Starting phenix.real_space_refine on Mon Oct 14 11:38:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmw_36428/10_2024/8jmw_36428.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 43614 2.51 5 N 11700 2.21 5 O 14040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 69552 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3864 Classifications: {'peptide': 517} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 487} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 12.27, per 1000 atoms: 0.18 Number of scatterers: 69552 At special positions: 0 Unit cell: (164.85, 162.75, 232.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 14040 8.00 N 11700 7.00 C 43614 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=0, symmetry=0 Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 7.0 seconds 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16596 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 180 sheets defined 20.5% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.09 Creating SS restraints... Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 563 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 586 through 592 Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER B 264 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 529 through 532 Processing helix chain 'B' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 563 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 586 through 592 Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 260 through 264 removed outlier: 4.252A pdb=" N SER C 264 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 529 through 532 Processing helix chain 'C' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 563 Processing helix chain 'C' and resid 576 through 581 Processing helix chain 'C' and resid 586 through 592 Processing helix chain 'D' and resid 160 through 166 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER D 264 " --> pdb=" O PRO D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 280 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 529 through 532 Processing helix chain 'D' and resid 533 through 548 removed outlier: 3.676A pdb=" N VAL D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 563 Processing helix chain 'D' and resid 576 through 581 Processing helix chain 'D' and resid 586 through 592 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 166 through 173 Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER E 264 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 298 through 307 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 529 through 532 Processing helix chain 'E' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 563 Processing helix chain 'E' and resid 576 through 581 Processing helix chain 'E' and resid 586 through 592 Processing helix chain 'F' and resid 160 through 166 Processing helix chain 'F' and resid 166 through 173 Processing helix chain 'F' and resid 229 through 239 Processing helix chain 'F' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER F 264 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 280 Processing helix chain 'F' and resid 298 through 307 Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 529 through 532 Processing helix chain 'F' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 576 through 581 Processing helix chain 'F' and resid 586 through 592 Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 166 through 173 Processing helix chain 'G' and resid 229 through 239 Processing helix chain 'G' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER G 264 " --> pdb=" O PRO G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 280 Processing helix chain 'G' and resid 298 through 307 Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 529 through 532 Processing helix chain 'G' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 563 Processing helix chain 'G' and resid 576 through 581 Processing helix chain 'G' and resid 586 through 592 Processing helix chain 'H' and resid 160 through 166 Processing helix chain 'H' and resid 166 through 173 Processing helix chain 'H' and resid 229 through 239 Processing helix chain 'H' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER H 264 " --> pdb=" O PRO H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 280 Processing helix chain 'H' and resid 298 through 307 Processing helix chain 'H' and resid 330 through 334 Processing helix chain 'H' and resid 529 through 532 Processing helix chain 'H' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL H 537 " --> pdb=" O ALA H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 563 Processing helix chain 'H' and resid 576 through 581 Processing helix chain 'H' and resid 586 through 592 Processing helix chain 'I' and resid 160 through 166 Processing helix chain 'I' and resid 166 through 173 Processing helix chain 'I' and resid 229 through 239 Processing helix chain 'I' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER I 264 " --> pdb=" O PRO I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 280 Processing helix chain 'I' and resid 298 through 307 Processing helix chain 'I' and resid 330 through 334 Processing helix chain 'I' and resid 529 through 532 Processing helix chain 'I' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL I 537 " --> pdb=" O ALA I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 563 Processing helix chain 'I' and resid 576 through 581 Processing helix chain 'I' and resid 586 through 592 Processing helix chain 'J' and resid 160 through 166 Processing helix chain 'J' and resid 166 through 173 Processing helix chain 'J' and resid 229 through 239 Processing helix chain 'J' and resid 260 through 264 removed outlier: 4.252A pdb=" N SER J 264 " --> pdb=" O PRO J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 280 Processing helix chain 'J' and resid 298 through 307 Processing helix chain 'J' and resid 330 through 334 Processing helix chain 'J' and resid 529 through 532 Processing helix chain 'J' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL J 537 " --> pdb=" O ALA J 533 " (cutoff:3.500A) Processing helix chain 'J' and resid 552 through 563 Processing helix chain 'J' and resid 576 through 581 Processing helix chain 'J' and resid 586 through 592 Processing helix chain 'K' and resid 160 through 166 Processing helix chain 'K' and resid 166 through 173 Processing helix chain 'K' and resid 229 through 239 Processing helix chain 'K' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 280 Processing helix chain 'K' and resid 298 through 307 Processing helix chain 'K' and resid 330 through 334 Processing helix chain 'K' and resid 529 through 532 Processing helix chain 'K' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL K 537 " --> pdb=" O ALA K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 552 through 563 Processing helix chain 'K' and resid 576 through 581 Processing helix chain 'K' and resid 586 through 592 Processing helix chain 'L' and resid 160 through 166 Processing helix chain 'L' and resid 166 through 173 Processing helix chain 'L' and resid 229 through 239 Processing helix chain 'L' and resid 260 through 264 removed outlier: 4.252A pdb=" N SER L 264 " --> pdb=" O PRO L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 280 Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 330 through 334 Processing helix chain 'L' and resid 529 through 532 Processing helix chain 'L' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL L 537 " --> pdb=" O ALA L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 576 through 581 Processing helix chain 'L' and resid 586 through 592 Processing helix chain 'M' and resid 160 through 166 Processing helix chain 'M' and resid 166 through 173 Processing helix chain 'M' and resid 229 through 239 Processing helix chain 'M' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER M 264 " --> pdb=" O PRO M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 280 Processing helix chain 'M' and resid 298 through 307 Processing helix chain 'M' and resid 330 through 334 Processing helix chain 'M' and resid 529 through 532 Processing helix chain 'M' and resid 533 through 548 removed outlier: 3.676A pdb=" N VAL M 537 " --> pdb=" O ALA M 533 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 563 Processing helix chain 'M' and resid 576 through 581 Processing helix chain 'M' and resid 586 through 592 Processing helix chain 'N' and resid 160 through 166 Processing helix chain 'N' and resid 166 through 173 Processing helix chain 'N' and resid 229 through 239 Processing helix chain 'N' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER N 264 " --> pdb=" O PRO N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 280 Processing helix chain 'N' and resid 298 through 307 Processing helix chain 'N' and resid 330 through 334 Processing helix chain 'N' and resid 529 through 532 Processing helix chain 'N' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL N 537 " --> pdb=" O ALA N 533 " (cutoff:3.500A) Processing helix chain 'N' and resid 552 through 563 Processing helix chain 'N' and resid 576 through 581 Processing helix chain 'N' and resid 586 through 592 Processing helix chain 'O' and resid 160 through 166 Processing helix chain 'O' and resid 166 through 173 Processing helix chain 'O' and resid 229 through 239 Processing helix chain 'O' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER O 264 " --> pdb=" O PRO O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 280 Processing helix chain 'O' and resid 298 through 307 Processing helix chain 'O' and resid 330 through 334 Processing helix chain 'O' and resid 529 through 532 Processing helix chain 'O' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL O 537 " --> pdb=" O ALA O 533 " (cutoff:3.500A) Processing helix chain 'O' and resid 552 through 563 Processing helix chain 'O' and resid 576 through 581 Processing helix chain 'O' and resid 586 through 592 Processing helix chain 'P' and resid 160 through 166 Processing helix chain 'P' and resid 166 through 173 Processing helix chain 'P' and resid 229 through 239 Processing helix chain 'P' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER P 264 " --> pdb=" O PRO P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 280 Processing helix chain 'P' and resid 298 through 307 Processing helix chain 'P' and resid 330 through 334 Processing helix chain 'P' and resid 529 through 532 Processing helix chain 'P' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL P 537 " --> pdb=" O ALA P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 552 through 563 Processing helix chain 'P' and resid 576 through 581 Processing helix chain 'P' and resid 586 through 592 Processing helix chain 'Q' and resid 160 through 166 Processing helix chain 'Q' and resid 166 through 173 Processing helix chain 'Q' and resid 229 through 239 Processing helix chain 'Q' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER Q 264 " --> pdb=" O PRO Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 280 Processing helix chain 'Q' and resid 298 through 307 Processing helix chain 'Q' and resid 330 through 334 Processing helix chain 'Q' and resid 529 through 532 Processing helix chain 'Q' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL Q 537 " --> pdb=" O ALA Q 533 " (cutoff:3.500A) Processing helix chain 'Q' and resid 552 through 563 Processing helix chain 'Q' and resid 576 through 581 Processing helix chain 'Q' and resid 586 through 592 Processing helix chain 'R' and resid 160 through 166 Processing helix chain 'R' and resid 166 through 173 Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'R' and resid 260 through 264 removed outlier: 4.251A pdb=" N SER R 264 " --> pdb=" O PRO R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 280 Processing helix chain 'R' and resid 298 through 307 Processing helix chain 'R' and resid 330 through 334 Processing helix chain 'R' and resid 529 through 532 Processing helix chain 'R' and resid 533 through 548 removed outlier: 3.675A pdb=" N VAL R 537 " --> pdb=" O ALA R 533 " (cutoff:3.500A) Processing helix chain 'R' and resid 552 through 563 Processing helix chain 'R' and resid 576 through 581 Processing helix chain 'R' and resid 586 through 592 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU A 253 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN A 202 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA A 255 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 204 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG A 257 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR A 206 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET A 285 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER A 317 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 287 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU A 253 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN A 202 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA A 255 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 204 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG A 257 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR A 206 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET A 285 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER A 317 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 287 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER A 339 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A 504 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY A 341 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 514 Processing sheet with id=AA4, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA5, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN A 657 " --> pdb=" O ASN A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE A 698 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A 606 " --> pdb=" O ILE A 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU A 685 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER A 709 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN A 748 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 738 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU A 732 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN A 748 " --> pdb=" O VAL A 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 738 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU A 732 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB2, first strand: chain 'B' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU B 253 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN B 202 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA B 255 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 204 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG B 257 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 206 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET B 285 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER B 317 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 287 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU B 253 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN B 202 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA B 255 " --> pdb=" O GLN B 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 204 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG B 257 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 206 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET B 285 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER B 317 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 287 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER B 339 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 504 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY B 341 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 514 Processing sheet with id=AB5, first strand: chain 'B' and resid 564 through 565 Processing sheet with id=AB6, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN B 657 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE B 698 " --> pdb=" O TYR B 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 606 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU B 685 " --> pdb=" O THR B 689 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER B 709 " --> pdb=" O TYR B 726 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN B 748 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 738 " --> pdb=" O GLN B 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU B 732 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN B 748 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 738 " --> pdb=" O GLN B 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU B 732 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 767 through 768 Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU C 253 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN C 202 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA C 255 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 204 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG C 257 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR C 206 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET C 285 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER C 317 " --> pdb=" O MET C 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 287 " --> pdb=" O SER C 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU C 253 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN C 202 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA C 255 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 204 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG C 257 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR C 206 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET C 285 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER C 317 " --> pdb=" O MET C 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU C 287 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER C 339 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA C 504 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY C 341 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 509 through 514 Processing sheet with id=AC6, first strand: chain 'C' and resid 564 through 565 Processing sheet with id=AC7, first strand: chain 'C' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN C 657 " --> pdb=" O ASN C 624 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE C 698 " --> pdb=" O TYR C 604 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR C 606 " --> pdb=" O ILE C 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR C 689 " --> pdb=" O GLU C 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU C 685 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER C 709 " --> pdb=" O TYR C 726 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN C 748 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 738 " --> pdb=" O GLN C 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU C 732 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN C 748 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 738 " --> pdb=" O GLN C 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU C 732 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 767 through 768 Processing sheet with id=AD4, first strand: chain 'D' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU D 253 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN D 202 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA D 255 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS D 204 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG D 257 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR D 206 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET D 285 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER D 317 " --> pdb=" O MET D 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU D 287 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU D 253 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN D 202 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA D 255 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS D 204 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG D 257 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR D 206 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET D 285 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER D 317 " --> pdb=" O MET D 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU D 287 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER D 339 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA D 504 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY D 341 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 509 through 514 Processing sheet with id=AD7, first strand: chain 'D' and resid 564 through 565 Processing sheet with id=AD8, first strand: chain 'D' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN D 657 " --> pdb=" O ASN D 624 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE D 698 " --> pdb=" O TYR D 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR D 606 " --> pdb=" O ILE D 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU D 685 " --> pdb=" O THR D 689 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER D 709 " --> pdb=" O TYR D 726 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN D 748 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 738 " --> pdb=" O GLN D 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU D 732 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN D 748 " --> pdb=" O VAL D 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 738 " --> pdb=" O GLN D 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU D 732 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 767 through 768 Processing sheet with id=AE5, first strand: chain 'E' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU E 253 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN E 202 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA E 255 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS E 204 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG E 257 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR E 206 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET E 285 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER E 317 " --> pdb=" O MET E 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 287 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU E 253 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN E 202 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA E 255 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS E 204 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG E 257 " --> pdb=" O LYS E 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR E 206 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET E 285 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER E 317 " --> pdb=" O MET E 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 287 " --> pdb=" O SER E 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER E 339 " --> pdb=" O VAL E 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA E 504 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY E 341 " --> pdb=" O ALA E 504 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 509 through 514 Processing sheet with id=AE8, first strand: chain 'E' and resid 564 through 565 Processing sheet with id=AE9, first strand: chain 'E' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN E 657 " --> pdb=" O ASN E 624 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE E 698 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR E 606 " --> pdb=" O ILE E 698 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR E 689 " --> pdb=" O GLU E 685 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU E 685 " --> pdb=" O THR E 689 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER E 709 " --> pdb=" O TYR E 726 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN E 748 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL E 738 " --> pdb=" O GLN E 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU E 732 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN E 748 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL E 738 " --> pdb=" O GLN E 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU E 732 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 767 through 768 Processing sheet with id=AF6, first strand: chain 'F' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU F 253 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN F 202 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA F 255 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS F 204 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG F 257 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR F 206 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET F 285 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER F 317 " --> pdb=" O MET F 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU F 287 " --> pdb=" O SER F 317 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU F 253 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN F 202 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA F 255 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS F 204 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG F 257 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR F 206 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET F 285 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER F 317 " --> pdb=" O MET F 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU F 287 " --> pdb=" O SER F 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER F 339 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA F 504 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY F 341 " --> pdb=" O ALA F 504 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 509 through 514 Processing sheet with id=AF9, first strand: chain 'F' and resid 564 through 565 Processing sheet with id=AG1, first strand: chain 'F' and resid 595 through 598 removed outlier: 3.622A pdb=" N GLN F 657 " --> pdb=" O ASN F 624 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE F 698 " --> pdb=" O TYR F 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR F 606 " --> pdb=" O ILE F 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU F 685 " --> pdb=" O THR F 689 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER F 709 " --> pdb=" O TYR F 726 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN F 748 " --> pdb=" O VAL F 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL F 738 " --> pdb=" O GLN F 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU F 732 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN F 748 " --> pdb=" O VAL F 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL F 738 " --> pdb=" O GLN F 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU F 732 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 767 through 768 Processing sheet with id=AG7, first strand: chain 'G' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU G 253 " --> pdb=" O PHE G 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN G 202 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA G 255 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS G 204 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG G 257 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR G 206 " --> pdb=" O ARG G 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET G 285 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER G 317 " --> pdb=" O MET G 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU G 287 " --> pdb=" O SER G 317 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU G 253 " --> pdb=" O PHE G 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN G 202 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA G 255 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS G 204 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG G 257 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR G 206 " --> pdb=" O ARG G 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET G 285 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER G 317 " --> pdb=" O MET G 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU G 287 " --> pdb=" O SER G 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER G 339 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA G 504 " --> pdb=" O SER G 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY G 341 " --> pdb=" O ALA G 504 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 509 through 514 Processing sheet with id=AH1, first strand: chain 'G' and resid 564 through 565 Processing sheet with id=AH2, first strand: chain 'G' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN G 657 " --> pdb=" O ASN G 624 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE G 698 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR G 606 " --> pdb=" O ILE G 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR G 689 " --> pdb=" O GLU G 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU G 685 " --> pdb=" O THR G 689 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER G 709 " --> pdb=" O TYR G 726 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN G 748 " --> pdb=" O VAL G 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL G 738 " --> pdb=" O GLN G 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU G 732 " --> pdb=" O LYS G 754 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN G 748 " --> pdb=" O VAL G 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL G 738 " --> pdb=" O GLN G 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU G 732 " --> pdb=" O LYS G 754 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 767 through 768 Processing sheet with id=AH8, first strand: chain 'H' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU H 253 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN H 202 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA H 255 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS H 204 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG H 257 " --> pdb=" O LYS H 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR H 206 " --> pdb=" O ARG H 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET H 285 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER H 317 " --> pdb=" O MET H 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU H 287 " --> pdb=" O SER H 317 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU H 253 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN H 202 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA H 255 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS H 204 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG H 257 " --> pdb=" O LYS H 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR H 206 " --> pdb=" O ARG H 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET H 285 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER H 317 " --> pdb=" O MET H 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU H 287 " --> pdb=" O SER H 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER H 339 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA H 504 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY H 341 " --> pdb=" O ALA H 504 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 509 through 514 Processing sheet with id=AI2, first strand: chain 'H' and resid 564 through 565 Processing sheet with id=AI3, first strand: chain 'H' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN H 657 " --> pdb=" O ASN H 624 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE H 698 " --> pdb=" O TYR H 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR H 606 " --> pdb=" O ILE H 698 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR H 689 " --> pdb=" O GLU H 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU H 685 " --> pdb=" O THR H 689 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER H 709 " --> pdb=" O TYR H 726 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN H 748 " --> pdb=" O VAL H 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL H 738 " --> pdb=" O GLN H 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU H 732 " --> pdb=" O LYS H 754 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN H 748 " --> pdb=" O VAL H 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL H 738 " --> pdb=" O GLN H 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU H 732 " --> pdb=" O LYS H 754 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'H' and resid 767 through 768 Processing sheet with id=AI9, first strand: chain 'I' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU I 253 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN I 202 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA I 255 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS I 204 " --> pdb=" O ALA I 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG I 257 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR I 206 " --> pdb=" O ARG I 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET I 285 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER I 317 " --> pdb=" O MET I 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU I 287 " --> pdb=" O SER I 317 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU I 253 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN I 202 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA I 255 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS I 204 " --> pdb=" O ALA I 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG I 257 " --> pdb=" O LYS I 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR I 206 " --> pdb=" O ARG I 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET I 285 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER I 317 " --> pdb=" O MET I 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU I 287 " --> pdb=" O SER I 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER I 339 " --> pdb=" O VAL I 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA I 504 " --> pdb=" O SER I 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY I 341 " --> pdb=" O ALA I 504 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 509 through 514 Processing sheet with id=AJ3, first strand: chain 'I' and resid 564 through 565 Processing sheet with id=AJ4, first strand: chain 'I' and resid 595 through 598 removed outlier: 3.622A pdb=" N GLN I 657 " --> pdb=" O ASN I 624 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE I 698 " --> pdb=" O TYR I 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR I 606 " --> pdb=" O ILE I 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR I 689 " --> pdb=" O GLU I 685 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU I 685 " --> pdb=" O THR I 689 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER I 709 " --> pdb=" O TYR I 726 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN I 748 " --> pdb=" O VAL I 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL I 738 " --> pdb=" O GLN I 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU I 732 " --> pdb=" O LYS I 754 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN I 748 " --> pdb=" O VAL I 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL I 738 " --> pdb=" O GLN I 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU I 732 " --> pdb=" O LYS I 754 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'I' and resid 767 through 768 Processing sheet with id=AK1, first strand: chain 'J' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU J 253 " --> pdb=" O PHE J 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN J 202 " --> pdb=" O LEU J 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA J 255 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS J 204 " --> pdb=" O ALA J 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG J 257 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR J 206 " --> pdb=" O ARG J 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET J 285 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER J 317 " --> pdb=" O MET J 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU J 287 " --> pdb=" O SER J 317 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU J 253 " --> pdb=" O PHE J 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN J 202 " --> pdb=" O LEU J 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA J 255 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS J 204 " --> pdb=" O ALA J 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG J 257 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR J 206 " --> pdb=" O ARG J 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET J 285 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER J 317 " --> pdb=" O MET J 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU J 287 " --> pdb=" O SER J 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER J 339 " --> pdb=" O VAL J 502 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA J 504 " --> pdb=" O SER J 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY J 341 " --> pdb=" O ALA J 504 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 509 through 514 Processing sheet with id=AK4, first strand: chain 'J' and resid 564 through 565 Processing sheet with id=AK5, first strand: chain 'J' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN J 657 " --> pdb=" O ASN J 624 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE J 698 " --> pdb=" O TYR J 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR J 606 " --> pdb=" O ILE J 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR J 689 " --> pdb=" O GLU J 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU J 685 " --> pdb=" O THR J 689 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER J 709 " --> pdb=" O TYR J 726 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN J 748 " --> pdb=" O VAL J 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL J 738 " --> pdb=" O GLN J 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU J 732 " --> pdb=" O LYS J 754 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN J 748 " --> pdb=" O VAL J 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL J 738 " --> pdb=" O GLN J 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU J 732 " --> pdb=" O LYS J 754 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 767 through 768 Processing sheet with id=AL2, first strand: chain 'K' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU K 253 " --> pdb=" O PHE K 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN K 202 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA K 255 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS K 204 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG K 257 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR K 206 " --> pdb=" O ARG K 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET K 285 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER K 317 " --> pdb=" O MET K 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU K 287 " --> pdb=" O SER K 317 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU K 253 " --> pdb=" O PHE K 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN K 202 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA K 255 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS K 204 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG K 257 " --> pdb=" O LYS K 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR K 206 " --> pdb=" O ARG K 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET K 285 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER K 317 " --> pdb=" O MET K 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU K 287 " --> pdb=" O SER K 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER K 339 " --> pdb=" O VAL K 502 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA K 504 " --> pdb=" O SER K 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY K 341 " --> pdb=" O ALA K 504 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 509 through 514 Processing sheet with id=AL5, first strand: chain 'K' and resid 564 through 565 Processing sheet with id=AL6, first strand: chain 'K' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN K 657 " --> pdb=" O ASN K 624 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE K 698 " --> pdb=" O TYR K 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR K 606 " --> pdb=" O ILE K 698 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR K 689 " --> pdb=" O GLU K 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU K 685 " --> pdb=" O THR K 689 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER K 709 " --> pdb=" O TYR K 726 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN K 748 " --> pdb=" O VAL K 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL K 738 " --> pdb=" O GLN K 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU K 732 " --> pdb=" O LYS K 754 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'K' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN K 748 " --> pdb=" O VAL K 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL K 738 " --> pdb=" O GLN K 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU K 732 " --> pdb=" O LYS K 754 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 767 through 768 Processing sheet with id=AM3, first strand: chain 'L' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU L 253 " --> pdb=" O PHE L 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN L 202 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA L 255 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS L 204 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG L 257 " --> pdb=" O LYS L 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR L 206 " --> pdb=" O ARG L 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET L 285 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER L 317 " --> pdb=" O MET L 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU L 287 " --> pdb=" O SER L 317 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'L' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU L 253 " --> pdb=" O PHE L 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN L 202 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA L 255 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS L 204 " --> pdb=" O ALA L 255 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ARG L 257 " --> pdb=" O LYS L 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR L 206 " --> pdb=" O ARG L 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET L 285 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER L 317 " --> pdb=" O MET L 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU L 287 " --> pdb=" O SER L 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER L 339 " --> pdb=" O VAL L 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA L 504 " --> pdb=" O SER L 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY L 341 " --> pdb=" O ALA L 504 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'L' and resid 509 through 514 Processing sheet with id=AM6, first strand: chain 'L' and resid 564 through 565 Processing sheet with id=AM7, first strand: chain 'L' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN L 657 " --> pdb=" O ASN L 624 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'L' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE L 698 " --> pdb=" O TYR L 604 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR L 606 " --> pdb=" O ILE L 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR L 689 " --> pdb=" O GLU L 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU L 685 " --> pdb=" O THR L 689 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'L' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER L 709 " --> pdb=" O TYR L 726 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'L' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN L 748 " --> pdb=" O VAL L 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL L 738 " --> pdb=" O GLN L 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU L 732 " --> pdb=" O LYS L 754 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'L' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN L 748 " --> pdb=" O VAL L 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL L 738 " --> pdb=" O GLN L 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU L 732 " --> pdb=" O LYS L 754 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'L' and resid 767 through 768 Processing sheet with id=AN4, first strand: chain 'M' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU M 253 " --> pdb=" O PHE M 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN M 202 " --> pdb=" O LEU M 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA M 255 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS M 204 " --> pdb=" O ALA M 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG M 257 " --> pdb=" O LYS M 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR M 206 " --> pdb=" O ARG M 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET M 285 " --> pdb=" O VAL M 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER M 317 " --> pdb=" O MET M 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU M 287 " --> pdb=" O SER M 317 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU M 253 " --> pdb=" O PHE M 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN M 202 " --> pdb=" O LEU M 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA M 255 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS M 204 " --> pdb=" O ALA M 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG M 257 " --> pdb=" O LYS M 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR M 206 " --> pdb=" O ARG M 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET M 285 " --> pdb=" O VAL M 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER M 317 " --> pdb=" O MET M 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU M 287 " --> pdb=" O SER M 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER M 339 " --> pdb=" O VAL M 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA M 504 " --> pdb=" O SER M 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY M 341 " --> pdb=" O ALA M 504 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'M' and resid 509 through 514 Processing sheet with id=AN7, first strand: chain 'M' and resid 564 through 565 Processing sheet with id=AN8, first strand: chain 'M' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN M 657 " --> pdb=" O ASN M 624 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'M' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE M 698 " --> pdb=" O TYR M 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR M 606 " --> pdb=" O ILE M 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR M 689 " --> pdb=" O GLU M 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU M 685 " --> pdb=" O THR M 689 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'M' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER M 709 " --> pdb=" O TYR M 726 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'M' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN M 748 " --> pdb=" O VAL M 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL M 738 " --> pdb=" O GLN M 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU M 732 " --> pdb=" O LYS M 754 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'M' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN M 748 " --> pdb=" O VAL M 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL M 738 " --> pdb=" O GLN M 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU M 732 " --> pdb=" O LYS M 754 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'M' and resid 767 through 768 Processing sheet with id=AO5, first strand: chain 'N' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU N 253 " --> pdb=" O PHE N 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN N 202 " --> pdb=" O LEU N 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA N 255 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS N 204 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG N 257 " --> pdb=" O LYS N 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR N 206 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET N 285 " --> pdb=" O VAL N 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER N 317 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU N 287 " --> pdb=" O SER N 317 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'N' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU N 253 " --> pdb=" O PHE N 200 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN N 202 " --> pdb=" O LEU N 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA N 255 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS N 204 " --> pdb=" O ALA N 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG N 257 " --> pdb=" O LYS N 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR N 206 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET N 285 " --> pdb=" O VAL N 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER N 317 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU N 287 " --> pdb=" O SER N 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER N 339 " --> pdb=" O VAL N 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA N 504 " --> pdb=" O SER N 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY N 341 " --> pdb=" O ALA N 504 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'N' and resid 509 through 514 Processing sheet with id=AO8, first strand: chain 'N' and resid 564 through 565 Processing sheet with id=AO9, first strand: chain 'N' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN N 657 " --> pdb=" O ASN N 624 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'N' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE N 698 " --> pdb=" O TYR N 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR N 606 " --> pdb=" O ILE N 698 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR N 689 " --> pdb=" O GLU N 685 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU N 685 " --> pdb=" O THR N 689 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'N' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER N 709 " --> pdb=" O TYR N 726 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'N' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN N 748 " --> pdb=" O VAL N 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL N 738 " --> pdb=" O GLN N 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU N 732 " --> pdb=" O LYS N 754 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'N' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN N 748 " --> pdb=" O VAL N 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL N 738 " --> pdb=" O GLN N 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU N 732 " --> pdb=" O LYS N 754 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'N' and resid 767 through 768 Processing sheet with id=AP6, first strand: chain 'O' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU O 253 " --> pdb=" O PHE O 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN O 202 " --> pdb=" O LEU O 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA O 255 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS O 204 " --> pdb=" O ALA O 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG O 257 " --> pdb=" O LYS O 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR O 206 " --> pdb=" O ARG O 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET O 285 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER O 317 " --> pdb=" O MET O 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU O 287 " --> pdb=" O SER O 317 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'O' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU O 253 " --> pdb=" O PHE O 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN O 202 " --> pdb=" O LEU O 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA O 255 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS O 204 " --> pdb=" O ALA O 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG O 257 " --> pdb=" O LYS O 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR O 206 " --> pdb=" O ARG O 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET O 285 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER O 317 " --> pdb=" O MET O 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU O 287 " --> pdb=" O SER O 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER O 339 " --> pdb=" O VAL O 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA O 504 " --> pdb=" O SER O 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY O 341 " --> pdb=" O ALA O 504 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'O' and resid 509 through 514 Processing sheet with id=AP9, first strand: chain 'O' and resid 564 through 565 Processing sheet with id=AQ1, first strand: chain 'O' and resid 595 through 598 removed outlier: 3.622A pdb=" N GLN O 657 " --> pdb=" O ASN O 624 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'O' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE O 698 " --> pdb=" O TYR O 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR O 606 " --> pdb=" O ILE O 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU O 685 " --> pdb=" O THR O 689 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'O' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER O 709 " --> pdb=" O TYR O 726 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'O' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN O 748 " --> pdb=" O VAL O 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL O 738 " --> pdb=" O GLN O 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU O 732 " --> pdb=" O LYS O 754 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'O' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN O 748 " --> pdb=" O VAL O 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL O 738 " --> pdb=" O GLN O 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU O 732 " --> pdb=" O LYS O 754 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'O' and resid 767 through 768 Processing sheet with id=AQ7, first strand: chain 'P' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU P 253 " --> pdb=" O PHE P 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN P 202 " --> pdb=" O LEU P 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA P 255 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS P 204 " --> pdb=" O ALA P 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG P 257 " --> pdb=" O LYS P 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR P 206 " --> pdb=" O ARG P 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET P 285 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER P 317 " --> pdb=" O MET P 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU P 287 " --> pdb=" O SER P 317 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'P' and resid 200 through 207 removed outlier: 6.486A pdb=" N LEU P 253 " --> pdb=" O PHE P 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN P 202 " --> pdb=" O LEU P 253 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ALA P 255 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS P 204 " --> pdb=" O ALA P 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG P 257 " --> pdb=" O LYS P 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR P 206 " --> pdb=" O ARG P 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET P 285 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER P 317 " --> pdb=" O MET P 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU P 287 " --> pdb=" O SER P 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER P 339 " --> pdb=" O VAL P 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA P 504 " --> pdb=" O SER P 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY P 341 " --> pdb=" O ALA P 504 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'P' and resid 509 through 514 Processing sheet with id=AR1, first strand: chain 'P' and resid 564 through 565 Processing sheet with id=AR2, first strand: chain 'P' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN P 657 " --> pdb=" O ASN P 624 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'P' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE P 698 " --> pdb=" O TYR P 604 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR P 606 " --> pdb=" O ILE P 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR P 689 " --> pdb=" O GLU P 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU P 685 " --> pdb=" O THR P 689 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'P' and resid 709 through 714 removed outlier: 3.993A pdb=" N SER P 709 " --> pdb=" O TYR P 726 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'P' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN P 748 " --> pdb=" O VAL P 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL P 738 " --> pdb=" O GLN P 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU P 732 " --> pdb=" O LYS P 754 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'P' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN P 748 " --> pdb=" O VAL P 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL P 738 " --> pdb=" O GLN P 748 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU P 732 " --> pdb=" O LYS P 754 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'P' and resid 767 through 768 Processing sheet with id=AR8, first strand: chain 'Q' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU Q 253 " --> pdb=" O PHE Q 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN Q 202 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA Q 255 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS Q 204 " --> pdb=" O ALA Q 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG Q 257 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR Q 206 " --> pdb=" O ARG Q 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET Q 285 " --> pdb=" O VAL Q 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER Q 317 " --> pdb=" O MET Q 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU Q 287 " --> pdb=" O SER Q 317 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'Q' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU Q 253 " --> pdb=" O PHE Q 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN Q 202 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA Q 255 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS Q 204 " --> pdb=" O ALA Q 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG Q 257 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR Q 206 " --> pdb=" O ARG Q 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET Q 285 " --> pdb=" O VAL Q 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER Q 317 " --> pdb=" O MET Q 285 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU Q 287 " --> pdb=" O SER Q 317 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER Q 339 " --> pdb=" O VAL Q 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA Q 504 " --> pdb=" O SER Q 339 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY Q 341 " --> pdb=" O ALA Q 504 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'Q' and resid 509 through 514 Processing sheet with id=AS2, first strand: chain 'Q' and resid 564 through 565 Processing sheet with id=AS3, first strand: chain 'Q' and resid 595 through 598 removed outlier: 3.621A pdb=" N GLN Q 657 " --> pdb=" O ASN Q 624 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'Q' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE Q 698 " --> pdb=" O TYR Q 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR Q 606 " --> pdb=" O ILE Q 698 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR Q 689 " --> pdb=" O GLU Q 685 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU Q 685 " --> pdb=" O THR Q 689 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'Q' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER Q 709 " --> pdb=" O TYR Q 726 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'Q' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN Q 748 " --> pdb=" O VAL Q 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL Q 738 " --> pdb=" O GLN Q 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU Q 732 " --> pdb=" O LYS Q 754 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'Q' and resid 745 through 755 removed outlier: 5.633A pdb=" N GLN Q 748 " --> pdb=" O VAL Q 738 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL Q 738 " --> pdb=" O GLN Q 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU Q 732 " --> pdb=" O LYS Q 754 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'Q' and resid 767 through 768 Processing sheet with id=AS9, first strand: chain 'R' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU R 253 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN R 202 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA R 255 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS R 204 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG R 257 " --> pdb=" O LYS R 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR R 206 " --> pdb=" O ARG R 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET R 285 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER R 317 " --> pdb=" O MET R 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU R 287 " --> pdb=" O SER R 317 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'R' and resid 200 through 207 removed outlier: 6.485A pdb=" N LEU R 253 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN R 202 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA R 255 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS R 204 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ARG R 257 " --> pdb=" O LYS R 204 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR R 206 " --> pdb=" O ARG R 257 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET R 285 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER R 317 " --> pdb=" O MET R 285 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU R 287 " --> pdb=" O SER R 317 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER R 339 " --> pdb=" O VAL R 502 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA R 504 " --> pdb=" O SER R 339 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY R 341 " --> pdb=" O ALA R 504 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'R' and resid 509 through 514 Processing sheet with id=AT3, first strand: chain 'R' and resid 564 through 565 Processing sheet with id=AT4, first strand: chain 'R' and resid 595 through 598 removed outlier: 3.622A pdb=" N GLN R 657 " --> pdb=" O ASN R 624 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'R' and resid 602 through 607 removed outlier: 6.258A pdb=" N ILE R 698 " --> pdb=" O TYR R 604 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR R 606 " --> pdb=" O ILE R 698 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR R 689 " --> pdb=" O GLU R 685 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU R 685 " --> pdb=" O THR R 689 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'R' and resid 709 through 714 removed outlier: 3.994A pdb=" N SER R 709 " --> pdb=" O TYR R 726 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'R' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN R 748 " --> pdb=" O VAL R 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL R 738 " --> pdb=" O GLN R 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU R 732 " --> pdb=" O LYS R 754 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'R' and resid 745 through 755 removed outlier: 5.632A pdb=" N GLN R 748 " --> pdb=" O VAL R 738 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL R 738 " --> pdb=" O GLN R 748 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU R 732 " --> pdb=" O LYS R 754 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'R' and resid 767 through 768 3312 hydrogen bonds defined for protein. 8910 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: 36.94 Time building geometry restraints manager: 14.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20011 1.33 - 1.45: 11239 1.45 - 1.57: 39400 1.57 - 1.69: 0 1.69 - 1.80: 396 Bond restraints: 71046 Sorted by residual: bond pdb=" CA THR J 563 " pdb=" CB THR J 563 " ideal model delta sigma weight residual 1.526 1.489 0.038 1.76e-02 3.23e+03 4.54e+00 bond pdb=" CA THR E 563 " pdb=" CB THR E 563 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.42e+00 bond pdb=" CA THR N 563 " pdb=" CB THR N 563 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.42e+00 bond pdb=" CA THR Q 563 " pdb=" CB THR Q 563 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.41e+00 bond pdb=" CA THR H 563 " pdb=" CB THR H 563 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.41e+00 ... (remaining 71041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 94163 1.66 - 3.31: 2195 3.31 - 4.97: 266 4.97 - 6.62: 18 6.62 - 8.28: 18 Bond angle restraints: 96660 Sorted by residual: angle pdb=" CB MET P 532 " pdb=" CG MET P 532 " pdb=" SD MET P 532 " ideal model delta sigma weight residual 112.70 104.42 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" CB MET G 532 " pdb=" CG MET G 532 " pdb=" SD MET G 532 " ideal model delta sigma weight residual 112.70 104.42 8.28 3.00e+00 1.11e-01 7.61e+00 angle pdb=" CB MET R 532 " pdb=" CG MET R 532 " pdb=" SD MET R 532 " ideal model delta sigma weight residual 112.70 104.43 8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" CB MET I 532 " pdb=" CG MET I 532 " pdb=" SD MET I 532 " ideal model delta sigma weight residual 112.70 104.43 8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" CB MET C 532 " pdb=" CG MET C 532 " pdb=" SD MET C 532 " ideal model delta sigma weight residual 112.70 104.44 8.26 3.00e+00 1.11e-01 7.59e+00 ... (remaining 96655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 37550 17.63 - 35.26: 3482 35.26 - 52.89: 728 52.89 - 70.51: 270 70.51 - 88.14: 162 Dihedral angle restraints: 42192 sinusoidal: 15876 harmonic: 26316 Sorted by residual: dihedral pdb=" CA TRP D 306 " pdb=" C TRP D 306 " pdb=" N ALA D 307 " pdb=" CA ALA D 307 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TRP M 306 " pdb=" C TRP M 306 " pdb=" N ALA M 307 " pdb=" CA ALA M 307 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TRP N 306 " pdb=" C TRP N 306 " pdb=" N ALA N 307 " pdb=" CA ALA N 307 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 42189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5517 0.030 - 0.060: 3088 0.060 - 0.090: 1435 0.090 - 0.121: 578 0.121 - 0.151: 128 Chirality restraints: 10746 Sorted by residual: chirality pdb=" CA ILE F 723 " pdb=" N ILE F 723 " pdb=" C ILE F 723 " pdb=" CB ILE F 723 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE O 723 " pdb=" N ILE O 723 " pdb=" C ILE O 723 " pdb=" CB ILE O 723 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA ILE K 723 " pdb=" N ILE K 723 " pdb=" C ILE K 723 " pdb=" CB ILE K 723 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 10743 not shown) Planarity restraints: 12672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 517 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO I 518 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 518 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 518 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 517 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO R 518 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO R 518 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 518 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Q 517 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO Q 518 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO Q 518 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO Q 518 " -0.032 5.00e-02 4.00e+02 ... (remaining 12669 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 8889 2.74 - 3.28: 66932 3.28 - 3.82: 118515 3.82 - 4.36: 146833 4.36 - 4.90: 255583 Nonbonded interactions: 596752 Sorted by model distance: nonbonded pdb=" O GLN G 202 " pdb=" OH TYR J 739 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 739 " pdb=" O GLN P 202 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR C 739 " pdb=" O GLN J 202 " model vdw 2.224 3.040 nonbonded pdb=" O GLN A 202 " pdb=" OH TYR L 739 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP J 297 " pdb=" NH2 ARG J 335 " model vdw 2.248 3.120 ... (remaining 596747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.080 Extract box with map and model: 1.980 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 115.410 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:9.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 71046 Z= 0.485 Angle : 0.640 8.276 96660 Z= 0.355 Chirality : 0.047 0.151 10746 Planarity : 0.005 0.057 12672 Dihedral : 15.803 88.142 25596 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 18.83 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.08), residues: 9234 helix: 0.99 (0.14), residues: 1530 sheet: 0.30 (0.09), residues: 2988 loop : -1.18 (0.08), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 306 HIS 0.003 0.001 HIS N 656 PHE 0.007 0.001 PHE M 208 TYR 0.010 0.001 TYR B 203 ARG 0.006 0.001 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 5.788 Fit side-chains REVERT: A 493 MET cc_start: 0.9205 (mmm) cc_final: 0.8858 (mmm) REVERT: B 158 MET cc_start: 0.7466 (tpt) cc_final: 0.7262 (tpp) REVERT: D 483 MET cc_start: 0.8699 (mmm) cc_final: 0.8063 (mmm) REVERT: H 497 MET cc_start: 0.9368 (ttm) cc_final: 0.9156 (ttm) REVERT: H 588 MET cc_start: 0.8780 (mmm) cc_final: 0.8565 (mmm) REVERT: I 483 MET cc_start: 0.8769 (mmm) cc_final: 0.8239 (tpp) REVERT: J 493 MET cc_start: 0.9204 (mmm) cc_final: 0.8856 (mmm) REVERT: K 158 MET cc_start: 0.7467 (tpt) cc_final: 0.7264 (tpp) REVERT: M 483 MET cc_start: 0.8700 (mmm) cc_final: 0.8065 (mmm) REVERT: Q 497 MET cc_start: 0.9368 (ttm) cc_final: 0.9157 (ttm) REVERT: Q 588 MET cc_start: 0.8779 (mmm) cc_final: 0.8562 (mmm) REVERT: R 483 MET cc_start: 0.8770 (mmm) cc_final: 0.8241 (tpp) outliers start: 0 outliers final: 4 residues processed: 286 average time/residue: 1.8785 time to fit residues: 674.8558 Evaluate side-chains 218 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain Q residue 160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 775 optimal weight: 10.0000 chunk 695 optimal weight: 8.9990 chunk 386 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 chunk 371 optimal weight: 6.9990 chunk 719 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 437 optimal weight: 5.9990 chunk 535 optimal weight: 5.9990 chunk 833 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 71046 Z= 0.382 Angle : 0.587 7.322 96660 Z= 0.317 Chirality : 0.047 0.155 10746 Planarity : 0.005 0.051 12672 Dihedral : 4.796 80.917 9908 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.50 % Allowed : 17.69 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 9234 helix: 1.47 (0.13), residues: 1602 sheet: 0.34 (0.09), residues: 3006 loop : -1.00 (0.09), residues: 4626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 306 HIS 0.004 0.001 HIS A 233 PHE 0.009 0.001 PHE Q 208 TYR 0.014 0.002 TYR H 256 ARG 0.007 0.001 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 218 time to evaluate : 6.184 Fit side-chains REVERT: A 493 MET cc_start: 0.9205 (mmm) cc_final: 0.8836 (mmm) REVERT: E 224 ARG cc_start: 0.9299 (mtm-85) cc_final: 0.9092 (mtm-85) REVERT: H 497 MET cc_start: 0.9291 (ttm) cc_final: 0.9001 (ttm) REVERT: I 483 MET cc_start: 0.9077 (mmm) cc_final: 0.8863 (tpp) REVERT: J 493 MET cc_start: 0.9206 (mmm) cc_final: 0.8835 (mmm) REVERT: N 224 ARG cc_start: 0.9299 (mtm-85) cc_final: 0.9091 (mtm-85) REVERT: Q 497 MET cc_start: 0.9291 (ttm) cc_final: 0.9001 (ttm) REVERT: R 483 MET cc_start: 0.9077 (mmm) cc_final: 0.8862 (tpp) outliers start: 184 outliers final: 56 residues processed: 372 average time/residue: 1.5125 time to fit residues: 739.4593 Evaluate side-chains 270 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 214 time to evaluate : 5.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 665 VAL Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 665 VAL Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 665 VAL Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain K residue 665 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 611 LYS Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain M residue 665 VAL Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 308 MET Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain O residue 665 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 308 MET Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 665 VAL Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 665 VAL Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 463 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 693 optimal weight: 7.9990 chunk 567 optimal weight: 0.2980 chunk 229 optimal weight: 5.9990 chunk 835 optimal weight: 8.9990 chunk 902 optimal weight: 0.0370 chunk 743 optimal weight: 6.9990 chunk 828 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 669 optimal weight: 2.9990 overall best weight: 3.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 ASN ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 71046 Z= 0.233 Angle : 0.522 6.091 96660 Z= 0.280 Chirality : 0.045 0.141 10746 Planarity : 0.005 0.047 12672 Dihedral : 4.495 79.088 9908 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.09), residues: 9234 helix: 2.01 (0.13), residues: 1602 sheet: 0.36 (0.09), residues: 2970 loop : -0.97 (0.09), residues: 4662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 306 HIS 0.005 0.001 HIS I 230 PHE 0.008 0.001 PHE J 208 TYR 0.010 0.001 TYR J 256 ARG 0.007 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 218 time to evaluate : 6.024 Fit side-chains REVERT: A 493 MET cc_start: 0.9196 (mmm) cc_final: 0.8780 (mmm) REVERT: A 532 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: C 158 MET cc_start: 0.7486 (mmm) cc_final: 0.7256 (mmm) REVERT: D 181 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8514 (mtpt) REVERT: E 696 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9232 (tt) REVERT: H 160 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7416 (t0) REVERT: H 181 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8255 (ttpt) REVERT: H 497 MET cc_start: 0.9250 (ttm) cc_final: 0.8987 (ttm) REVERT: I 483 MET cc_start: 0.9093 (mmm) cc_final: 0.8890 (tpp) REVERT: J 493 MET cc_start: 0.9196 (mmm) cc_final: 0.8781 (mmm) REVERT: J 532 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: L 158 MET cc_start: 0.7485 (mmm) cc_final: 0.7254 (mmm) REVERT: M 181 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: N 696 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9232 (tt) REVERT: Q 160 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7418 (t0) REVERT: Q 181 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8255 (ttpt) REVERT: Q 497 MET cc_start: 0.9250 (ttm) cc_final: 0.8988 (ttm) REVERT: R 483 MET cc_start: 0.9092 (mmm) cc_final: 0.8890 (tpp) outliers start: 160 outliers final: 42 residues processed: 352 average time/residue: 1.4479 time to fit residues: 687.4407 Evaluate side-chains 268 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 216 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain I residue 696 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 532 MET Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain N residue 696 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 308 MET Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 658 THR Chi-restraints excluded: chain R residue 696 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 825 optimal weight: 10.0000 chunk 627 optimal weight: 6.9990 chunk 433 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 560 optimal weight: 8.9990 chunk 838 optimal weight: 10.0000 chunk 887 optimal weight: 9.9990 chunk 437 optimal weight: 9.9990 chunk 794 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 71046 Z= 0.319 Angle : 0.539 6.440 96660 Z= 0.288 Chirality : 0.046 0.143 10746 Planarity : 0.005 0.044 12672 Dihedral : 4.438 69.802 9908 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.93 % Allowed : 18.34 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.09), residues: 9234 helix: 2.09 (0.13), residues: 1602 sheet: 0.39 (0.09), residues: 3006 loop : -0.96 (0.09), residues: 4626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 306 HIS 0.004 0.001 HIS G 230 PHE 0.007 0.001 PHE B 638 TYR 0.011 0.001 TYR J 256 ARG 0.008 0.000 ARG J 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 216 time to evaluate : 5.926 Fit side-chains REVERT: A 493 MET cc_start: 0.9211 (mmm) cc_final: 0.8820 (mmm) REVERT: A 532 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 638 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: D 181 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: E 696 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9243 (tt) REVERT: H 160 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7531 (t0) REVERT: H 181 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8298 (ttpt) REVERT: H 497 MET cc_start: 0.9236 (ttm) cc_final: 0.8968 (ttm) REVERT: I 483 MET cc_start: 0.9080 (mmm) cc_final: 0.8743 (tpp) REVERT: J 493 MET cc_start: 0.9211 (mmm) cc_final: 0.8820 (mmm) REVERT: J 532 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8337 (mmm) REVERT: K 638 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: M 181 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: N 696 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9244 (tt) REVERT: Q 160 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7533 (t0) REVERT: Q 181 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8298 (ttpt) REVERT: Q 497 MET cc_start: 0.9237 (ttm) cc_final: 0.8969 (ttm) REVERT: R 483 MET cc_start: 0.9081 (mmm) cc_final: 0.8743 (tpp) outliers start: 142 outliers final: 66 residues processed: 336 average time/residue: 1.4901 time to fit residues: 660.9974 Evaluate side-chains 292 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 214 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 651 VAL Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 493 MET Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain I residue 696 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 532 MET Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 628 ILE Chi-restraints excluded: chain K residue 638 PHE Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 271 ILE Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 304 LEU Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 651 VAL Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain N residue 696 LEU Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 308 MET Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain P residue 173 LEU Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 173 LEU Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Chi-restraints excluded: chain R residue 696 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 739 optimal weight: 0.9990 chunk 503 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 660 optimal weight: 0.4980 chunk 366 optimal weight: 10.0000 chunk 757 optimal weight: 10.0000 chunk 613 optimal weight: 8.9990 chunk 1 optimal weight: 0.0060 chunk 453 optimal weight: 10.0000 chunk 796 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 71046 Z= 0.189 Angle : 0.496 7.224 96660 Z= 0.263 Chirality : 0.044 0.137 10746 Planarity : 0.004 0.042 12672 Dihedral : 4.204 63.401 9908 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.04 % Allowed : 18.49 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 9234 helix: 2.31 (0.13), residues: 1602 sheet: 0.43 (0.09), residues: 2970 loop : -0.95 (0.09), residues: 4662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 496 HIS 0.004 0.001 HIS G 230 PHE 0.007 0.001 PHE A 208 TYR 0.009 0.001 TYR A 256 ARG 0.008 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 224 time to evaluate : 5.912 Fit side-chains REVERT: A 493 MET cc_start: 0.9214 (mmm) cc_final: 0.8760 (mmm) REVERT: B 638 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: D 181 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: D 638 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: H 160 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7527 (t0) REVERT: H 181 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8297 (ttpt) REVERT: I 224 ARG cc_start: 0.8921 (mpp80) cc_final: 0.8699 (mtm180) REVERT: I 483 MET cc_start: 0.9098 (mmm) cc_final: 0.8834 (tpp) REVERT: J 493 MET cc_start: 0.9212 (mmm) cc_final: 0.8758 (mmm) REVERT: J 756 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8525 (t0) REVERT: K 638 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: M 181 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8495 (mtpt) REVERT: M 638 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: Q 160 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7529 (t0) REVERT: Q 181 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8296 (ttpt) REVERT: R 224 ARG cc_start: 0.8918 (mpp80) cc_final: 0.8695 (mtm180) REVERT: R 483 MET cc_start: 0.9100 (mmm) cc_final: 0.8836 (tpp) outliers start: 150 outliers final: 63 residues processed: 346 average time/residue: 1.5184 time to fit residues: 691.6503 Evaluate side-chains 286 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 212 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 638 PHE Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 493 MET Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain I residue 696 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 756 ASP Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 638 PHE Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 651 VAL Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 638 PHE Chi-restraints excluded: chain M residue 651 VAL Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain P residue 173 LEU Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 743 LEU Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Chi-restraints excluded: chain R residue 696 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 298 optimal weight: 10.0000 chunk 799 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 520 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 888 optimal weight: 10.0000 chunk 737 optimal weight: 3.9990 chunk 411 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 293 optimal weight: 0.0570 chunk 466 optimal weight: 9.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 578 ASN ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 71046 Z= 0.275 Angle : 0.520 9.023 96660 Z= 0.275 Chirality : 0.045 0.141 10746 Planarity : 0.004 0.041 12672 Dihedral : 4.224 58.076 9908 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.56 % Allowed : 19.10 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 9234 helix: 2.26 (0.13), residues: 1602 sheet: 0.52 (0.10), residues: 2862 loop : -0.94 (0.09), residues: 4770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 326 HIS 0.004 0.001 HIS G 230 PHE 0.007 0.001 PHE J 800 TYR 0.010 0.001 TYR A 256 ARG 0.009 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 220 time to evaluate : 5.902 Fit side-chains REVERT: A 493 MET cc_start: 0.9218 (mmm) cc_final: 0.8799 (mmm) REVERT: B 638 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: D 181 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8516 (mtpt) REVERT: E 638 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: H 160 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7572 (t0) REVERT: H 181 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8363 (ttpt) REVERT: I 224 ARG cc_start: 0.8929 (mpp80) cc_final: 0.8679 (mtm180) REVERT: I 483 MET cc_start: 0.9097 (mmm) cc_final: 0.8739 (tpp) REVERT: I 532 MET cc_start: 0.9149 (mmt) cc_final: 0.8874 (mmm) REVERT: I 638 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: J 493 MET cc_start: 0.9215 (mmm) cc_final: 0.8789 (mmm) REVERT: K 638 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: M 181 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8516 (mtpt) REVERT: N 638 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: Q 160 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7576 (t0) REVERT: Q 181 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8362 (ttpt) REVERT: R 224 ARG cc_start: 0.8927 (mpp80) cc_final: 0.8677 (mtm180) REVERT: R 483 MET cc_start: 0.9097 (mmm) cc_final: 0.8740 (tpp) REVERT: R 532 MET cc_start: 0.9149 (mmt) cc_final: 0.8875 (mmm) REVERT: R 638 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8262 (m-80) outliers start: 115 outliers final: 61 residues processed: 320 average time/residue: 1.4981 time to fit residues: 632.2828 Evaluate side-chains 285 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 212 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 638 PHE Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 638 PHE Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 330 SER Chi-restraints excluded: chain H residue 493 MET Chi-restraints excluded: chain H residue 651 VAL Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 638 PHE Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 638 PHE Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 638 PHE Chi-restraints excluded: chain M residue 651 VAL Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 638 PHE Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 330 SER Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain Q residue 651 VAL Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 638 PHE Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 856 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 506 optimal weight: 4.9990 chunk 648 optimal weight: 0.8980 chunk 502 optimal weight: 10.0000 chunk 747 optimal weight: 9.9990 chunk 495 optimal weight: 7.9990 chunk 884 optimal weight: 10.0000 chunk 553 optimal weight: 5.9990 chunk 539 optimal weight: 9.9990 chunk 408 optimal weight: 30.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 71046 Z= 0.280 Angle : 0.519 7.717 96660 Z= 0.275 Chirality : 0.045 0.142 10746 Planarity : 0.004 0.041 12672 Dihedral : 4.216 51.282 9908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.83 % Allowed : 19.29 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 9234 helix: 2.23 (0.13), residues: 1602 sheet: 0.53 (0.10), residues: 2862 loop : -0.95 (0.09), residues: 4770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 326 HIS 0.004 0.001 HIS G 230 PHE 0.007 0.001 PHE K 800 TYR 0.010 0.001 TYR A 256 ARG 0.008 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 214 time to evaluate : 6.051 Fit side-chains REVERT: A 493 MET cc_start: 0.9221 (mmm) cc_final: 0.8796 (mmm) REVERT: B 638 PHE cc_start: 0.9248 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: D 181 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: E 638 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: F 756 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8285 (t0) REVERT: G 756 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8351 (t0) REVERT: H 181 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8338 (ttpt) REVERT: I 158 MET cc_start: 0.8020 (mmm) cc_final: 0.7756 (tpt) REVERT: I 224 ARG cc_start: 0.8953 (mpp80) cc_final: 0.8681 (mtm180) REVERT: I 483 MET cc_start: 0.9096 (mmm) cc_final: 0.8734 (tpp) REVERT: I 532 MET cc_start: 0.9158 (mmt) cc_final: 0.8880 (mmm) REVERT: J 493 MET cc_start: 0.9216 (mmm) cc_final: 0.8782 (mmm) REVERT: K 638 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: M 181 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: N 638 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: O 756 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8285 (t0) REVERT: P 756 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8350 (t0) REVERT: Q 181 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: R 158 MET cc_start: 0.8022 (mmm) cc_final: 0.7758 (tpt) REVERT: R 224 ARG cc_start: 0.8952 (mpp80) cc_final: 0.8678 (mtm180) REVERT: R 483 MET cc_start: 0.9095 (mmm) cc_final: 0.8734 (tpp) REVERT: R 532 MET cc_start: 0.9158 (mmt) cc_final: 0.8880 (mmm) outliers start: 135 outliers final: 67 residues processed: 335 average time/residue: 1.4446 time to fit residues: 642.6927 Evaluate side-chains 289 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 210 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 638 PHE Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 713 GLN Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 768 VAL Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain G residue 756 ASP Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 330 SER Chi-restraints excluded: chain H residue 493 MET Chi-restraints excluded: chain H residue 651 VAL Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 768 VAL Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 638 PHE Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain K residue 665 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 651 VAL Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 638 PHE Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain N residue 713 GLN Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain O residue 756 ASP Chi-restraints excluded: chain O residue 768 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 756 ASP Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 330 SER Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain Q residue 651 VAL Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 547 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 528 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 562 optimal weight: 5.9990 chunk 602 optimal weight: 0.8980 chunk 437 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 695 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 71046 Z= 0.264 Angle : 0.515 6.963 96660 Z= 0.273 Chirality : 0.045 0.158 10746 Planarity : 0.004 0.040 12672 Dihedral : 4.306 82.731 9908 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.70 % Allowed : 19.51 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.09), residues: 9234 helix: 2.25 (0.13), residues: 1602 sheet: 0.55 (0.10), residues: 2844 loop : -0.95 (0.09), residues: 4788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 326 HIS 0.003 0.001 HIS G 230 PHE 0.007 0.001 PHE J 800 TYR 0.010 0.001 TYR A 256 ARG 0.008 0.000 ARG N 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 210 time to evaluate : 5.831 Fit side-chains REVERT: A 493 MET cc_start: 0.9217 (mmm) cc_final: 0.8777 (mmm) REVERT: B 483 MET cc_start: 0.8766 (mmm) cc_final: 0.8507 (mmt) REVERT: B 638 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: C 532 MET cc_start: 0.8825 (mmm) cc_final: 0.8544 (mmm) REVERT: D 181 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8503 (mtpt) REVERT: E 638 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: F 756 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8283 (t0) REVERT: G 285 MET cc_start: 0.9022 (mtp) cc_final: 0.8767 (mtp) REVERT: G 756 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8350 (t0) REVERT: H 181 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8334 (ttpt) REVERT: I 224 ARG cc_start: 0.8953 (mpp80) cc_final: 0.8672 (mtm180) REVERT: I 483 MET cc_start: 0.9060 (mmm) cc_final: 0.8691 (tpp) REVERT: I 532 MET cc_start: 0.9146 (mmt) cc_final: 0.8866 (mmm) REVERT: J 493 MET cc_start: 0.9216 (mmm) cc_final: 0.8775 (mmm) REVERT: K 483 MET cc_start: 0.8765 (mmm) cc_final: 0.8506 (mmt) REVERT: K 638 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: L 532 MET cc_start: 0.8828 (mmm) cc_final: 0.8546 (mmm) REVERT: M 181 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8505 (mtpt) REVERT: N 638 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: O 756 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8281 (t0) REVERT: P 285 MET cc_start: 0.9024 (mtp) cc_final: 0.8768 (mtp) REVERT: P 756 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8349 (t0) REVERT: Q 181 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8334 (ttpt) REVERT: R 224 ARG cc_start: 0.8950 (mpp80) cc_final: 0.8669 (mtm180) REVERT: R 483 MET cc_start: 0.9061 (mmm) cc_final: 0.8691 (tpp) REVERT: R 532 MET cc_start: 0.9146 (mmt) cc_final: 0.8866 (mmm) outliers start: 125 outliers final: 80 residues processed: 320 average time/residue: 1.4408 time to fit residues: 613.2365 Evaluate side-chains 302 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 210 time to evaluate : 5.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 638 PHE Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain D residue 181 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 638 PHE Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 713 GLN Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 768 VAL Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 696 LEU Chi-restraints excluded: chain G residue 756 ASP Chi-restraints excluded: chain G residue 768 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 330 SER Chi-restraints excluded: chain H residue 493 MET Chi-restraints excluded: chain H residue 651 VAL Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 497 MET Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 768 VAL Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 638 PHE Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain K residue 665 VAL Chi-restraints excluded: chain K residue 768 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain L residue 768 VAL Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 651 VAL Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 638 PHE Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain N residue 713 GLN Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain O residue 665 VAL Chi-restraints excluded: chain O residue 756 ASP Chi-restraints excluded: chain O residue 768 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 696 LEU Chi-restraints excluded: chain P residue 756 ASP Chi-restraints excluded: chain P residue 768 VAL Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 330 SER Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain Q residue 651 VAL Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 804 optimal weight: 9.9990 chunk 847 optimal weight: 5.9990 chunk 773 optimal weight: 0.9990 chunk 824 optimal weight: 1.9990 chunk 496 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 647 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 745 optimal weight: 0.5980 chunk 779 optimal weight: 5.9990 chunk 821 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 71046 Z= 0.145 Angle : 0.482 10.049 96660 Z= 0.253 Chirality : 0.044 0.158 10746 Planarity : 0.004 0.040 12672 Dihedral : 4.001 64.787 9908 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.26 % Allowed : 20.12 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 9234 helix: 2.52 (0.13), residues: 1602 sheet: 0.68 (0.10), residues: 2754 loop : -0.96 (0.09), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 496 HIS 0.003 0.001 HIS G 230 PHE 0.008 0.001 PHE J 208 TYR 0.010 0.001 TYR O 780 ARG 0.009 0.000 ARG E 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 218 time to evaluate : 5.946 Fit side-chains REVERT: A 158 MET cc_start: 0.7839 (tpt) cc_final: 0.7601 (mmm) REVERT: A 493 MET cc_start: 0.9210 (mmm) cc_final: 0.8632 (mmm) REVERT: C 532 MET cc_start: 0.8721 (mmm) cc_final: 0.8486 (mmm) REVERT: F 756 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8278 (t0) REVERT: G 285 MET cc_start: 0.8881 (mtp) cc_final: 0.8640 (mtp) REVERT: G 756 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8428 (t0) REVERT: H 160 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7502 (t0) REVERT: H 181 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8338 (ttpt) REVERT: I 224 ARG cc_start: 0.8950 (mpp80) cc_final: 0.8670 (mtm180) REVERT: I 483 MET cc_start: 0.9117 (mmm) cc_final: 0.8754 (tpp) REVERT: I 532 MET cc_start: 0.9120 (mmt) cc_final: 0.8851 (mmm) REVERT: J 493 MET cc_start: 0.9209 (mmm) cc_final: 0.8627 (mmm) REVERT: L 532 MET cc_start: 0.8722 (mmm) cc_final: 0.8490 (mmm) REVERT: O 756 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8277 (t0) REVERT: P 285 MET cc_start: 0.8883 (mtp) cc_final: 0.8642 (mtp) REVERT: P 756 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8429 (t0) REVERT: Q 160 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7503 (t0) REVERT: Q 181 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8341 (ttpt) REVERT: R 224 ARG cc_start: 0.8948 (mpp80) cc_final: 0.8667 (mtm180) REVERT: R 483 MET cc_start: 0.9117 (mmm) cc_final: 0.8754 (tpp) REVERT: R 532 MET cc_start: 0.9121 (mmt) cc_final: 0.8852 (mmm) outliers start: 93 outliers final: 54 residues processed: 305 average time/residue: 1.5263 time to fit residues: 613.7695 Evaluate side-chains 268 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 206 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 768 VAL Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 756 ASP Chi-restraints excluded: chain G residue 768 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 330 SER Chi-restraints excluded: chain H residue 651 VAL Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain K residue 768 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 710 ILE Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain O residue 756 ASP Chi-restraints excluded: chain O residue 768 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 756 ASP Chi-restraints excluded: chain P residue 768 VAL Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 330 SER Chi-restraints excluded: chain Q residue 651 VAL Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 541 optimal weight: 5.9990 chunk 871 optimal weight: 9.9990 chunk 532 optimal weight: 0.3980 chunk 413 optimal weight: 2.9990 chunk 606 optimal weight: 5.9990 chunk 914 optimal weight: 20.0000 chunk 841 optimal weight: 5.9990 chunk 728 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 562 optimal weight: 0.9980 chunk 446 optimal weight: 0.0670 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 482 GLN ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 71046 Z= 0.187 Angle : 0.492 10.714 96660 Z= 0.257 Chirality : 0.044 0.173 10746 Planarity : 0.004 0.040 12672 Dihedral : 3.969 58.532 9908 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.15 % Allowed : 20.33 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 9234 helix: 2.51 (0.13), residues: 1602 sheet: 0.70 (0.10), residues: 2754 loop : -0.94 (0.09), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 496 HIS 0.003 0.001 HIS P 516 PHE 0.007 0.001 PHE J 800 TYR 0.009 0.001 TYR E 256 ARG 0.009 0.000 ARG N 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18468 Ramachandran restraints generated. 9234 Oldfield, 0 Emsley, 9234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 5.861 Fit side-chains REVERT: A 158 MET cc_start: 0.7867 (tpt) cc_final: 0.7660 (mmm) REVERT: A 493 MET cc_start: 0.9214 (mmm) cc_final: 0.8632 (mmm) REVERT: B 756 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8140 (t0) REVERT: F 756 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8277 (t0) REVERT: G 285 MET cc_start: 0.8946 (mtp) cc_final: 0.8729 (mtp) REVERT: H 160 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7521 (t0) REVERT: H 181 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8409 (ttpt) REVERT: I 224 ARG cc_start: 0.8935 (mpp80) cc_final: 0.8657 (mtm180) REVERT: I 483 MET cc_start: 0.9128 (mmm) cc_final: 0.8807 (tpp) REVERT: I 532 MET cc_start: 0.9122 (mmt) cc_final: 0.8842 (mmm) REVERT: J 493 MET cc_start: 0.9216 (mmm) cc_final: 0.8655 (mmm) REVERT: K 483 MET cc_start: 0.8656 (mmm) cc_final: 0.8412 (mmt) REVERT: K 756 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8145 (t0) REVERT: M 181 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8486 (mtpt) REVERT: O 756 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8276 (t0) REVERT: P 285 MET cc_start: 0.8949 (mtp) cc_final: 0.8731 (mtp) REVERT: Q 160 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7523 (t0) REVERT: Q 181 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8429 (ttpt) REVERT: R 224 ARG cc_start: 0.8931 (mpp80) cc_final: 0.8652 (mtm180) REVERT: R 483 MET cc_start: 0.9128 (mmm) cc_final: 0.8807 (tpp) REVERT: R 532 MET cc_start: 0.9124 (mmt) cc_final: 0.8844 (mmm) outliers start: 85 outliers final: 57 residues processed: 287 average time/residue: 1.5061 time to fit residues: 571.0696 Evaluate side-chains 274 residues out of total 7362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 208 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 756 ASP Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 658 THR Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain D residue 658 THR Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 768 VAL Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 328 VAL Chi-restraints excluded: chain G residue 645 VAL Chi-restraints excluded: chain G residue 658 THR Chi-restraints excluded: chain G residue 768 VAL Chi-restraints excluded: chain H residue 160 ASP Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 330 SER Chi-restraints excluded: chain H residue 651 VAL Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 781 MET Chi-restraints excluded: chain I residue 645 VAL Chi-restraints excluded: chain I residue 658 THR Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 651 VAL Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 658 THR Chi-restraints excluded: chain K residue 756 ASP Chi-restraints excluded: chain K residue 768 VAL Chi-restraints excluded: chain L residue 186 ASP Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 710 ILE Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 658 THR Chi-restraints excluded: chain N residue 658 THR Chi-restraints excluded: chain O residue 173 LEU Chi-restraints excluded: chain O residue 628 ILE Chi-restraints excluded: chain O residue 658 THR Chi-restraints excluded: chain O residue 756 ASP Chi-restraints excluded: chain O residue 768 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain P residue 645 VAL Chi-restraints excluded: chain P residue 658 THR Chi-restraints excluded: chain P residue 768 VAL Chi-restraints excluded: chain Q residue 160 ASP Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 330 SER Chi-restraints excluded: chain Q residue 651 VAL Chi-restraints excluded: chain Q residue 658 THR Chi-restraints excluded: chain Q residue 781 MET Chi-restraints excluded: chain R residue 645 VAL Chi-restraints excluded: chain R residue 658 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 918 random chunks: chunk 578 optimal weight: 2.9990 chunk 775 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 671 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 729 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 749 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 134 optimal weight: 0.0970 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051173 restraints weight = 190834.700| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.87 r_work: 0.2748 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 71046 Z= 0.190 Angle : 0.493 11.175 96660 Z= 0.258 Chirality : 0.044 0.164 10746 Planarity : 0.004 0.040 12672 Dihedral : 3.957 50.225 9908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.15 % Allowed : 20.44 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 9234 helix: 2.52 (0.13), residues: 1602 sheet: 0.69 (0.10), residues: 2754 loop : -0.94 (0.09), residues: 4878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 496 HIS 0.003 0.001 HIS H 230 PHE 0.007 0.001 PHE Q 486 TYR 0.009 0.001 TYR A 256 ARG 0.007 0.000 ARG A 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12383.12 seconds wall clock time: 221 minutes 26.08 seconds (13286.08 seconds total)