Starting phenix.real_space_refine on Tue Aug 26 10:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk7_19263/08_2025/8rk7_19263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk7_19263/08_2025/8rk7_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_19263/08_2025/8rk7_19263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk7_19263/08_2025/8rk7_19263.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk7_19263/08_2025/8rk7_19263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk7_19263/08_2025/8rk7_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35877 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2099 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 13, 'TRANS': 258} Chain: "C" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4278 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 30, 'TRANS': 523} Chain: "M" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5581 Classifications: {'peptide': 727} Link IDs: {'PTRANS': 40, 'TRANS': 686} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, E, B, F, D, G Time building chain proxies: 8.29, per 1000 atoms: 0.23 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 9282 Ramachandran restraints generated. 4641 Oldfield, 0 Emsley, 4641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8472 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 57 sheets defined 15.3% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 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: 6.15 Time building geometry restraints manager: 3.46 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: 0.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 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 aren 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 covalent geometry : bond 0.00194 (36666) covalent geometry : angle 0.45416 (50004) hydrogen bonds : bond 0.24020 ( 801) hydrogen bonds : angle 9.69361 ( 2097) Misc. bond : bond 0.41076 ( 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 : 1.525 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: 0.7521 (tmm) REVERT: C 306 LEU cc_start: 0.8129 (mt) cc_final: 0.7718 (mp) REVERT: C 501 THR cc_start: 0.5669 (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: 0.6448 (mt) cc_final: 0.6150 (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: 0.7199 (p0) REVERT: D 186 THR cc_start: 0.8079 (m) cc_final: 0.7778 (p) REVERT: D 351 ILE cc_start: 0.7664 (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: 0.7293 (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: 0.4952 (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: 0.7737 (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: 0.7112 (m) cc_final: 0.6128 (t) REVERT: G 557 ASP cc_start: 0.7190 (t70) cc_final: 0.6881 (t70) outliers start: 0 outliers final: 0 residues processed: 948 average time/residue: 0.2411 time to fit residues: 366.2897 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 : 1.187 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.108009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096317 restraints weight = 171630.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097388 restraints weight = 110136.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098138 restraints weight = 70084.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098637 restraints weight = 50326.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.098933 restraints weight = 38371.398| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2897 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= 0.225 Angle : 0.846 33.144 50004 Z= 0.437 Chirality : 0.052 0.497 5610 Planarity : 0.016 0.431 6576 Dihedral : 5.756 116.621 5142 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.08 % Favored : 93.73 % Rotamer: Outliers : 0.77 % Allowed : 4.49 % 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 aren not related in a simple way. whole: -0.86 (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 G 214 Details of bonding type rmsd covalent geometry : bond 0.00491 (36666) covalent geometry : angle 0.84646 (50004) hydrogen bonds : bond 0.05484 ( 801) hydrogen bonds : angle 7.64794 ( 2097) Misc. bond : bond 0.01341 ( 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 627 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 598 time to evaluate : 1.428 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: 0.7490 (tp) cc_final: 0.7270 (tp) REVERT: I 134 MET cc_start: 0.7655 (mmt) cc_final: 0.7397 (mmt) REVERT: I 203 ASN cc_start: 0.6947 (m-40) cc_final: 0.6494 (m-40) REVERT: I 268 ASP cc_start: 0.7069 (p0) cc_final: 0.6844 (p0) REVERT: I 270 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7122 (p0) REVERT: C 501 THR cc_start: 0.5733 (p) cc_final: 0.5434 (t) REVERT: M 218 GLU cc_start: 0.6548 (mp0) cc_final: 0.6258 (mp0) REVERT: M 528 TYR cc_start: 0.6782 (t80) cc_final: 0.6237 (m-80) REVERT: M 539 CYS cc_start: 0.7564 (m) cc_final: 0.6684 (t) REVERT: A 92 LEU cc_start: 0.7600 (tp) cc_final: 0.7398 (tp) REVERT: A 270 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 83 MET cc_start: 0.4360 (mpp) cc_final: 0.3859 (mpp) REVERT: B 282 MET cc_start: 0.7718 (ttt) cc_final: 0.7306 (tmm) REVERT: B 501 THR cc_start: 0.5580 (p) cc_final: 0.5240 (t) REVERT: B 513 ASP cc_start: 0.7280 (p0) cc_final: 0.7005 (p0) REVERT: D 56 GLU cc_start: 0.7149 (pm20) cc_final: 0.5676 (pt0) REVERT: D 218 GLU cc_start: 0.6510 (mp0) cc_final: 0.6284 (mp0) REVERT: D 528 TYR cc_start: 0.6706 (t80) cc_final: 0.6182 (m-80) REVERT: D 539 CYS cc_start: 0.7530 (m) cc_final: 0.6706 (t) REVERT: D 556 TYR cc_start: 0.7412 (p90) cc_final: 0.7111 (p90) REVERT: E 23 ARG cc_start: 0.8313 (ttt180) cc_final: 0.7709 (ttt90) REVERT: E 268 ASP cc_start: 0.6683 (p0) cc_final: 0.6322 (p0) REVERT: E 270 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6879 (p0) REVERT: F 83 MET cc_start: 0.4740 (mpp) cc_final: 0.3872 (ptp) REVERT: F 340 THR cc_start: 0.8637 (p) cc_final: 0.8243 (t) REVERT: F 501 THR cc_start: 0.5596 (p) cc_final: 0.5290 (t) REVERT: G 528 TYR cc_start: 0.6647 (t80) cc_final: 0.6139 (m-80) REVERT: G 539 CYS cc_start: 0.7379 (m) cc_final: 0.6254 (t) outliers start: 29 outliers final: 6 residues processed: 619 average time/residue: 0.2012 time to fit residues: 204.3585 Evaluate side-chains 372 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 363 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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: 2.9990 chunk 428 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 337 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 437 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN C 494 HIS M 8 GLN ** M 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 HIS A 271 GLN 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** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN F 74 ASN F 124 GLN G 8 GLN G 256 GLN G 281 GLN ** G 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.084507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.072666 restraints weight = 166840.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073364 restraints weight = 108064.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.073764 restraints weight = 70622.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074107 restraints weight = 53156.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074457 restraints weight = 41967.785| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 36723 Z= 0.350 Angle : 0.975 23.804 50004 Z= 0.511 Chirality : 0.066 2.261 5610 Planarity : 0.011 0.269 6576 Dihedral : 7.356 170.155 5142 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.78 % Rotamer: Outliers : 0.74 % Allowed : 7.22 % Favored : 92.04 % Cbeta Deviations : 0.05 % 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 aren not related in a simple way. whole: -1.62 (0.12), residues: 4641 helix: -0.24 (0.22), residues: 483 sheet: -0.46 (0.14), residues: 1305 loop : -1.58 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.002 ARG G 323 TYR 0.035 0.003 TYR B 385 PHE 0.042 0.004 PHE F 427 TRP 0.024 0.002 TRP G 198 HIS 0.015 0.002 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00739 (36666) covalent geometry : angle 0.97538 (50004) hydrogen bonds : bond 0.05614 ( 801) hydrogen bonds : angle 7.09576 ( 2097) Misc. bond : bond 0.01357 ( 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 459 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 431 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: symmetry clash revert: 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: 0.7621 (mmt) cc_final: 0.7417 (mmm) REVERT: I 175 TRP cc_start: 0.6558 (m100) cc_final: 0.6316 (m100) REVERT: C 83 MET cc_start: 0.4958 (mpp) cc_final: 0.4393 (mtm) REVERT: C 186 SER cc_start: 0.8609 (m) cc_final: 0.8169 (p) REVERT: C 513 ASP cc_start: 0.7219 (p0) cc_final: 0.6987 (p0) REVERT: C 531 MET cc_start: 0.7226 (mtp) cc_final: 0.6781 (mtm) REVERT: M 194 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7628 (pp) REVERT: M 218 GLU cc_start: 0.6753 (mp0) cc_final: 0.6410 (mp0) REVERT: B 83 MET cc_start: 0.4824 (mpp) cc_final: 0.4171 (mtm) REVERT: B 186 SER cc_start: 0.8625 (m) cc_final: 0.8194 (p) REVERT: D 233 LEU cc_start: 0.8780 (mt) cc_final: 0.8537 (mt) REVERT: D 369 GLU cc_start: 0.7363 (pt0) cc_final: 0.7126 (pt0) REVERT: D 528 TYR cc_start: 0.7192 (t80) cc_final: 0.6846 (t80) REVERT: D 557 ASP cc_start: 0.7195 (t70) cc_final: 0.6874 (t0) REVERT: E 270 ASP cc_start: 0.7340 (p0) cc_final: 0.7110 (p0) REVERT: F 83 MET cc_start: 0.5057 (mpp) cc_final: 0.4352 (mtm) REVERT: F 186 SER cc_start: 0.8561 (m) cc_final: 0.8258 (p) REVERT: G 322 MET cc_start: 0.7451 (tmm) cc_final: 0.7160 (tmm) REVERT: G 369 GLU cc_start: 0.7231 (pt0) cc_final: 0.6515 (pt0) REVERT: G 379 THR cc_start: 0.8542 (m) cc_final: 0.8290 (p) REVERT: G 557 ASP cc_start: 0.7214 (t70) cc_final: 0.6776 (t0) outliers start: 28 outliers final: 11 residues processed: 456 average time/residue: 0.2137 time to fit residues: 158.8539 Evaluate side-chains 265 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 253 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 5.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 159 optimal weight: 6.9990 chunk 340 optimal weight: 0.3980 chunk 315 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 203 ASN I 251 ASN I 254 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 287 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN D 268 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN D 371 ASN E 251 ASN E 254 ASN F 87 ASN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 371 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.087826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074928 restraints weight = 167515.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075834 restraints weight = 109451.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.076245 restraints weight = 73140.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076643 restraints weight = 55491.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.076977 restraints weight = 44617.149| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 36723 Z= 0.213 Angle : 0.783 30.492 50004 Z= 0.398 Chirality : 0.049 0.353 5610 Planarity : 0.007 0.188 6576 Dihedral : 6.810 171.487 5142 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % 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 aren not related in a simple way. whole: -1.51 (0.12), residues: 4641 helix: 0.12 (0.23), residues: 477 sheet: -0.53 (0.15), residues: 1230 loop : -1.46 (0.11), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.001 ARG D 323 TYR 0.022 0.002 TYR D 136 PHE 0.071 0.002 PHE I 208 TRP 0.025 0.002 TRP E 117 HIS 0.005 0.001 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00467 (36666) covalent geometry : angle 0.78336 (50004) hydrogen bonds : bond 0.04222 ( 801) hydrogen bonds : angle 6.55461 ( 2097) Misc. bond : bond 0.01332 ( 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 404 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 396 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 134 MET cc_start: 0.7637 (mmt) cc_final: 0.6957 (mmt) REVERT: I 270 ASP cc_start: 0.7049 (p0) cc_final: 0.6715 (p0) REVERT: C 186 SER cc_start: 0.8607 (m) cc_final: 0.8075 (p) REVERT: C 233 ASP cc_start: 0.7215 (t0) cc_final: 0.6591 (m-30) REVERT: M 15 TYR cc_start: 0.6688 (m-80) cc_final: 0.3345 (p90) REVERT: M 233 LEU cc_start: 0.8718 (mt) cc_final: 0.8471 (mt) REVERT: M 369 GLU cc_start: 0.6955 (pt0) cc_final: 0.6270 (pt0) REVERT: M 557 ASP cc_start: 0.7446 (t70) cc_final: 0.7163 (t0) REVERT: B 83 MET cc_start: 0.4306 (mpp) cc_final: 0.3736 (mtp) REVERT: B 186 SER cc_start: 0.8613 (m) cc_final: 0.8161 (p) REVERT: B 513 ASP cc_start: 0.7250 (p0) cc_final: 0.7018 (p0) REVERT: D 15 TYR cc_start: 0.6863 (m-80) cc_final: 0.3406 (p90) REVERT: D 477 ASP cc_start: 0.8355 (t70) cc_final: 0.8135 (t0) REVERT: D 557 ASP cc_start: 0.7127 (t70) cc_final: 0.6788 (t0) REVERT: E 270 ASP cc_start: 0.7202 (p0) cc_final: 0.6864 (p0) REVERT: F 83 MET cc_start: 0.4840 (mpp) cc_final: 0.4415 (mtm) REVERT: F 178 THR cc_start: 0.7773 (p) cc_final: 0.7536 (p) REVERT: F 186 SER cc_start: 0.8571 (m) cc_final: 0.8232 (p) REVERT: F 501 THR cc_start: 0.6974 (p) cc_final: 0.6711 (t) REVERT: G 15 TYR cc_start: 0.6713 (m-80) cc_final: 0.3545 (p90) REVERT: G 268 GLN cc_start: 0.6766 (tt0) cc_final: 0.6536 (tt0) REVERT: G 369 GLU cc_start: 0.7174 (pt0) cc_final: 0.6227 (pt0) REVERT: G 379 THR cc_start: 0.8563 (m) cc_final: 0.8296 (p) REVERT: G 557 ASP cc_start: 0.7386 (t70) cc_final: 0.7066 (t0) outliers start: 8 outliers final: 3 residues processed: 404 average time/residue: 0.2061 time to fit residues: 138.0667 Evaluate side-chains 255 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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: 4.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 240 optimal weight: 0.0980 chunk 135 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 288 ASN M 371 ASN M 713 HIS B 74 ASN D 49 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 713 HIS E 271 GLN G 371 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 = 0.3517 r_free = 0.3517 target = 0.083752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070789 restraints weight = 168799.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.071611 restraints weight = 109661.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.071982 restraints weight = 73730.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.072318 restraints weight = 55655.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072607 restraints weight = 44446.999| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 36723 Z= 0.260 Angle : 0.820 28.768 50004 Z= 0.417 Chirality : 0.050 0.453 5610 Planarity : 0.008 0.166 6576 Dihedral : 6.634 176.006 5142 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.17 % Favored : 91.70 % Rotamer: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.12), residues: 4641 helix: 0.00 (0.23), residues: 483 sheet: -0.70 (0.14), residues: 1287 loop : -1.53 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG B 480 TYR 0.025 0.002 TYR B 385 PHE 0.091 0.003 PHE I 208 TRP 0.029 0.002 TRP D 12 HIS 0.010 0.002 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00565 (36666) covalent geometry : angle 0.81966 (50004) hydrogen bonds : bond 0.04356 ( 801) hydrogen bonds : angle 6.32024 ( 2097) Misc. bond : bond 0.01489 ( 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 333 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 328 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 134 MET cc_start: 0.7528 (mmt) cc_final: 0.6979 (mmt) REVERT: C 186 SER cc_start: 0.8744 (m) cc_final: 0.8351 (p) REVERT: C 513 ASP cc_start: 0.7454 (p0) cc_final: 0.7172 (p0) REVERT: M 15 TYR cc_start: 0.6748 (m-80) cc_final: 0.3449 (p90) REVERT: M 528 TYR cc_start: 0.7315 (t80) cc_final: 0.6603 (t80) REVERT: M 557 ASP cc_start: 0.7472 (t70) cc_final: 0.7131 (t0) REVERT: M 688 MET cc_start: 0.4147 (mmm) cc_final: 0.3727 (mmm) REVERT: A 134 MET cc_start: 0.7475 (mmt) cc_final: 0.6861 (mmt) REVERT: A 270 ASP cc_start: 0.7373 (p0) cc_final: 0.7088 (p0) REVERT: B 83 MET cc_start: 0.4277 (mpp) cc_final: 0.3745 (mtp) REVERT: B 178 THR cc_start: 0.7719 (p) cc_final: 0.7508 (p) REVERT: B 186 SER cc_start: 0.8805 (m) cc_final: 0.8387 (p) REVERT: B 513 ASP cc_start: 0.7195 (p0) cc_final: 0.6967 (p0) REVERT: D 15 TYR cc_start: 0.6806 (m-80) cc_final: 0.3569 (p90) REVERT: D 322 MET cc_start: 0.7631 (tmm) cc_final: 0.7429 (tmm) REVERT: D 557 ASP cc_start: 0.7420 (t70) cc_final: 0.7088 (t0) REVERT: F 83 MET cc_start: 0.4698 (mpp) cc_final: 0.4458 (mpp) REVERT: F 186 SER cc_start: 0.8777 (m) cc_final: 0.8376 (p) REVERT: G 15 TYR cc_start: 0.6807 (m-80) cc_final: 0.3587 (p90) REVERT: G 287 ASN cc_start: 0.8204 (m-40) cc_final: 0.7997 (m110) REVERT: G 322 MET cc_start: 0.7662 (tmm) cc_final: 0.7276 (tmm) REVERT: G 557 ASP cc_start: 0.7505 (t70) cc_final: 0.7137 (t0) outliers start: 5 outliers final: 2 residues processed: 332 average time/residue: 0.2023 time to fit residues: 112.0338 Evaluate side-chains 229 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 7.9990 chunk 417 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 314 optimal weight: 5.9990 chunk 442 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 251 ASN I 254 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 GLN M 268 GLN M 287 ASN M 288 ASN 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** D 713 HIS E 251 ASN E 254 ASN F 61 GLN G 268 GLN G 288 ASN G 371 ASN G 713 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.082805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069767 restraints weight = 168521.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070640 restraints weight = 110323.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071081 restraints weight = 74310.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071448 restraints weight = 56302.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.071867 restraints weight = 44515.167| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 36723 Z= 0.226 Angle : 0.780 25.823 50004 Z= 0.395 Chirality : 0.049 0.410 5610 Planarity : 0.007 0.149 6576 Dihedral : 6.584 177.916 5142 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.37 % Rotamer: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.12), residues: 4641 helix: 0.14 (0.23), residues: 486 sheet: -0.77 (0.14), residues: 1323 loop : -1.52 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.001 ARG B 480 TYR 0.027 0.002 TYR F 102 PHE 0.082 0.003 PHE A 208 TRP 0.035 0.002 TRP M 198 HIS 0.006 0.001 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00504 (36666) covalent geometry : angle 0.78012 (50004) hydrogen bonds : bond 0.03972 ( 801) hydrogen bonds : angle 6.16379 ( 2097) Misc. bond : bond 0.01254 ( 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 338 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 335 time to evaluate : 1.467 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: 0.7577 (mmt) cc_final: 0.7307 (mmt) REVERT: I 270 ASP cc_start: 0.7279 (p0) cc_final: 0.6982 (p0) REVERT: C 186 SER cc_start: 0.8733 (m) cc_final: 0.8340 (p) REVERT: C 513 ASP cc_start: 0.7387 (p0) cc_final: 0.7124 (p0) REVERT: C 531 MET cc_start: 0.7219 (mtp) cc_final: 0.6864 (mtm) REVERT: M 159 TYR cc_start: 0.8145 (t80) cc_final: 0.7879 (t80) REVERT: M 268 GLN cc_start: 0.7184 (tt0) cc_final: 0.6944 (tt0) REVERT: M 408 THR cc_start: 0.6987 (p) cc_final: 0.6061 (p) REVERT: M 528 TYR cc_start: 0.7231 (t80) cc_final: 0.6580 (t80) REVERT: M 636 ILE cc_start: 0.7049 (mm) cc_final: 0.6766 (mm) REVERT: M 688 MET cc_start: 0.4004 (mmm) cc_final: 0.3704 (mmm) REVERT: B 83 MET cc_start: 0.4308 (mpp) cc_final: 0.3890 (mtp) REVERT: B 186 SER cc_start: 0.8707 (m) cc_final: 0.8239 (p) REVERT: B 531 MET cc_start: 0.7392 (mtp) cc_final: 0.6902 (mtm) REVERT: D 15 TYR cc_start: 0.6860 (m-80) cc_final: 0.3691 (p90) REVERT: D 118 LYS cc_start: 0.2016 (tttt) cc_final: 0.1711 (tttm) REVERT: E 224 GLU cc_start: 0.6743 (mp0) cc_final: 0.6511 (mp0) REVERT: F 186 SER cc_start: 0.8772 (m) cc_final: 0.8368 (p) REVERT: F 228 GLU cc_start: 0.8194 (mp0) cc_final: 0.7991 (mt-10) REVERT: F 417 ILE cc_start: 0.8846 (mp) cc_final: 0.8551 (mm) REVERT: G 15 TYR cc_start: 0.6766 (m-80) cc_final: 0.3591 (p90) REVERT: G 322 MET cc_start: 0.7506 (tmm) cc_final: 0.7057 (tmm) REVERT: G 528 TYR cc_start: 0.7097 (t80) cc_final: 0.6542 (t80) REVERT: G 688 MET cc_start: 0.4341 (mmp) cc_final: 0.3996 (mmm) outliers start: 3 outliers final: 2 residues processed: 337 average time/residue: 0.2115 time to fit residues: 118.9117 Evaluate side-chains 227 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 375 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 285 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 413 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN C 87 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 ASN M 371 ASN M 720 HIS D 268 GLN D 283 GLN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 HIS E 20 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 371 ASN ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066255 restraints weight = 154220.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067180 restraints weight = 94572.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.067584 restraints weight = 62801.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.067959 restraints weight = 47409.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068353 restraints weight = 35529.624| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 36723 Z= 0.183 Angle : 0.755 25.624 50004 Z= 0.378 Chirality : 0.048 0.320 5610 Planarity : 0.007 0.170 6576 Dihedral : 6.468 179.679 5142 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.19 % Favored : 91.68 % Rotamer: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.12), residues: 4641 helix: 0.32 (0.24), residues: 486 sheet: -0.69 (0.14), residues: 1302 loop : -1.50 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.001 ARG B 480 TYR 0.024 0.001 TYR F 102 PHE 0.109 0.002 PHE C 237 TRP 0.020 0.002 TRP I 117 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00395 (36666) covalent geometry : angle 0.75482 (50004) hydrogen bonds : bond 0.03689 ( 801) hydrogen bonds : angle 6.00001 ( 2097) Misc. bond : bond 0.01267 ( 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: 2 poor density : 325 time to evaluate : 1.307 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: C 186 SER cc_start: 0.8729 (m) cc_final: 0.8325 (p) REVERT: C 513 ASP cc_start: 0.7357 (p0) cc_final: 0.7094 (p0) REVERT: C 531 MET cc_start: 0.7301 (mtp) cc_final: 0.6980 (mtm) REVERT: M 159 TYR cc_start: 0.8169 (t80) cc_final: 0.7884 (t80) REVERT: M 528 TYR cc_start: 0.7239 (t80) cc_final: 0.6575 (t80) REVERT: M 688 MET cc_start: 0.4004 (mmm) cc_final: 0.3681 (mmm) REVERT: B 83 MET cc_start: 0.4741 (mpp) cc_final: 0.4396 (mtp) REVERT: B 178 THR cc_start: 0.7787 (p) cc_final: 0.7585 (p) REVERT: B 186 SER cc_start: 0.8671 (m) cc_final: 0.8232 (p) REVERT: B 401 VAL cc_start: 0.8817 (p) cc_final: 0.8606 (m) REVERT: B 531 MET cc_start: 0.7417 (mtp) cc_final: 0.6889 (mtm) REVERT: D 15 TYR cc_start: 0.6856 (m-80) cc_final: 0.3757 (p90) REVERT: D 16 PHE cc_start: 0.4189 (m-10) cc_final: 0.3976 (m-10) REVERT: E 224 GLU cc_start: 0.6644 (mp0) cc_final: 0.6435 (mp0) REVERT: E 270 ASP cc_start: 0.7147 (p0) cc_final: 0.6815 (p0) REVERT: F 186 SER cc_start: 0.8751 (m) cc_final: 0.8338 (p) REVERT: F 417 ILE cc_start: 0.8809 (mp) cc_final: 0.8577 (mm) REVERT: G 528 TYR cc_start: 0.7111 (t80) cc_final: 0.6544 (t80) REVERT: G 688 MET cc_start: 0.4264 (mmp) cc_final: 0.3895 (mmm) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.1918 time to fit residues: 106.6045 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 : 0.982 ------------------------------------------------------------------------------- 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: 0.0980 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 309 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 258 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 overall best weight: 3.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 GLN I 20 GLN C 61 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 371 ASN M 713 HIS B 61 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN D 371 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 371 ASN ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS G 720 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.075965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064272 restraints weight = 153631.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065210 restraints weight = 93686.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065682 restraints weight = 62479.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066085 restraints weight = 43674.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066391 restraints weight = 32812.825| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 36723 Z= 0.245 Angle : 0.808 26.499 50004 Z= 0.408 Chirality : 0.049 0.310 5610 Planarity : 0.007 0.131 6576 Dihedral : 6.661 179.941 5142 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.92 % Favored : 90.95 % Rotamer: Outliers : 0.08 % Allowed : 1.80 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.12), residues: 4641 helix: 0.23 (0.24), residues: 486 sheet: -0.84 (0.14), residues: 1308 loop : -1.60 (0.11), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.001 ARG B 480 TYR 0.021 0.002 TYR F 102 PHE 0.108 0.003 PHE A 208 TRP 0.041 0.002 TRP D 198 HIS 0.007 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00547 (36666) covalent geometry : angle 0.80760 (50004) hydrogen bonds : bond 0.03990 ( 801) hydrogen bonds : angle 6.08784 ( 2097) Misc. bond : bond 0.01286 ( 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 301 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 SER cc_start: 0.8815 (m) cc_final: 0.8442 (p) REVERT: C 513 ASP cc_start: 0.7339 (p0) cc_final: 0.7074 (p0) REVERT: C 531 MET cc_start: 0.7172 (mtp) cc_final: 0.6789 (mtm) REVERT: M 528 TYR cc_start: 0.7291 (t80) cc_final: 0.6548 (t80) REVERT: M 688 MET cc_start: 0.3854 (mmm) cc_final: 0.3537 (mmm) REVERT: B 83 MET cc_start: 0.4760 (mpp) cc_final: 0.4268 (mtp) REVERT: B 178 THR cc_start: 0.7808 (p) cc_final: 0.7596 (p) REVERT: B 186 SER cc_start: 0.8788 (m) cc_final: 0.8338 (p) REVERT: B 401 VAL cc_start: 0.8891 (p) cc_final: 0.8679 (m) REVERT: B 531 MET cc_start: 0.7435 (mtp) cc_final: 0.6871 (mtm) REVERT: D 15 TYR cc_start: 0.6927 (m-80) cc_final: 0.3712 (p90) REVERT: D 198 TRP cc_start: 0.6119 (m100) cc_final: 0.3029 (p-90) REVERT: D 288 ASN cc_start: 0.5654 (OUTLIER) cc_final: 0.5261 (m-40) REVERT: D 369 GLU cc_start: 0.7355 (pt0) cc_final: 0.7076 (pt0) REVERT: D 528 TYR cc_start: 0.7381 (t80) cc_final: 0.7140 (t80) REVERT: E 224 GLU cc_start: 0.6925 (mp0) cc_final: 0.6723 (mp0) REVERT: E 270 ASP cc_start: 0.7171 (p0) cc_final: 0.6782 (p0) REVERT: F 186 SER cc_start: 0.8883 (m) cc_final: 0.8506 (p) REVERT: F 417 ILE cc_start: 0.8825 (mp) cc_final: 0.8565 (mm) REVERT: G 118 LYS cc_start: 0.1460 (tttt) cc_final: 0.0181 (tptt) REVERT: G 288 ASN cc_start: 0.5881 (OUTLIER) cc_final: 0.5312 (t0) REVERT: G 322 MET cc_start: 0.7781 (tpt) cc_final: 0.7498 (tpt) REVERT: G 528 TYR cc_start: 0.7051 (t80) cc_final: 0.6565 (t80) REVERT: G 688 MET cc_start: 0.4318 (mmp) cc_final: 0.3933 (mmm) outliers start: 3 outliers final: 1 residues processed: 300 average time/residue: 0.1994 time to fit residues: 102.1634 Evaluate side-chains 214 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 211 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 461 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN D 288 ASN D 386 GLN D 713 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 288 ASN G 371 ASN ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066345 restraints weight = 151313.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067269 restraints weight = 91629.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067814 restraints weight = 60436.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068216 restraints weight = 42059.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068546 restraints weight = 32308.106| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.8493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 36723 Z= 0.160 Angle : 0.761 24.965 50004 Z= 0.380 Chirality : 0.047 0.341 5610 Planarity : 0.007 0.231 6576 Dihedral : 6.425 179.771 5142 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.12), residues: 4641 helix: 0.32 (0.24), residues: 486 sheet: -0.81 (0.14), residues: 1305 loop : -1.50 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.001 ARG B 480 TYR 0.023 0.001 TYR G 159 PHE 0.099 0.002 PHE E 208 TRP 0.071 0.002 TRP M 12 HIS 0.006 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00331 (36666) covalent geometry : angle 0.76137 (50004) hydrogen bonds : bond 0.03441 ( 801) hydrogen bonds : angle 5.86257 ( 2097) Misc. bond : bond 0.01314 ( 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 336 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.587 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: symmetry clash REVERT: C 186 SER cc_start: 0.8671 (m) cc_final: 0.8252 (p) REVERT: C 513 ASP cc_start: 0.7328 (p0) cc_final: 0.7071 (p0) REVERT: C 531 MET cc_start: 0.7079 (mtp) cc_final: 0.6785 (mtm) REVERT: M 15 TYR cc_start: 0.6833 (m-80) cc_final: 0.3580 (p90) REVERT: M 159 TYR cc_start: 0.8070 (t80) cc_final: 0.7805 (t80) REVERT: M 528 TYR cc_start: 0.7033 (t80) cc_final: 0.6462 (t80) REVERT: M 688 MET cc_start: 0.3809 (mmm) cc_final: 0.3484 (mmm) REVERT: B 83 MET cc_start: 0.4699 (mpp) cc_final: 0.4434 (mtp) REVERT: B 178 THR cc_start: 0.7676 (p) cc_final: 0.7410 (p) REVERT: B 186 SER cc_start: 0.8616 (m) cc_final: 0.8147 (p) REVERT: B 401 VAL cc_start: 0.8809 (p) cc_final: 0.8609 (m) REVERT: B 531 MET cc_start: 0.7298 (mtp) cc_final: 0.6711 (mtm) REVERT: D 15 TYR cc_start: 0.7015 (m-80) cc_final: 0.3818 (p90) REVERT: E 268 ASP cc_start: 0.7042 (p0) cc_final: 0.6479 (p0) REVERT: E 270 ASP cc_start: 0.7018 (p0) cc_final: 0.6768 (p0) REVERT: F 83 MET cc_start: 0.5004 (mpp) cc_final: 0.4476 (ptp) REVERT: F 178 THR cc_start: 0.7910 (p) cc_final: 0.7709 (p) REVERT: F 186 SER cc_start: 0.8712 (m) cc_final: 0.8302 (p) REVERT: F 417 ILE cc_start: 0.8778 (mp) cc_final: 0.8483 (mm) REVERT: F 531 MET cc_start: 0.7149 (mtp) cc_final: 0.6755 (ttm) REVERT: G 118 LYS cc_start: 0.1403 (tttt) cc_final: 0.0716 (mtpt) REVERT: G 287 ASN cc_start: 0.8158 (m-40) cc_final: 0.7760 (m-40) REVERT: G 322 MET cc_start: 0.7768 (tpt) cc_final: 0.7476 (tpt) REVERT: G 528 TYR cc_start: 0.6907 (t80) cc_final: 0.6363 (t80) REVERT: G 688 MET cc_start: 0.4206 (mmp) cc_final: 0.3823 (mmm) outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.1870 time to fit residues: 108.2400 Evaluate side-chains 221 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 1.9990 chunk 159 optimal weight: 0.7980 chunk 446 optimal weight: 9.9990 chunk 236 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 148 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 713 HIS ** 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN G 371 ASN ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 713 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065859 restraints weight = 152117.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066684 restraints weight = 91624.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.067206 restraints weight = 62308.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067665 restraints weight = 43540.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068031 restraints weight = 32781.392| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.8625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 36723 Z= 0.170 Angle : 0.772 26.253 50004 Z= 0.382 Chirality : 0.047 0.315 5610 Planarity : 0.008 0.236 6576 Dihedral : 6.385 178.807 5142 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.10 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.12), residues: 4641 helix: 0.46 (0.24), residues: 483 sheet: -0.79 (0.14), residues: 1341 loop : -1.48 (0.11), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.001 ARG B 480 TYR 0.022 0.001 TYR B 102 PHE 0.086 0.002 PHE E 208 TRP 0.053 0.002 TRP M 12 HIS 0.007 0.001 HIS F 57 Details of bonding type rmsd covalent geometry : bond 0.00362 (36666) covalent geometry : angle 0.77215 (50004) hydrogen bonds : bond 0.03473 ( 801) hydrogen bonds : angle 5.77394 ( 2097) Misc. bond : bond 0.01293 ( 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 306 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.063 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: C 186 SER cc_start: 0.8680 (m) cc_final: 0.8255 (p) REVERT: C 233 ASP cc_start: 0.7254 (t70) cc_final: 0.6972 (t70) REVERT: C 513 ASP cc_start: 0.7246 (p0) cc_final: 0.7008 (p0) REVERT: C 531 MET cc_start: 0.7148 (mtp) cc_final: 0.6821 (mtm) REVERT: M 15 TYR cc_start: 0.7033 (m-80) cc_final: 0.3640 (p90) REVERT: M 159 TYR cc_start: 0.8089 (t80) cc_final: 0.7188 (t80) REVERT: M 528 TYR cc_start: 0.7074 (t80) cc_final: 0.6527 (t80) REVERT: M 688 MET cc_start: 0.3842 (mmm) cc_final: 0.3511 (mmm) REVERT: A 270 ASP cc_start: 0.7076 (p0) cc_final: 0.6862 (p0) REVERT: B 83 MET cc_start: 0.4651 (mpp) cc_final: 0.4311 (mtp) REVERT: B 178 THR cc_start: 0.7515 (p) cc_final: 0.7284 (p) REVERT: B 186 SER cc_start: 0.8634 (m) cc_final: 0.8173 (p) REVERT: B 531 MET cc_start: 0.7288 (mtp) cc_final: 0.6781 (mtm) REVERT: D 15 TYR cc_start: 0.7029 (m-80) cc_final: 0.3861 (p90) REVERT: D 159 TYR cc_start: 0.7992 (t80) cc_final: 0.7584 (t80) REVERT: D 578 LEU cc_start: 0.8463 (mt) cc_final: 0.8247 (mt) REVERT: D 580 ASN cc_start: 0.9105 (m-40) cc_final: 0.8590 (m110) REVERT: E 270 ASP cc_start: 0.7155 (p0) cc_final: 0.6819 (p0) REVERT: F 178 THR cc_start: 0.7920 (p) cc_final: 0.7719 (p) REVERT: F 186 SER cc_start: 0.8741 (m) cc_final: 0.8341 (p) REVERT: F 531 MET cc_start: 0.7310 (mtp) cc_final: 0.6589 (mtm) REVERT: G 118 LYS cc_start: 0.1299 (tttt) cc_final: 0.0070 (tptt) REVERT: G 287 ASN cc_start: 0.8246 (m-40) cc_final: 0.8011 (m-40) REVERT: G 322 MET cc_start: 0.7748 (tpt) cc_final: 0.7437 (tpt) REVERT: G 528 TYR cc_start: 0.6931 (t80) cc_final: 0.6389 (t80) REVERT: G 688 MET cc_start: 0.4288 (mmp) cc_final: 0.3898 (mmm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2020 time to fit residues: 104.4883 Evaluate side-chains 220 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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: 9.9990 chunk 122 optimal weight: 0.9980 chunk 380 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 303 optimal weight: 1.9990 chunk 423 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 268 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 ASN ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066463 restraints weight = 151953.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067358 restraints weight = 92689.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067705 restraints weight = 62821.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068118 restraints weight = 47471.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.068478 restraints weight = 35192.981| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.8736 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= 0.157 Angle : 0.737 23.092 50004 Z= 0.366 Chirality : 0.046 0.316 5610 Planarity : 0.007 0.243 6576 Dihedral : 6.253 178.814 5142 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4641 helix: 0.35 (0.24), residues: 501 sheet: -0.74 (0.14), residues: 1326 loop : -1.44 (0.12), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.001 ARG B 480 TYR 0.020 0.001 TYR B 102 PHE 0.082 0.002 PHE E 208 TRP 0.044 0.002 TRP A 117 HIS 0.003 0.001 HIS I 212 Details of bonding type rmsd covalent geometry : bond 0.00329 (36666) covalent geometry : angle 0.73714 (50004) hydrogen bonds : bond 0.03337 ( 801) hydrogen bonds : angle 5.69851 ( 2097) Misc. bond : bond 0.01232 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.62 seconds wall clock time: 102 minutes 11.05 seconds (6131.05 seconds total)