdb=" CG LYS I 264 " pdb=" CE3 TRP D 402 " model vdw 0.568 3.740 nonbonded pdb=" CG LYS A 264 " pdb=" CE3 TRP G 402 " model vdw 0.568 3.740 ... (remaining 283349 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: 0.08 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: 14.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.970 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 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 : 0.016 0.809 36723 Z= 1.621 Angle : 0.454 6.175 50004 Z= 0.244 Chirality : 0.043 0.377 5610 Planarity : 0.004 0.066 6576 Dihedral : 13.293 89.519 13248 Min Nonbonded Distance : 0.452 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (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 C 102 PHE 0.008 0.001 PHE M 724 TRP 0.006 0.001 TRP C 99 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 (36666) covalent geometry : angle 0.45416 / 0.24 (50004) hydrogen bonds : bond 0.24020 / 16.50 ( 801) hydrogen bonds : angle 9.69361 / 6.87 ( 2097) Misc. bond : bond 0.41076 / 26.75 ( 57) *********************** 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 948 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 948 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 23 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8124 (ptm160) REVERT: C 83 MET cc_start: 0.5551 (mpp) cc_final: 0.4977 (mtp) REVERT: C 252 ILE cc_start: 0.7632 (tt) cc_final: 0.7113 (tt) REVERT: C 282 MET cc_start: 0.7841 (ttt) cc_final: 0.7522 (tmm) REVERT: C 306 LEU cc_start: 0.8129 (mt) cc_final: 0.7718 (mp) REVERT: C 501 THR cc_start: 0.5668 (p) cc_final: 0.5115 (t) REVERT: C 513 ASP cc_start: 0.7621 (p0) cc_final: 0.7121 (p0) REVERT: M 194 LEU cc_start: 0.6447 (mt) cc_final: 0.6149 (mt) REVERT: M 335 VAL cc_start: 0.7416 (t) cc_final: 0.7193 (t) REVERT: M 351 ILE cc_start: 0.7755 (pt) cc_final: 0.7385 (pt) REVERT: M 408 THR cc_start: 0.3567 (t) cc_final: 0.2997 (p) REVERT: M 528 TYR cc_start: 0.6340 (t80) cc_final: 0.5889 (m-80) REVERT: M 534 THR cc_start: 0.8560 (m) cc_final: 0.8283 (p) REVERT: M 539 CYS cc_start: 0.7353 (m) cc_final: 0.6264 (t) REVERT: M 557 ASP cc_start: 0.6974 (t70) cc_final: 0.6735 (t70) REVERT: A 23 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8019 (ptm160) REVERT: A 114 ASP cc_start: 0.4756 (t0) cc_final: 0.4122 (t0) REVERT: B 83 MET cc_start: 0.5577 (mpp) cc_final: 0.4677 (mtt) REVERT: B 282 MET cc_start: 0.7866 (ttt) cc_final: 0.7616 (tmm) REVERT: B 306 LEU cc_start: 0.8180 (mt) cc_final: 0.7879 (mp) REVERT: B 340 THR cc_start: 0.7859 (p) cc_final: 0.7297 (p) REVERT: B 501 THR cc_start: 0.5589 (p) cc_final: 0.5004 (t) REVERT: B 513 ASP cc_start: 0.7602 (p0) cc_final: 0.7198 (p0) REVERT: D 186 THR cc_start: 0.8079 (m) cc_final: 0.7778 (p) REVERT: D 351 ILE cc_start: 0.7663 (pt) cc_final: 0.7284 (pt) REVERT: D 408 THR cc_start: 0.3616 (t) cc_final: 0.3168 (p) REVERT: D 539 CYS cc_start: 0.7292 (m) cc_final: 0.6393 (t) REVERT: E 23 ARG cc_start: 0.8386 (ttt180) cc_final: 0.8056 (ptm160) REVERT: E 114 ASP cc_start: 0.5107 (t0) cc_final: 0.4764 (t0) REVERT: F 306 LEU cc_start: 0.8207 (mt) cc_final: 0.7823 (mp) REVERT: F 437 GLN cc_start: 0.6973 (mp10) cc_final: 0.6722 (mt0) REVERT: F 501 THR cc_start: 0.5469 (p) cc_final: 0.4953 (t) REVERT: F 513 ASP cc_start: 0.7506 (p0) cc_final: 0.7246 (p0) REVERT: G 186 THR cc_start: 0.8119 (m) cc_final: 0.7866 (p) REVERT: G 351 ILE cc_start: 0.7738 (pt) cc_final: 0.7384 (pt) REVERT: G 534 THR cc_start: 0.8512 (m) cc_final: 0.8281 (p) REVERT: G 539 CYS cc_start: 0.7111 (m) cc_final: 0.6128 (t) REVERT: G 557 ASP cc_start: 0.7190 (t70) cc_final: 0.6882 (t70) outliers start: 0 outliers final: 0 residues processed: 948 average time/residue: 0.2337 time to fit residues: 355.5561 Evaluate side-chains 438 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 6.9990 chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 0.9980 chunk 455 optimal weight: 0.0570 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.0060 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 98 HIS C 446 HIS C 494 HIS C 545 HIS M 49 GLN ** M 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN E 98 HIS F 446 HIS F 494 HIS G 49 GLN ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.108020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.096431 restraints weight = 171581.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097583 restraints weight = 113212.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097992 restraints weight = 75079.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.098301 restraints weight = 57101.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098732 restraints weight = 47657.442| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 36723 Z= 0.226 Angle : 0.848 33.252 50004 Z= 0.438 Chirality : 0.052 0.492 5610 Planarity : 0.015 0.431 6576 Dihedral : 5.748 116.490 5142 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.05 % Favored : 93.75 % Rotamer: Outliers : 0.79 % Allowed : 4.47 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.12), residues: 4641 helix: 0.55 (0.24), residues: 462 sheet: -0.02 (0.15), residues: 1278 loop : -1.03 (0.12), residues: 2901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG B 400 TYR 0.022 0.001 TYR D 136 PHE 0.029 0.002 PHE F 427 TRP 0.033 0.002 TRP M 402 HIS 0.004 0.001 HIS B 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (36666) covalent geometry : angle 0.84755 / 0.44 (50004) hydrogen bonds : bond 0.05505 / 3.80 ( 801) hydrogen bonds : angle 7.65577 / 5.38 ( 2097) Misc. bond : bond 0.01335 / 0.92 ( 57) *********************** 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 626 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 596 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 92 LEU cc_start: 0.7517 (tp) cc_final: 0.7293 (tp) REVERT: I 134 MET cc_start: 0.7608 (mmt) cc_final: 0.7346 (mmt) REVERT: I 203 ASN cc_start: 0.6958 (m-40) cc_final: 0.6514 (m-40) REVERT: I 268 ASP cc_start: 0.7125 (p0) cc_final: 0.6910 (p0) REVERT: I 270 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7164 (p0) REVERT: C 501 THR cc_start: 0.5791 (p) cc_final: 0.5491 (t) REVERT: M 218 GLU cc_start: 0.6555 (mp0) cc_final: 0.6265 (mp0) REVERT: M 528 TYR cc_start: 0.6856 (t80) cc_final: 0.6277 (m-80) REVERT: M 539 CYS cc_start: 0.7562 (m) cc_final: 0.6686 (t) REVERT: A 270 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7108 (p0) REVERT: B 83 MET cc_start: 0.4529 (mpp) cc_final: 0.4014 (mpp) REVERT: B 282 MET cc_start: 0.7722 (ttt) cc_final: 0.7294 (tmm) REVERT: B 501 THR cc_start: 0.5643 (p) cc_final: 0.5295 (t) REVERT: B 513 ASP cc_start: 0.7262 (p0) cc_final: 0.6985 (p0) REVERT: D 56 GLU cc_start: 0.7154 (pm20) cc_final: 0.5670 (pt0) REVERT: D 218 GLU cc_start: 0.6520 (mp0) cc_final: 0.6286 (mp0) REVERT: D 528 TYR cc_start: 0.6766 (t80) cc_final: 0.6206 (m-80) REVERT: D 539 CYS cc_start: 0.7527 (m) cc_final: 0.6704 (t) REVERT: E 23 ARG cc_start: 0.8298 (ttt180) cc_final: 0.7677 (ttt90) REVERT: E 268 ASP cc_start: 0.6752 (p0) cc_final: 0.6405 (p0) REVERT: E 270 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6876 (p0) REVERT: F 83 MET cc_start: 0.4919 (mpp) cc_final: 0.3954 (ptp) REVERT: F 340 THR cc_start: 0.8650 (p) cc_final: 0.8249 (t) REVERT: F 501 THR cc_start: 0.5667 (p) cc_final: 0.5375 (t) REVERT: G 528 TYR cc_start: 0.6702 (t80) cc_final: 0.6164 (m-80) REVERT: G 539 CYS cc_start: 0.7350 (m) cc_final: 0.6271 (t) outliers start: 30 outliers final: 6 residues processed: 618 average time/residue: 0.2293 time to fit residues: 232.1100 Evaluate side-chains 371 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 362 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 99 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 428 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 437 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN C 124 GLN C 494 HIS M 8 GLN ** M 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 713 HIS A 98 HIS B 74 ASN B 87 ASN B 124 GLN B 494 HIS D 8 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS E 20 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN F 74 ASN F 124 GLN G 8 GLN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 GLN ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071127 restraints weight = 170379.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071528 restraints weight = 113752.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072086 restraints weight = 90086.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.072653 restraints weight = 62935.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072812 restraints weight = 46853.805| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 36723 Z= 0.432 Angle : 1.103 23.350 50004 Z= 0.579 Chirality : 0.069 2.165 5610 Planarity : 0.012 0.518 6576 Dihedral : 7.796 168.922 5142 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.93 % Favored : 91.94 % Rotamer: Outliers : 0.90 % Allowed : 7.98 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.12), residues: 4641 helix: -0.50 (0.22), residues: 483 sheet: -0.65 (0.14), residues: 1278 loop : -1.78 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.002 ARG M 323 TYR 0.039 0.003 TYR B 385 PHE 0.039 0.004 PHE F 427 TRP 0.037 0.003 TRP I 117 HIS 0.018 0.003 HIS C 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00908 / 0.43 (36666) covalent geometry : angle 1.10290 / 0.58 (50004) hydrogen bonds : bond 0.06083 / 4.12 ( 801) hydrogen bonds : angle 7.34355 / 5.30 ( 2097) Misc. bond : bond 0.01801 / 1.24 ( 57) *********************** 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 436 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 402 time to evaluate : 1.455 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: I 134 MET cc_start: 0.7591 (mmt) cc_final: 0.7309 (mmm) REVERT: I 224 GLU cc_start: 0.6401 (mp0) cc_final: 0.6152 (mp0) REVERT: C 83 MET cc_start: 0.4977 (mpp) cc_final: 0.4303 (mtp) REVERT: C 186 SER cc_start: 0.8779 (m) cc_final: 0.8476 (p) REVERT: C 417 ILE cc_start: 0.8638 (pt) cc_final: 0.8426 (pt) REVERT: M 369 GLU cc_start: 0.7252 (pt0) cc_final: 0.6555 (pt0) REVERT: M 379 THR cc_start: 0.8700 (m) cc_final: 0.8412 (p) REVERT: M 557 ASP cc_start: 0.7406 (t70) cc_final: 0.7104 (t0) REVERT: M 636 ILE cc_start: 0.6722 (mm) cc_final: 0.6518 (mm) REVERT: B 83 MET cc_start: 0.4696 (mpp) cc_final: 0.3926 (mtp) REVERT: B 178 THR cc_start: 0.7703 (p) cc_final: 0.7484 (p) REVERT: B 186 SER cc_start: 0.8838 (m) cc_final: 0.8450 (p) REVERT: D 218 GLU cc_start: 0.6869 (mp0) cc_final: 0.6574 (mp0) REVERT: D 528 TYR cc_start: 0.7412 (t80) cc_final: 0.7210 (t80) REVERT: E 203 ASN cc_start: 0.7213 (m-40) cc_final: 0.6847 (m110) REVERT: E 270 ASP cc_start: 0.7418 (p0) cc_final: 0.7081 (p0) REVERT: F 83 MET cc_start: 0.5137 (mpp) cc_final: 0.4300 (mtt) REVERT: F 186 SER cc_start: 0.8783 (m) cc_final: 0.8467 (p) REVERT: G 322 MET cc_start: 0.7559 (tmm) cc_final: 0.7304 (tmm) REVERT: G 557 ASP cc_start: 0.7454 (t70) cc_final: 0.6975 (t0) REVERT: G 636 ILE cc_start: 0.6692 (mm) cc_final: 0.6487 (mm) REVERT: G 688 MET cc_start: 0.4568 (mmp) cc_final: 0.4343 (mmp) outliers start: 34 outliers final: 12 residues processed: 434 average time/residue: 0.2314 time to fit residues: 164.5352 Evaluate side-chains 259 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 157 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 340 optimal weight: 0.0770 chunk 315 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 335 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 268 GLN M 287 ASN M 713 HIS ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN D 268 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS E 271 GLN F 87 ASN G 268 GLN G 287 ASN G 713 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.084629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.072630 restraints weight = 163352.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073336 restraints weight = 106402.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073666 restraints weight = 70891.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074120 restraints weight = 52920.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074476 restraints weight = 40438.716| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 36723 Z= 0.177 Angle : 0.747 19.045 50004 Z= 0.383 Chirality : 0.051 1.219 5610 Planarity : 0.007 0.188 6576 Dihedral : 6.845 172.228 5142 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4641 helix: 0.04 (0.23), residues: 480 sheet: -0.50 (0.14), residues: 1302 loop : -1.57 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 211 TYR 0.021 0.001 TYR B 102 PHE 0.066 0.002 PHE I 208 TRP 0.021 0.002 TRP A 273 HIS 0.004 0.001 HIS G 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (36666) covalent geometry : angle 0.74701 / 0.38 (50004) hydrogen bonds : bond 0.03982 / 2.75 ( 801) hydrogen bonds : angle 6.53306 / 4.65 ( 2097) Misc. bond : bond 0.01273 / 0.92 ( 57) *********************** 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 454 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 449 time to evaluate : 1.359 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 134 MET cc_start: 0.7599 (mmt) cc_final: 0.6973 (mmt) REVERT: I 224 GLU cc_start: 0.6129 (mp0) cc_final: 0.5838 (mp0) REVERT: I 270 ASP cc_start: 0.7027 (p0) cc_final: 0.6776 (p0) REVERT: C 186 SER cc_start: 0.8637 (m) cc_final: 0.8094 (p) REVERT: C 233 ASP cc_start: 0.7140 (t0) cc_final: 0.6557 (m-30) REVERT: C 473 PHE cc_start: 0.7205 (m-10) cc_final: 0.6874 (m-10) REVERT: C 513 ASP cc_start: 0.7555 (p0) cc_final: 0.7302 (p0) REVERT: M 15 TYR cc_start: 0.6663 (m-80) cc_final: 0.3393 (p90) REVERT: M 130 TRP cc_start: 0.7822 (m100) cc_final: 0.7400 (m100) REVERT: M 218 GLU cc_start: 0.6871 (mp0) cc_final: 0.6669 (mp0) REVERT: M 557 ASP cc_start: 0.7418 (t70) cc_final: 0.6974 (t0) REVERT: M 688 MET cc_start: 0.3956 (mmm) cc_final: 0.3634 (mmm) REVERT: B 83 MET cc_start: 0.4648 (mpp) cc_final: 0.4211 (mtp) REVERT: B 186 SER cc_start: 0.8613 (m) cc_final: 0.8105 (p) REVERT: B 531 MET cc_start: 0.7215 (mtp) cc_final: 0.6812 (mtm) REVERT: D 15 TYR cc_start: 0.6771 (m-80) cc_final: 0.3569 (p90) REVERT: D 233 LEU cc_start: 0.8708 (mt) cc_final: 0.8426 (mt) REVERT: D 477 ASP cc_start: 0.8405 (t0) cc_final: 0.8199 (t0) REVERT: D 557 ASP cc_start: 0.7184 (t70) cc_final: 0.6630 (t0) REVERT: E 270 ASP cc_start: 0.7129 (p0) cc_final: 0.6677 (p0) REVERT: F 186 SER cc_start: 0.8632 (m) cc_final: 0.8260 (p) REVERT: F 473 PHE cc_start: 0.7276 (m-10) cc_final: 0.7009 (m-10) REVERT: F 501 THR cc_start: 0.7023 (p) cc_final: 0.6787 (t) REVERT: G 160 LEU cc_start: 0.7701 (tp) cc_final: 0.7483 (tp) REVERT: G 557 ASP cc_start: 0.7338 (t70) cc_final: 0.7026 (t0) REVERT: G 636 ILE cc_start: 0.6750 (mm) cc_final: 0.6514 (mm) REVERT: G 688 MET cc_start: 0.3941 (mmp) cc_final: 0.3651 (mmm) outliers start: 5 outliers final: 0 residues processed: 453 average time/residue: 0.2240 time to fit residues: 167.0437 Evaluate side-chains 264 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 370 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 11 optimal weight: 0.0570 chunk 242 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 371 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 20 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN E 254 ASN F 160 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.086717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073658 restraints weight = 168197.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.074395 restraints weight = 111889.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074953 restraints weight = 78836.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075392 restraints weight = 56437.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075787 restraints weight = 43711.567| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 36723 Z= 0.184 Angle : 0.724 24.355 50004 Z= 0.364 Chirality : 0.047 0.318 5610 Planarity : 0.007 0.167 6576 Dihedral : 6.278 175.000 5142 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.28 % Favored : 92.59 % Rotamer: Outliers : 0.16 % Allowed : 2.59 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.12), residues: 4641 helix: 0.07 (0.23), residues: 483 sheet: -0.47 (0.14), residues: 1353 loop : -1.48 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.001 ARG B 480 TYR 0.020 0.001 TYR C 102 PHE 0.095 0.002 PHE C 237 TRP 0.034 0.001 TRP G 135 HIS 0.007 0.001 HIS I 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (36666) covalent geometry : angle 0.72379 / 0.36 (50004) hydrogen bonds : bond 0.03755 / 2.59 ( 801) hydrogen bonds : angle 6.16987 / 4.43 ( 2097) Misc. bond : bond 0.01344 / 0.98 ( 57) *********************** 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 376 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 370 time to evaluate : 1.433 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 134 MET cc_start: 0.7572 (mmt) cc_final: 0.7031 (mmt) REVERT: I 224 GLU cc_start: 0.6309 (mp0) cc_final: 0.6063 (mp0) REVERT: I 270 ASP cc_start: 0.7257 (p0) cc_final: 0.6899 (p0) REVERT: C 186 SER cc_start: 0.8620 (m) cc_final: 0.8110 (p) REVERT: C 513 ASP cc_start: 0.7482 (p0) cc_final: 0.7260 (p0) REVERT: M 15 TYR cc_start: 0.6786 (m-80) cc_final: 0.3547 (p90) REVERT: M 369 GLU cc_start: 0.6614 (pt0) cc_final: 0.6109 (pt0) REVERT: M 379 THR cc_start: 0.8737 (m) cc_final: 0.8474 (p) REVERT: M 557 ASP cc_start: 0.7461 (t70) cc_final: 0.7183 (t0) REVERT: M 688 MET cc_start: 0.4108 (mmm) cc_final: 0.3716 (mmm) REVERT: B 83 MET cc_start: 0.4477 (mpp) cc_final: 0.3997 (mtp) REVERT: B 186 SER cc_start: 0.8623 (m) cc_final: 0.8086 (p) REVERT: B 513 ASP cc_start: 0.7321 (p0) cc_final: 0.7103 (p0) REVERT: B 531 MET cc_start: 0.7329 (mtp) cc_final: 0.6931 (mtm) REVERT: D 15 TYR cc_start: 0.6919 (m-80) cc_final: 0.3644 (p90) REVERT: D 377 LYS cc_start: 0.6257 (tttt) cc_final: 0.6046 (ptmt) REVERT: E 224 GLU cc_start: 0.6549 (mp0) cc_final: 0.6166 (mp0) REVERT: E 270 ASP cc_start: 0.7250 (p0) cc_final: 0.6783 (p0) REVERT: F 186 SER cc_start: 0.8700 (m) cc_final: 0.8230 (p) REVERT: F 501 THR cc_start: 0.7143 (p) cc_final: 0.6931 (t) REVERT: F 513 ASP cc_start: 0.7192 (p0) cc_final: 0.6982 (p0) REVERT: F 531 MET cc_start: 0.7627 (mtp) cc_final: 0.7233 (mtm) REVERT: G 557 ASP cc_start: 0.7308 (t70) cc_final: 0.6969 (t0) REVERT: G 636 ILE cc_start: 0.6800 (mm) cc_final: 0.6571 (mm) REVERT: G 688 MET cc_start: 0.4112 (mmp) cc_final: 0.3843 (mmm) outliers start: 6 outliers final: 1 residues processed: 375 average time/residue: 0.2164 time to fit residues: 135.9944 Evaluate side-chains 254 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 286 optimal weight: 8.9990 chunk 84 optimal weight: 0.0980 chunk 417 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 442 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 371 ASN M 713 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 713 HIS E 254 ASN G 287 ASN G 371 ASN G 713 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069078 restraints weight = 164929.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070146 restraints weight = 105761.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070335 restraints weight = 64515.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070680 restraints weight = 49521.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070920 restraints weight = 39024.608| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 36723 Z= 0.204 Angle : 0.748 22.151 50004 Z= 0.375 Chirality : 0.048 0.325 5610 Planarity : 0.007 0.153 6576 Dihedral : 6.346 176.864 5142 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.48 % Favored : 92.39 % Rotamer: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.12), residues: 4641 helix: 0.06 (0.23), residues: 492 sheet: -0.59 (0.14), residues: 1293 loop : -1.41 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.001 ARG B 480 TYR 0.017 0.001 TYR D 159 PHE 0.075 0.002 PHE I 208 TRP 0.025 0.002 TRP M 198 HIS 0.006 0.001 HIS E 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (36666) covalent geometry : angle 0.74809 / 0.38 (50004) hydrogen bonds : bond 0.03775 / 2.60 ( 801) hydrogen bonds : angle 6.00202 / 4.32 ( 2097) Misc. bond : bond 0.01276 / 0.92 ( 57) *********************** 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 334 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 1.398 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: I 134 MET cc_start: 0.7617 (mmt) cc_final: 0.7205 (mmt) REVERT: I 224 GLU cc_start: 0.6302 (mp0) cc_final: 0.5982 (mp0) REVERT: I 270 ASP cc_start: 0.7318 (p0) cc_final: 0.6961 (p0) REVERT: C 186 SER cc_start: 0.8676 (m) cc_final: 0.8255 (p) REVERT: C 513 ASP cc_start: 0.7530 (p0) cc_final: 0.7278 (p0) REVERT: M 15 TYR cc_start: 0.6820 (m-80) cc_final: 0.3623 (p90) REVERT: M 369 GLU cc_start: 0.6905 (pt0) cc_final: 0.6536 (pt0) REVERT: M 379 THR cc_start: 0.8803 (m) cc_final: 0.8558 (p) REVERT: M 557 ASP cc_start: 0.7443 (t70) cc_final: 0.7136 (t0) REVERT: M 636 ILE cc_start: 0.6798 (mm) cc_final: 0.6475 (mm) REVERT: M 688 MET cc_start: 0.4027 (mmm) cc_final: 0.3632 (mmm) REVERT: B 83 MET cc_start: 0.4731 (mpp) cc_final: 0.4334 (mtp) REVERT: B 186 SER cc_start: 0.8654 (m) cc_final: 0.8197 (p) REVERT: B 233 ASP cc_start: 0.7035 (t0) cc_final: 0.6761 (t70) REVERT: B 513 ASP cc_start: 0.7293 (p0) cc_final: 0.7086 (p0) REVERT: B 531 MET cc_start: 0.7529 (mtp) cc_final: 0.7081 (mtm) REVERT: D 15 TYR cc_start: 0.6698 (m-80) cc_final: 0.3545 (p90) REVERT: D 557 ASP cc_start: 0.7455 (t70) cc_final: 0.6942 (t0) REVERT: E 270 ASP cc_start: 0.7208 (p0) cc_final: 0.6606 (p0) REVERT: F 178 THR cc_start: 0.7951 (p) cc_final: 0.7734 (p) REVERT: F 186 SER cc_start: 0.8641 (m) cc_final: 0.8296 (p) REVERT: F 513 ASP cc_start: 0.7258 (p0) cc_final: 0.7044 (p0) REVERT: F 531 MET cc_start: 0.7644 (mtp) cc_final: 0.7132 (mtm) REVERT: G 557 ASP cc_start: 0.7337 (t70) cc_final: 0.7001 (t0) REVERT: G 636 ILE cc_start: 0.6938 (mm) cc_final: 0.6713 (mm) REVERT: G 688 MET cc_start: 0.4119 (mmp) cc_final: 0.3816 (mmm) outliers start: 2 outliers final: 1 residues processed: 333 average time/residue: 0.2079 time to fit residues: 116.4373 Evaluate side-chains 228 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 135 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 184 optimal weight: 0.0970 chunk 375 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 413 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 430 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 14 GLN I 20 GLN I 251 ASN I 254 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 371 ASN ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 713 HIS A 20 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN D 713 HIS E 203 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN G 371 ASN G 713 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.084501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071444 restraints weight = 168603.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072361 restraints weight = 110738.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.072720 restraints weight = 72454.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073056 restraints weight = 55572.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073343 restraints weight = 44069.354| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 36723 Z= 0.187 Angle : 0.768 36.221 50004 Z= 0.378 Chirality : 0.047 0.306 5610 Planarity : 0.007 0.195 6576 Dihedral : 6.306 178.484 5142 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4641 helix: 0.24 (0.24), residues: 492 sheet: -0.56 (0.14), residues: 1293 loop : -1.43 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.001 ARG B 480 TYR 0.027 0.001 TYR F 102 PHE 0.107 0.002 PHE C 237 TRP 0.027 0.001 TRP B 77 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (36666) covalent geometry : angle 0.76834 / 0.38 (50004) hydrogen bonds : bond 0.03572 / 2.47 ( 801) hydrogen bonds : angle 5.89719 / 4.26 ( 2097) Misc. bond : bond 0.01365 / 1.00 ( 57) *********************** 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 327 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.319 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: I 134 MET cc_start: 0.7516 (mmt) cc_final: 0.7217 (mmt) REVERT: I 270 ASP cc_start: 0.7316 (p0) cc_final: 0.6988 (p0) REVERT: C 186 SER cc_start: 0.8604 (m) cc_final: 0.8111 (p) REVERT: C 513 ASP cc_start: 0.7289 (p0) cc_final: 0.7038 (p0) REVERT: M 15 TYR cc_start: 0.6966 (m-80) cc_final: 0.3709 (p90) REVERT: M 369 GLU cc_start: 0.7023 (pt0) cc_final: 0.6327 (pt0) REVERT: M 379 THR cc_start: 0.8806 (m) cc_final: 0.8574 (p) REVERT: M 557 ASP cc_start: 0.7379 (t70) cc_final: 0.7062 (t0) REVERT: M 688 MET cc_start: 0.4073 (mmm) cc_final: 0.3797 (mmm) REVERT: B 83 MET cc_start: 0.4362 (mpp) cc_final: 0.3914 (mtp) REVERT: B 186 SER cc_start: 0.8647 (m) cc_final: 0.8160 (p) REVERT: D 15 TYR cc_start: 0.6844 (m-80) cc_final: 0.3633 (p90) REVERT: D 557 ASP cc_start: 0.7522 (t70) cc_final: 0.6989 (t0) REVERT: E 270 ASP cc_start: 0.7232 (p0) cc_final: 0.6797 (p0) REVERT: F 178 THR cc_start: 0.7970 (p) cc_final: 0.7766 (p) REVERT: F 186 SER cc_start: 0.8656 (m) cc_final: 0.8289 (p) REVERT: F 531 MET cc_start: 0.7614 (mtp) cc_final: 0.7068 (mtm) REVERT: G 15 TYR cc_start: 0.6690 (m-80) cc_final: 0.3721 (p90) REVERT: G 557 ASP cc_start: 0.7287 (t70) cc_final: 0.6950 (t0) REVERT: G 636 ILE cc_start: 0.7084 (mm) cc_final: 0.6827 (mm) REVERT: G 688 MET cc_start: 0.4289 (mmp) cc_final: 0.3956 (mmm) outliers start: 1 outliers final: 1 residues processed: 327 average time/residue: 0.2095 time to fit residues: 116.5898 Evaluate side-chains 232 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 352 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 258 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 20 GLN I 251 ASN I 254 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 GLN M 268 GLN M 371 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 ASN G 713 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069481 restraints weight = 164399.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.070384 restraints weight = 105973.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070743 restraints weight = 68898.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071066 restraints weight = 49864.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071448 restraints weight = 38726.260| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.7795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 36723 Z= 0.154 Angle : 0.741 32.789 50004 Z= 0.359 Chirality : 0.047 0.392 5610 Planarity : 0.006 0.140 6576 Dihedral : 6.642 179.450 5142 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.89 % Rotamer: Outliers : 0.03 % Allowed : 1.00 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4641 helix: 0.28 (0.24), residues: 489 sheet: -0.59 (0.14), residues: 1305 loop : -1.39 (0.12), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.001 ARG B 480 TYR 0.025 0.001 TYR F 102 PHE 0.098 0.002 PHE C 237 TRP 0.023 0.002 TRP F 77 HIS 0.003 0.001 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (36666) covalent geometry : angle 0.74116 / 0.36 (50004) hydrogen bonds : bond 0.03336 / 2.31 ( 801) hydrogen bonds : angle 5.80543 / 4.20 ( 2097) Misc. bond : bond 0.01213 / 0.88 ( 57) *********************** 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 341 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 1.415 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: I 103 GLU cc_start: 0.8217 (tp30) cc_final: 0.8012 (tp30) REVERT: I 134 MET cc_start: 0.7564 (mmt) cc_final: 0.7294 (mmt) REVERT: I 224 GLU cc_start: 0.6480 (mp0) cc_final: 0.6083 (mp0) REVERT: C 186 SER cc_start: 0.8539 (m) cc_final: 0.8026 (p) REVERT: C 513 ASP cc_start: 0.7296 (p0) cc_final: 0.7060 (p0) REVERT: M 15 TYR cc_start: 0.6897 (m-80) cc_final: 0.3765 (p90) REVERT: M 369 GLU cc_start: 0.6974 (pt0) cc_final: 0.6352 (pt0) REVERT: M 379 THR cc_start: 0.8847 (m) cc_final: 0.8625 (p) REVERT: M 557 ASP cc_start: 0.7334 (t70) cc_final: 0.7029 (t0) REVERT: M 688 MET cc_start: 0.3977 (mmm) cc_final: 0.3703 (mmm) REVERT: B 83 MET cc_start: 0.4573 (mpp) cc_final: 0.4214 (mtp) REVERT: B 186 SER cc_start: 0.8610 (m) cc_final: 0.8133 (p) REVERT: B 513 ASP cc_start: 0.7289 (p0) cc_final: 0.7075 (p0) REVERT: D 15 TYR cc_start: 0.6853 (m-80) cc_final: 0.3726 (p90) REVERT: D 557 ASP cc_start: 0.7432 (t70) cc_final: 0.6920 (t0) REVERT: F 178 THR cc_start: 0.7949 (p) cc_final: 0.7702 (p) REVERT: F 186 SER cc_start: 0.8607 (m) cc_final: 0.8234 (p) REVERT: F 531 MET cc_start: 0.7517 (mtp) cc_final: 0.7022 (mtm) REVERT: G 15 TYR cc_start: 0.6657 (m-80) cc_final: 0.3771 (p90) REVERT: G 557 ASP cc_start: 0.7311 (t70) cc_final: 0.6857 (t0) REVERT: G 636 ILE cc_start: 0.7085 (mm) cc_final: 0.6859 (mm) REVERT: G 688 MET cc_start: 0.4148 (mmp) cc_final: 0.3787 (mmm) outliers start: 1 outliers final: 1 residues processed: 340 average time/residue: 0.2148 time to fit residues: 123.4597 Evaluate side-chains 236 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 170 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 341 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 461 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 371 ASN M 713 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 371 ASN G 713 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068554 restraints weight = 165232.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.069573 restraints weight = 106110.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.069847 restraints weight = 66077.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070197 restraints weight = 49881.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070482 restraints weight = 38661.832| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 36723 Z= 0.174 Angle : 0.813 42.049 50004 Z= 0.387 Chirality : 0.047 0.365 5610 Planarity : 0.009 0.346 6576 Dihedral : 6.769 179.707 5142 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.13 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 are not related in a simple way. whole: -1.39 (0.12), residues: 4641 helix: 0.34 (0.24), residues: 489 sheet: -0.51 (0.14), residues: 1296 loop : -1.39 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.001 ARG B 480 TYR 0.024 0.001 TYR C 102 PHE 0.083 0.002 PHE C 237 TRP 0.024 0.001 TRP A 117 HIS 0.009 0.001 HIS E 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (36666) covalent geometry : angle 0.81298 / 0.39 (50004) hydrogen bonds : bond 0.03368 / 2.33 ( 801) hydrogen bonds : angle 5.71994 / 4.11 ( 2097) Misc. bond : bond 0.01258 / 0.92 ( 57) *********************** 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 319 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 2.587 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: I 134 MET cc_start: 0.7514 (mmt) cc_final: 0.7303 (mmt) REVERT: I 224 GLU cc_start: 0.6724 (mp0) cc_final: 0.6361 (mp0) REVERT: C 186 SER cc_start: 0.8562 (m) cc_final: 0.8050 (p) REVERT: C 513 ASP cc_start: 0.7311 (p0) cc_final: 0.7084 (p0) REVERT: M 15 TYR cc_start: 0.6955 (m-80) cc_final: 0.3703 (p90) REVERT: M 557 ASP cc_start: 0.7356 (t70) cc_final: 0.7013 (t0) REVERT: M 688 MET cc_start: 0.3970 (mmm) cc_final: 0.3684 (mmm) REVERT: B 83 MET cc_start: 0.4558 (mpp) cc_final: 0.4224 (mtp) REVERT: B 178 THR cc_start: 0.7912 (p) cc_final: 0.7682 (p) REVERT: B 186 SER cc_start: 0.8646 (m) cc_final: 0.8170 (p) REVERT: B 513 ASP cc_start: 0.7324 (p0) cc_final: 0.7090 (p0) REVERT: D 15 TYR cc_start: 0.6790 (m-80) cc_final: 0.3767 (p90) REVERT: D 288 ASN cc_start: 0.5984 (t160) cc_final: 0.5724 (t0) REVERT: D 557 ASP cc_start: 0.7567 (t70) cc_final: 0.7039 (t0) REVERT: F 178 THR cc_start: 0.7907 (p) cc_final: 0.7696 (p) REVERT: F 186 SER cc_start: 0.8664 (m) cc_final: 0.8275 (p) REVERT: F 531 MET cc_start: 0.7570 (mtp) cc_final: 0.7080 (mtm) REVERT: G 15 TYR cc_start: 0.6711 (m-80) cc_final: 0.3680 (p90) REVERT: G 557 ASP cc_start: 0.7299 (t70) cc_final: 0.6944 (t0) REVERT: G 636 ILE cc_start: 0.7123 (mm) cc_final: 0.6882 (mm) REVERT: G 688 MET cc_start: 0.4211 (mmp) cc_final: 0.3824 (mmm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2067 time to fit residues: 113.7817 Evaluate side-chains 223 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 311 optimal weight: 7.9990 chunk 159 optimal weight: 0.5980 chunk 446 optimal weight: 1.9990 chunk 236 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 405 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 354 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 371 ASN M 713 HIS D 268 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN G 288 ASN G 371 ASN G 713 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068162 restraints weight = 165795.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.068885 restraints weight = 107182.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069408 restraints weight = 73974.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069887 restraints weight = 50537.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070232 restraints weight = 37454.304| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.8170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 36723 Z= 0.174 Angle : 0.789 42.319 50004 Z= 0.379 Chirality : 0.047 0.374 5610 Planarity : 0.008 0.249 6576 Dihedral : 6.647 179.818 5142 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.12), residues: 4641 helix: 0.41 (0.24), residues: 486 sheet: -0.59 (0.14), residues: 1323 loop : -1.37 (0.12), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.001 ARG B 480 TYR 0.027 0.001 TYR C 102 PHE 0.080 0.002 PHE C 237 TRP 0.032 0.001 TRP I 117 HIS 0.005 0.001 HIS E 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (36666) covalent geometry : angle 0.78903 / 0.38 (50004) hydrogen bonds : bond 0.03437 / 2.39 ( 801) hydrogen bonds : angle 5.68970 / 4.07 ( 2097) Misc. bond : bond 0.01236 / 0.90 ( 57) ********************** 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 311 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.432 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: I 134 MET cc_start: 0.7530 (mmt) cc_final: 0.7318 (mmt) REVERT: I 270 ASP cc_start: 0.7306 (p0) cc_final: 0.7102 (p0) REVERT: C 186 SER cc_start: 0.8557 (m) cc_final: 0.8075 (p) REVERT: C 233 ASP cc_start: 0.7428 (t0) cc_final: 0.7128 (t70) REVERT: C 513 ASP cc_start: 0.7274 (p0) cc_final: 0.7047 (p0) REVERT: M 15 TYR cc_start: 0.6998 (m-80) cc_final: 0.3703 (p90) REVERT: M 688 MET cc_start: 0.3993 (mmm) cc_final: 0.3689 (mmm) REVERT: A 134 MET cc_start: 0.7075 (mmt) cc_final: 0.6619 (mmt) REVERT: B 83 MET cc_start: 0.4500 (mpp) cc_final: 0.4132 (mtp) REVERT: B 178 THR cc_start: 0.7783 (p) cc_final: 0.7566 (p) REVERT: B 186 SER cc_start: 0.8613 (m) cc_final: 0.8135 (p) REVERT: B 513 ASP cc_start: 0.7312 (p0) cc_final: 0.7101 (p0) REVERT: D 15 TYR cc_start: 0.6747 (m-80) cc_final: 0.3729 (p90) REVERT: F 178 THR cc_start: 0.7923 (p) cc_final: 0.7688 (p) REVERT: F 186 SER cc_start: 0.8665 (m) cc_final: 0.8265 (p) REVERT: F 531 MET cc_start: 0.7570 (mtp) cc_final: 0.7099 (mtm) REVERT: G 15 TYR cc_start: 0.6278 (m-80) cc_final: 0.3499 (p90) REVERT: G 636 ILE cc_start: 0.7142 (mm) cc_final: 0.6855 (mm) REVERT: G 688 MET cc_start: 0.4230 (mmp) cc_final: 0.3819 (mmm) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2120 time to fit residues: 112.9391 Evaluate side-chains 219 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 343 optimal weight: 7.9990 chunk 122 optimal weight: 0.0170 chunk 380 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 423 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 268 GLN M 371 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN G 288 ASN G 371 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067381 restraints weight = 153180.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.068292 restraints weight = 93767.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068724 restraints weight = 61892.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068966 restraints weight = 43822.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.069343 restraints weight = 37416.231| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 36723 Z= 0.153 Angle : 0.748 31.959 50004 Z= 0.364 Chirality : 0.047 0.429 5610 Planarity : 0.008 0.258 6576 Dihedral : 6.543 179.606 5142 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 4641 helix: 0.42 (0.24), residues: 486 sheet: -0.58 (0.14), residues: 1335 loop : -1.33 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.001 ARG B 480 TYR 0.025 0.001 TYR C 102 PHE 0.073 0.002 PHE C 237 TRP 0.030 0.001 TRP I 117 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (36666) covalent geometry : angle 0.74842 / 0.36 (50004) hydrogen bonds : bond 0.03239 / 2.25 ( 801) hydrogen bonds : angle 5.63102 / 4.01 ( 2097) Misc. bond : bond 0.01212 / 0.88 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6405.68 seconds wall clock time: 111 minutes 25.39 seconds (6685.39 seconds total)