Starting phenix.real_space_refine on Sat Sep 28 15:54:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k57_22676/09_2024/7k57_22676.cif" } resolution = 3.7 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= 0.010 sd= 0.102 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 372 5.16 5 C 44088 2.51 5 N 12360 2.21 5 O 13284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 70104 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5842 Classifications: {'peptide': 741} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 698} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 15.80, per 1000 atoms: 0.23 Number of scatterers: 70104 At special positions: 0 Unit cell: (178.538, 178.538, 218.903, 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 372 16.00 O 13284 8.00 N 12360 7.00 C 44088 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 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16728 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 72 sheets defined 42.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN A 692 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.214A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.554A pdb=" N ILE B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 751 through 762 removed outlier: 3.650A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 4.138A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.569A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.212A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.712A pdb=" N LEU C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE C 479 " --> pdb=" O TRP C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 660 Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 692 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS C 695 " --> pdb=" O CYS C 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG D 64 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU D 381 " --> pdb=" O ARG D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.606A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 660 Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN D 692 " --> pdb=" O THR D 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 751 through 762 removed outlier: 3.648A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.138A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE E 479 " --> pdb=" O TRP E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR E 549 " --> pdb=" O PRO E 545 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA E 566 " --> pdb=" O ILE E 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 660 Processing helix chain 'E' and resid 672 through 677 Processing helix chain 'E' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN E 692 " --> pdb=" O THR E 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.567A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE F 479 " --> pdb=" O TRP F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA F 566 " --> pdb=" O ILE F 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 660 Processing helix chain 'F' and resid 672 through 677 Processing helix chain 'F' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 196 Processing helix chain 'G' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE G 206 " --> pdb=" O TYR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE G 230 " --> pdb=" O HIS G 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 261 Processing helix chain 'G' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE G 274 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 312 through 316 Processing helix chain 'G' and resid 319 through 334 Processing helix chain 'G' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG G 358 " --> pdb=" O PRO G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 402 Processing helix chain 'G' and resid 407 through 425 Processing helix chain 'G' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE G 452 " --> pdb=" O THR G 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER G 459 " --> pdb=" O ALA G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE G 479 " --> pdb=" O TRP G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 494 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'G' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE G 506 " --> pdb=" O LYS G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA G 530 " --> pdb=" O LEU G 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE G 531 " --> pdb=" O LEU G 527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 532 " --> pdb=" O ALA G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR G 549 " --> pdb=" O PRO G 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET G 550 " --> pdb=" O GLU G 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP G 551 " --> pdb=" O LEU G 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY G 553 " --> pdb=" O THR G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA G 566 " --> pdb=" O ILE G 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA G 569 " --> pdb=" O LYS G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU G 607 " --> pdb=" O GLN G 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG G 635 " --> pdb=" O ALA G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 660 Processing helix chain 'G' and resid 672 through 677 Processing helix chain 'G' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE G 690 " --> pdb=" O ASP G 686 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS G 691 " --> pdb=" O LEU G 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN G 692 " --> pdb=" O THR G 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS G 695 " --> pdb=" O CYS G 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU G 701 " --> pdb=" O LEU G 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 706 " --> pdb=" O SER G 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 707 " --> pdb=" O ILE G 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 708 " --> pdb=" O GLU G 704 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG G 709 " --> pdb=" O SER G 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 710 " --> pdb=" O GLU G 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE G 736 " --> pdb=" O ARG G 732 " (cutoff:3.500A) Processing helix chain 'G' and resid 741 through 743 No H-bonds generated for 'chain 'G' and resid 741 through 743' Processing helix chain 'G' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR G 755 " --> pdb=" O ASP G 751 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 130 through 135 Processing helix chain 'H' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU H 140 " --> pdb=" O LYS H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE H 206 " --> pdb=" O TYR H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE H 230 " --> pdb=" O HIS H 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 261 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE H 274 " --> pdb=" O GLY H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 296 Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 312 through 316 Processing helix chain 'H' and resid 319 through 334 Processing helix chain 'H' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG H 358 " --> pdb=" O PRO H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU H 381 " --> pdb=" O ARG H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 402 Processing helix chain 'H' and resid 407 through 425 Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE H 452 " --> pdb=" O THR H 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER H 459 " --> pdb=" O ALA H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE H 479 " --> pdb=" O TRP H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 494 Processing helix chain 'H' and resid 494 through 499 Processing helix chain 'H' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE H 506 " --> pdb=" O LYS H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 524 through 535 removed outlier: 4.183A pdb=" N ALA H 530 " --> pdb=" O LEU H 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE H 531 " --> pdb=" O LEU H 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 532 " --> pdb=" O ALA H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR H 549 " --> pdb=" O PRO H 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET H 550 " --> pdb=" O GLU H 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP H 551 " --> pdb=" O LEU H 547 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY H 553 " --> pdb=" O THR H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA H 566 " --> pdb=" O ILE H 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA H 569 " --> pdb=" O LYS H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU H 607 " --> pdb=" O GLN H 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP H 609 " --> pdb=" O LEU H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG H 635 " --> pdb=" O ALA H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 660 Processing helix chain 'H' and resid 672 through 677 Processing helix chain 'H' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE H 690 " --> pdb=" O ASP H 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS H 691 " --> pdb=" O LEU H 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN H 692 " --> pdb=" O THR H 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS H 695 " --> pdb=" O CYS H 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU H 701 " --> pdb=" O LEU H 697 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU H 706 " --> pdb=" O SER H 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE H 707 " --> pdb=" O ILE H 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG H 708 " --> pdb=" O GLU H 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 709 " --> pdb=" O SER H 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU H 710 " --> pdb=" O GLU H 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE H 736 " --> pdb=" O ARG H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 741 through 743 No H-bonds generated for 'chain 'H' and resid 741 through 743' Processing helix chain 'H' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR H 755 " --> pdb=" O ASP H 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG I 64 " --> pdb=" O GLY I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 92 Processing helix chain 'I' and resid 130 through 135 Processing helix chain 'I' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU I 140 " --> pdb=" O LYS I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 196 Processing helix chain 'I' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE I 206 " --> pdb=" O TYR I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 226 removed outlier: 4.656A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE I 230 " --> pdb=" O HIS I 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 261 Processing helix chain 'I' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE I 274 " --> pdb=" O GLY I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 Processing helix chain 'I' and resid 306 through 309 Processing helix chain 'I' and resid 312 through 316 Processing helix chain 'I' and resid 319 through 334 Processing helix chain 'I' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG I 358 " --> pdb=" O PRO I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU I 381 " --> pdb=" O ARG I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 402 Processing helix chain 'I' and resid 407 through 425 Processing helix chain 'I' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE I 452 " --> pdb=" O THR I 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER I 459 " --> pdb=" O ALA I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE I 479 " --> pdb=" O TRP I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 494 Processing helix chain 'I' and resid 494 through 499 Processing helix chain 'I' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE I 506 " --> pdb=" O LYS I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA I 530 " --> pdb=" O LEU I 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE I 531 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA I 532 " --> pdb=" O ALA I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR I 549 " --> pdb=" O PRO I 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET I 550 " --> pdb=" O GLU I 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP I 551 " --> pdb=" O LEU I 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY I 553 " --> pdb=" O THR I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA I 566 " --> pdb=" O ILE I 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 569 " --> pdb=" O LYS I 565 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU I 607 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP I 609 " --> pdb=" O LEU I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 635 removed outlier: 3.664A pdb=" N ARG I 635 " --> pdb=" O ALA I 632 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 660 Processing helix chain 'I' and resid 672 through 677 Processing helix chain 'I' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS I 691 " --> pdb=" O LEU I 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN I 692 " --> pdb=" O THR I 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS I 695 " --> pdb=" O CYS I 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU I 701 " --> pdb=" O LEU I 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU I 706 " --> pdb=" O SER I 702 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 707 " --> pdb=" O ILE I 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG I 708 " --> pdb=" O GLU I 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG I 709 " --> pdb=" O SER I 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU I 710 " --> pdb=" O GLU I 706 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE I 736 " --> pdb=" O ARG I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 741 through 743 No H-bonds generated for 'chain 'I' and resid 741 through 743' Processing helix chain 'I' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR I 755 " --> pdb=" O ASP I 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.136A pdb=" N ARG J 64 " --> pdb=" O GLY J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 92 Processing helix chain 'J' and resid 130 through 135 Processing helix chain 'J' and resid 135 through 140 removed outlier: 4.449A pdb=" N LEU J 140 " --> pdb=" O LYS J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 196 Processing helix chain 'J' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE J 206 " --> pdb=" O TYR J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU J 222 " --> pdb=" O GLU J 218 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE J 230 " --> pdb=" O HIS J 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 261 Processing helix chain 'J' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE J 274 " --> pdb=" O GLY J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 312 through 316 Processing helix chain 'J' and resid 319 through 334 Processing helix chain 'J' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG J 358 " --> pdb=" O PRO J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU J 381 " --> pdb=" O ARG J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 402 Processing helix chain 'J' and resid 407 through 425 Processing helix chain 'J' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE J 452 " --> pdb=" O THR J 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER J 459 " --> pdb=" O ALA J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE J 479 " --> pdb=" O TRP J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 494 Processing helix chain 'J' and resid 494 through 499 Processing helix chain 'J' and resid 501 through 506 removed outlier: 3.914A pdb=" N PHE J 506 " --> pdb=" O LYS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 535 removed outlier: 4.181A pdb=" N ALA J 530 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE J 531 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA J 532 " --> pdb=" O ALA J 528 " (cutoff:3.500A) Processing helix chain 'J' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR J 549 " --> pdb=" O PRO J 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET J 550 " --> pdb=" O GLU J 546 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP J 551 " --> pdb=" O LEU J 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY J 553 " --> pdb=" O THR J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA J 566 " --> pdb=" O ILE J 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA J 569 " --> pdb=" O LYS J 565 " (cutoff:3.500A) Processing helix chain 'J' and resid 600 through 609 removed outlier: 3.581A pdb=" N GLU J 607 " --> pdb=" O GLN J 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP J 609 " --> pdb=" O LEU J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 635 removed outlier: 3.666A pdb=" N ARG J 635 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 660 Processing helix chain 'J' and resid 672 through 677 Processing helix chain 'J' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE J 690 " --> pdb=" O ASP J 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS J 691 " --> pdb=" O LEU J 687 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN J 692 " --> pdb=" O THR J 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS J 695 " --> pdb=" O CYS J 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU J 701 " --> pdb=" O LEU J 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU J 706 " --> pdb=" O SER J 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 707 " --> pdb=" O ILE J 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG J 708 " --> pdb=" O GLU J 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 709 " --> pdb=" O SER J 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU J 710 " --> pdb=" O GLU J 706 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 740 removed outlier: 4.232A pdb=" N PHE J 736 " --> pdb=" O ARG J 732 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 743 No H-bonds generated for 'chain 'J' and resid 741 through 743' Processing helix chain 'J' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR J 755 " --> pdb=" O ASP J 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG K 64 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 92 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 135 through 140 removed outlier: 4.451A pdb=" N LEU K 140 " --> pdb=" O LYS K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 196 Processing helix chain 'K' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE K 206 " --> pdb=" O TYR K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 226 removed outlier: 4.654A pdb=" N LEU K 222 " --> pdb=" O GLU K 218 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE K 230 " --> pdb=" O HIS K 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS K 231 " --> pdb=" O PRO K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 261 Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.553A pdb=" N ILE K 274 " --> pdb=" O GLY K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 296 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 312 through 316 Processing helix chain 'K' and resid 319 through 334 Processing helix chain 'K' and resid 354 through 358 removed outlier: 3.702A pdb=" N ARG K 358 " --> pdb=" O PRO K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU K 381 " --> pdb=" O ARG K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 402 Processing helix chain 'K' and resid 407 through 425 Processing helix chain 'K' and resid 448 through 459 removed outlier: 3.584A pdb=" N PHE K 452 " --> pdb=" O THR K 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER K 459 " --> pdb=" O ALA K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 479 removed outlier: 3.518A pdb=" N ILE K 479 " --> pdb=" O TRP K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 494 Processing helix chain 'K' and resid 494 through 499 Processing helix chain 'K' and resid 501 through 506 removed outlier: 3.913A pdb=" N PHE K 506 " --> pdb=" O LYS K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA K 530 " --> pdb=" O LEU K 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE K 531 " --> pdb=" O LEU K 527 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K 532 " --> pdb=" O ALA K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR K 549 " --> pdb=" O PRO K 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET K 550 " --> pdb=" O GLU K 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP K 551 " --> pdb=" O LEU K 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY K 553 " --> pdb=" O THR K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 569 removed outlier: 3.887A pdb=" N ALA K 566 " --> pdb=" O ILE K 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA K 569 " --> pdb=" O LYS K 565 " (cutoff:3.500A) Processing helix chain 'K' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU K 607 " --> pdb=" O GLN K 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP K 609 " --> pdb=" O LEU K 605 " (cutoff:3.500A) Processing helix chain 'K' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG K 635 " --> pdb=" O ALA K 632 " (cutoff:3.500A) Processing helix chain 'K' and resid 649 through 660 Processing helix chain 'K' and resid 672 through 677 Processing helix chain 'K' and resid 686 through 711 removed outlier: 3.653A pdb=" N ILE K 690 " --> pdb=" O ASP K 686 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS K 691 " --> pdb=" O LEU K 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN K 692 " --> pdb=" O THR K 688 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS K 695 " --> pdb=" O CYS K 691 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU K 701 " --> pdb=" O LEU K 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU K 706 " --> pdb=" O SER K 702 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE K 707 " --> pdb=" O ILE K 703 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG K 708 " --> pdb=" O GLU K 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 709 " --> pdb=" O SER K 705 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU K 710 " --> pdb=" O GLU K 706 " (cutoff:3.500A) Processing helix chain 'K' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE K 736 " --> pdb=" O ARG K 732 " (cutoff:3.500A) Processing helix chain 'K' and resid 741 through 743 No H-bonds generated for 'chain 'K' and resid 741 through 743' Processing helix chain 'K' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR K 755 " --> pdb=" O ASP K 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 4.137A pdb=" N ARG L 64 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 92 Processing helix chain 'L' and resid 130 through 135 Processing helix chain 'L' and resid 135 through 140 removed outlier: 4.450A pdb=" N LEU L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 196 Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.568A pdb=" N ILE L 206 " --> pdb=" O TYR L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 226 removed outlier: 4.655A pdb=" N LEU L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 226 through 234 removed outlier: 4.213A pdb=" N PHE L 230 " --> pdb=" O HIS L 226 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 261 Processing helix chain 'L' and resid 271 through 275 removed outlier: 3.552A pdb=" N ILE L 274 " --> pdb=" O GLY L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 Processing helix chain 'L' and resid 306 through 309 Processing helix chain 'L' and resid 312 through 316 Processing helix chain 'L' and resid 319 through 334 Processing helix chain 'L' and resid 354 through 358 removed outlier: 3.701A pdb=" N ARG L 358 " --> pdb=" O PRO L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 383 removed outlier: 3.711A pdb=" N LEU L 381 " --> pdb=" O ARG L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 402 Processing helix chain 'L' and resid 407 through 425 Processing helix chain 'L' and resid 448 through 459 removed outlier: 3.583A pdb=" N PHE L 452 " --> pdb=" O THR L 448 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER L 459 " --> pdb=" O ALA L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 479 removed outlier: 3.519A pdb=" N ILE L 479 " --> pdb=" O TRP L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 482 through 494 Processing helix chain 'L' and resid 494 through 499 Processing helix chain 'L' and resid 501 through 506 removed outlier: 3.912A pdb=" N PHE L 506 " --> pdb=" O LYS L 502 " (cutoff:3.500A) Processing helix chain 'L' and resid 524 through 535 removed outlier: 4.182A pdb=" N ALA L 530 " --> pdb=" O LEU L 526 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 531 " --> pdb=" O LEU L 527 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA L 532 " --> pdb=" O ALA L 528 " (cutoff:3.500A) Processing helix chain 'L' and resid 543 through 553 removed outlier: 3.605A pdb=" N THR L 549 " --> pdb=" O PRO L 545 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET L 550 " --> pdb=" O GLU L 546 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP L 551 " --> pdb=" O LEU L 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY L 553 " --> pdb=" O THR L 549 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 569 removed outlier: 3.888A pdb=" N ALA L 566 " --> pdb=" O ILE L 562 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA L 569 " --> pdb=" O LYS L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 600 through 609 removed outlier: 3.580A pdb=" N GLU L 607 " --> pdb=" O GLN L 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP L 609 " --> pdb=" O LEU L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 635 removed outlier: 3.665A pdb=" N ARG L 635 " --> pdb=" O ALA L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 649 through 660 Processing helix chain 'L' and resid 672 through 677 Processing helix chain 'L' and resid 686 through 711 removed outlier: 3.654A pdb=" N ILE L 690 " --> pdb=" O ASP L 686 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS L 691 " --> pdb=" O LEU L 687 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN L 692 " --> pdb=" O THR L 688 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS L 695 " --> pdb=" O CYS L 691 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU L 701 " --> pdb=" O LEU L 697 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU L 706 " --> pdb=" O SER L 702 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE L 707 " --> pdb=" O ILE L 703 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG L 708 " --> pdb=" O GLU L 704 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 709 " --> pdb=" O SER L 705 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU L 710 " --> pdb=" O GLU L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 740 removed outlier: 4.231A pdb=" N PHE L 736 " --> pdb=" O ARG L 732 " (cutoff:3.500A) Processing helix chain 'L' and resid 741 through 743 No H-bonds generated for 'chain 'L' and resid 741 through 743' Processing helix chain 'L' and resid 751 through 762 removed outlier: 3.649A pdb=" N TYR L 755 " --> pdb=" O ASP L 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 67 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE A 342 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA6, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.467A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE B 342 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 514 through 517 Processing sheet with id=AB3, first strand: chain 'B' and resid 573 through 575 removed outlier: 6.465A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB6, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 514 through 517 Processing sheet with id=AB9, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP D 74 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 67 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AC4, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE D 342 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 514 through 517 Processing sheet with id=AC6, first strand: chain 'D' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC9, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD1, first strand: chain 'E' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE E 342 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 514 through 517 Processing sheet with id=AD3, first strand: chain 'E' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP F 74 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD6, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AD7, first strand: chain 'F' and resid 266 through 269 removed outlier: 3.586A pdb=" N ILE F 342 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD9, first strand: chain 'F' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP G 74 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 67 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER G 101 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 145 through 147 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'G' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE G 342 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG G 365 " --> pdb=" O GLY G 240 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 514 through 517 Processing sheet with id=AE6, first strand: chain 'G' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU G 574 " --> pdb=" O ILE G 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP H 74 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 67 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER H 101 " --> pdb=" O LYS H 60 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 145 through 147 Processing sheet with id=AE9, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AF1, first strand: chain 'H' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE H 342 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 365 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 514 through 517 Processing sheet with id=AF3, first strand: chain 'H' and resid 573 through 575 removed outlier: 6.467A pdb=" N LEU H 574 " --> pdb=" O ILE H 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP I 74 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 67 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER I 101 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 145 through 147 Processing sheet with id=AF6, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AF7, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE I 342 " --> pdb=" O ALA I 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG I 365 " --> pdb=" O GLY I 240 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 514 through 517 Processing sheet with id=AF9, first strand: chain 'I' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU I 574 " --> pdb=" O ILE I 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'J' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP J 74 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA J 67 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 101 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 145 through 147 Processing sheet with id=AG3, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AG4, first strand: chain 'J' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE J 342 " --> pdb=" O ALA J 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG J 365 " --> pdb=" O GLY J 240 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 514 through 517 Processing sheet with id=AG6, first strand: chain 'J' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU J 574 " --> pdb=" O ILE J 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'K' and resid 38 through 42 removed outlier: 3.608A pdb=" N ASP K 74 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 67 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER K 101 " --> pdb=" O LYS K 60 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 145 through 147 Processing sheet with id=AG9, first strand: chain 'K' and resid 153 through 155 Processing sheet with id=AH1, first strand: chain 'K' and resid 266 through 269 removed outlier: 3.588A pdb=" N ILE K 342 " --> pdb=" O ALA K 299 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 365 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 514 through 517 Processing sheet with id=AH3, first strand: chain 'K' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU K 574 " --> pdb=" O ILE K 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 38 through 42 removed outlier: 3.607A pdb=" N ASP L 74 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 67 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER L 101 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 147 Processing sheet with id=AH6, first strand: chain 'L' and resid 153 through 155 Processing sheet with id=AH7, first strand: chain 'L' and resid 266 through 269 removed outlier: 3.587A pdb=" N ILE L 342 " --> pdb=" O ALA L 299 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 365 " --> pdb=" O GLY L 240 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 514 through 517 Processing sheet with id=AH9, first strand: chain 'L' and resid 573 through 575 removed outlier: 6.466A pdb=" N LEU L 574 " --> pdb=" O ILE L 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 2220 hydrogen bonds defined for protein. 6300 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: 26.27 Time building geometry restraints manager: 15.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23934 1.34 - 1.46: 11990 1.46 - 1.58: 34756 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 71280 Sorted by residual: bond pdb=" CB VAL B 600 " pdb=" CG2 VAL B 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL I 600 " pdb=" CG2 VAL I 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB VAL G 600 " pdb=" CG2 VAL G 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB VAL L 600 " pdb=" CG2 VAL L 600 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB VAL C 600 " pdb=" CG2 VAL C 600 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 ... (remaining 71275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 93398 2.54 - 5.08: 2261 5.08 - 7.62: 463 7.62 - 10.16: 82 10.16 - 12.70: 48 Bond angle restraints: 96252 Sorted by residual: angle pdb=" C LEU J 140 " pdb=" N GLU J 141 " pdb=" CA GLU J 141 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C LEU B 140 " pdb=" N GLU B 141 " pdb=" CA GLU B 141 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C LEU F 140 " pdb=" N GLU F 141 " pdb=" CA GLU F 141 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C LEU E 140 " pdb=" N GLU E 141 " pdb=" CA GLU E 141 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C LEU L 140 " pdb=" N GLU L 141 " pdb=" CA GLU L 141 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 96247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 38733 17.31 - 34.62: 4514 34.62 - 51.93: 865 51.93 - 69.24: 228 69.24 - 86.55: 108 Dihedral angle restraints: 44448 sinusoidal: 18720 harmonic: 25728 Sorted by residual: dihedral pdb=" CA PHE K 506 " pdb=" C PHE K 506 " pdb=" N GLY K 507 " pdb=" CA GLY K 507 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE J 506 " pdb=" C PHE J 506 " pdb=" N GLY J 507 " pdb=" CA GLY J 507 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PHE L 506 " pdb=" C PHE L 506 " pdb=" N GLY L 507 " pdb=" CA GLY L 507 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 44445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7365 0.054 - 0.107: 2613 0.107 - 0.161: 678 0.161 - 0.215: 107 0.215 - 0.269: 49 Chirality restraints: 10812 Sorted by residual: chirality pdb=" CA GLN A 50 " pdb=" N GLN A 50 " pdb=" C GLN A 50 " pdb=" CB GLN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLN G 50 " pdb=" N GLN G 50 " pdb=" C GLN G 50 " pdb=" CB GLN G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLN B 50 " pdb=" N GLN B 50 " pdb=" C GLN B 50 " pdb=" CB GLN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 10809 not shown) Planarity restraints: 12780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 552 " 0.022 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE B 552 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 552 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 552 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 552 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 552 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 552 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 552 " -0.022 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE F 552 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE F 552 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE F 552 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 552 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 552 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE F 552 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 552 " -0.022 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE I 552 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE I 552 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE I 552 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE I 552 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 552 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE I 552 " 0.001 2.00e-02 2.50e+03 ... (remaining 12777 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1315 2.67 - 3.22: 63528 3.22 - 3.78: 107010 3.78 - 4.34: 132074 4.34 - 4.90: 214713 Nonbonded interactions: 518640 Sorted by model distance: nonbonded pdb=" OG SER B 276 " pdb=" OG SER C 326 " model vdw 2.107 3.040 nonbonded pdb=" OG SER H 276 " pdb=" OG SER I 326 " model vdw 2.222 3.040 nonbonded pdb=" O GLU E 712 " pdb=" OG1 THR E 715 " model vdw 2.239 3.040 nonbonded pdb=" O GLU A 712 " pdb=" OG1 THR A 715 " model vdw 2.239 3.040 nonbonded pdb=" O GLU B 712 " pdb=" OG1 THR B 715 " model vdw 2.239 3.040 ... (remaining 518635 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.970 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 104.280 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.200 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 0.065 71280 Z= 0.473 Angle : 1.026 12.704 96252 Z= 0.538 Chirality : 0.060 0.269 10812 Planarity : 0.007 0.067 12780 Dihedral : 15.808 86.547 27720 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.94 % Allowed : 9.38 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -4.46 (0.07), residues: 8844 helix: -3.24 (0.06), residues: 3228 sheet: -2.98 (0.13), residues: 1140 loop : -2.68 (0.08), residues: 4476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP I 551 HIS 0.006 0.001 HIS J 317 PHE 0.055 0.003 PHE B 552 TYR 0.013 0.002 TYR B 244 ARG 0.012 0.001 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 672 time to evaluate : 6.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5985 (ttt) cc_final: 0.5658 (ppp) REVERT: A 582 ILE cc_start: 0.8937 (pt) cc_final: 0.8722 (mp) REVERT: B 464 LEU cc_start: 0.7117 (tp) cc_final: 0.6733 (tp) REVERT: B 611 MET cc_start: 0.8151 (ttp) cc_final: 0.7918 (tmm) REVERT: B 740 MET cc_start: 0.8802 (tpt) cc_final: 0.8573 (mmm) REVERT: B 757 MET cc_start: 0.7963 (tmm) cc_final: 0.7721 (tmm) REVERT: C 275 MET cc_start: 0.8291 (mmm) cc_final: 0.8055 (tpp) REVERT: C 449 MET cc_start: 0.7998 (tpt) cc_final: 0.7482 (tpt) REVERT: C 577 ASP cc_start: 0.8152 (t0) cc_final: 0.6337 (t0) REVERT: C 757 MET cc_start: 0.7649 (tmm) cc_final: 0.7339 (tmm) REVERT: D 307 ASP cc_start: 0.7901 (p0) cc_final: 0.7640 (p0) REVERT: D 582 ILE cc_start: 0.8984 (pt) cc_final: 0.8735 (tt) REVERT: D 678 MET cc_start: 0.8522 (tpp) cc_final: 0.8189 (tpp) REVERT: E 550 MET cc_start: 0.7565 (mtt) cc_final: 0.7226 (mtm) REVERT: E 740 MET cc_start: 0.9049 (tpt) cc_final: 0.8793 (mmm) REVERT: E 757 MET cc_start: 0.7921 (tmm) cc_final: 0.7658 (tmm) REVERT: F 449 MET cc_start: 0.8000 (tpt) cc_final: 0.7153 (tpt) REVERT: F 550 MET cc_start: 0.7667 (mtt) cc_final: 0.7405 (mtt) REVERT: F 757 MET cc_start: 0.7960 (tmm) cc_final: 0.7652 (tmm) REVERT: G 158 MET cc_start: 0.5750 (ttt) cc_final: 0.5493 (ppp) REVERT: G 757 MET cc_start: 0.7998 (tmm) cc_final: 0.7664 (tmm) REVERT: H 46 MET cc_start: 0.1500 (mmp) cc_final: 0.1216 (mmm) REVERT: H 550 MET cc_start: 0.7641 (mtt) cc_final: 0.7244 (mtt) REVERT: H 740 MET cc_start: 0.8986 (tpt) cc_final: 0.8706 (mmm) REVERT: I 427 MET cc_start: 0.8371 (ttm) cc_final: 0.8127 (tpp) REVERT: I 562 ILE cc_start: 0.9414 (pt) cc_final: 0.9172 (tp) REVERT: I 757 MET cc_start: 0.8029 (tmm) cc_final: 0.7723 (tmm) REVERT: J 158 MET cc_start: 0.5223 (ttt) cc_final: 0.4975 (ppp) REVERT: J 307 ASP cc_start: 0.7871 (p0) cc_final: 0.7641 (p0) REVERT: J 330 THR cc_start: 0.8631 (m) cc_final: 0.8412 (t) REVERT: J 442 MET cc_start: 0.8652 (mtm) cc_final: 0.8442 (mtt) REVERT: J 582 ILE cc_start: 0.8953 (pt) cc_final: 0.8656 (mp) REVERT: K 550 MET cc_start: 0.7642 (mtt) cc_final: 0.7432 (mtt) REVERT: L 46 MET cc_start: 0.0822 (mmp) cc_final: 0.0599 (mmp) REVERT: L 158 MET cc_start: 0.5697 (ttt) cc_final: 0.5432 (tmm) REVERT: L 449 MET cc_start: 0.7970 (tpt) cc_final: 0.7351 (tpt) REVERT: L 757 MET cc_start: 0.7898 (tmm) cc_final: 0.7598 (tmm) outliers start: 72 outliers final: 48 residues processed: 744 average time/residue: 0.6649 time to fit residues: 862.5684 Evaluate side-chains 496 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 448 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 746 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 746 SER Chi-restraints excluded: chain G residue 69 CYS Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 69 CYS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 746 SER Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 746 SER Chi-restraints excluded: chain J residue 69 CYS Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 746 SER Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 69 CYS Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 746 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 40.0000 chunk 673 optimal weight: 40.0000 chunk 373 optimal weight: 4.9990 chunk 229 optimal weight: 40.0000 chunk 454 optimal weight: 40.0000 chunk 359 optimal weight: 5.9990 chunk 696 optimal weight: 4.9990 chunk 269 optimal weight: 0.5980 chunk 423 optimal weight: 5.9990 chunk 518 optimal weight: 30.0000 chunk 806 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 91 ASN A 199 ASN A 285 ASN A 384 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 602 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 91 ASN B 199 ASN B 285 ASN B 384 HIS ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 602 ASN C 90 ASN C 91 ASN C 199 ASN C 285 ASN C 384 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN C 602 ASN ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN D 91 ASN D 199 ASN D 285 ASN D 384 HIS ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 602 ASN E 90 ASN E 91 ASN E 199 ASN E 285 ASN E 384 HIS ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN E 602 ASN F 90 ASN F 91 ASN F 199 ASN F 285 ASN F 384 HIS ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN F 602 ASN ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 91 ASN G 199 ASN G 285 ASN G 384 HIS ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 538 ASN G 602 ASN ** G 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN H 91 ASN H 115 HIS H 199 ASN H 285 ASN H 384 HIS ** H 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 ASN H 602 ASN I 90 ASN I 91 ASN I 199 ASN I 285 ASN I 384 HIS ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 538 ASN I 602 ASN ** I 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 91 ASN J 199 ASN J 285 ASN J 384 HIS ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 538 ASN J 602 ASN K 90 ASN K 91 ASN K 199 ASN K 285 ASN K 384 HIS ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 538 ASN K 602 ASN L 90 ASN L 91 ASN L 199 ASN L 285 ASN L 384 HIS ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 538 ASN L 602 ASN ** L 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 71280 Z= 0.398 Angle : 0.733 10.058 96252 Z= 0.370 Chirality : 0.047 0.156 10812 Planarity : 0.005 0.044 12780 Dihedral : 5.921 58.386 9739 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.51 % Allowed : 14.03 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.75 (0.08), residues: 8844 helix: -1.35 (0.09), residues: 3276 sheet: -2.63 (0.14), residues: 1140 loop : -1.91 (0.09), residues: 4428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 454 HIS 0.004 0.001 HIS E 499 PHE 0.028 0.002 PHE E 506 TYR 0.020 0.001 TYR L 244 ARG 0.006 0.001 ARG H 772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 468 time to evaluate : 6.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5845 (ttt) cc_final: 0.5550 (ppp) REVERT: A 582 ILE cc_start: 0.9115 (pt) cc_final: 0.8889 (mp) REVERT: A 757 MET cc_start: 0.7996 (tmm) cc_final: 0.7558 (tmm) REVERT: B 552 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8526 (t80) REVERT: B 757 MET cc_start: 0.7978 (tmm) cc_final: 0.7593 (tmm) REVERT: C 230 PHE cc_start: 0.7008 (m-80) cc_final: 0.6803 (m-80) REVERT: C 449 MET cc_start: 0.7973 (tpt) cc_final: 0.7307 (tpt) REVERT: C 577 ASP cc_start: 0.8249 (t0) cc_final: 0.8027 (t0) REVERT: C 757 MET cc_start: 0.7725 (tmm) cc_final: 0.7264 (tmm) REVERT: D 404 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7215 (t-90) REVERT: D 582 ILE cc_start: 0.9135 (pt) cc_final: 0.8859 (tt) REVERT: D 757 MET cc_start: 0.7833 (tmm) cc_final: 0.7388 (tmm) REVERT: E 550 MET cc_start: 0.7838 (mtt) cc_final: 0.7542 (mtt) REVERT: E 552 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8676 (t80) REVERT: E 582 ILE cc_start: 0.8827 (pt) cc_final: 0.8552 (tt) REVERT: E 757 MET cc_start: 0.7861 (tmm) cc_final: 0.7474 (tmm) REVERT: F 678 MET cc_start: 0.8268 (tpp) cc_final: 0.7786 (mpp) REVERT: F 757 MET cc_start: 0.8028 (tmm) cc_final: 0.7520 (tmm) REVERT: G 275 MET cc_start: 0.8260 (mmm) cc_final: 0.7962 (mmm) REVERT: G 757 MET cc_start: 0.8010 (tmm) cc_final: 0.7519 (tmm) REVERT: H 550 MET cc_start: 0.7771 (mtt) cc_final: 0.7252 (mtt) REVERT: H 552 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8564 (t80) REVERT: I 757 MET cc_start: 0.8080 (tmm) cc_final: 0.7556 (tmm) REVERT: J 158 MET cc_start: 0.5303 (ttt) cc_final: 0.4980 (ppp) REVERT: J 404 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: J 582 ILE cc_start: 0.9123 (pt) cc_final: 0.8899 (mp) REVERT: J 757 MET cc_start: 0.7747 (tmm) cc_final: 0.7379 (tmm) REVERT: K 552 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8666 (t80) REVERT: K 577 ASP cc_start: 0.8426 (t0) cc_final: 0.8212 (t0) REVERT: K 757 MET cc_start: 0.7967 (tmm) cc_final: 0.7669 (tmm) REVERT: L 46 MET cc_start: 0.0949 (mmp) cc_final: 0.0621 (mmm) REVERT: L 158 MET cc_start: 0.5397 (ttt) cc_final: 0.5154 (tmm) REVERT: L 449 MET cc_start: 0.7904 (tpt) cc_final: 0.7143 (tpt) REVERT: L 757 MET cc_start: 0.7986 (tmm) cc_final: 0.7454 (tmm) outliers start: 192 outliers final: 97 residues processed: 649 average time/residue: 0.5702 time to fit residues: 671.6968 Evaluate side-chains 514 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 411 time to evaluate : 6.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 552 PHE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 686 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 552 PHE Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 404 HIS Chi-restraints excluded: chain G residue 436 THR Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain G residue 686 ASP Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 404 HIS Chi-restraints excluded: chain H residue 436 THR Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 548 LEU Chi-restraints excluded: chain H residue 552 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 540 ILE Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 300 ILE Chi-restraints excluded: chain J residue 404 HIS Chi-restraints excluded: chain J residue 436 THR Chi-restraints excluded: chain J residue 540 ILE Chi-restraints excluded: chain J residue 552 PHE Chi-restraints excluded: chain J residue 686 ASP Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 404 HIS Chi-restraints excluded: chain K residue 436 THR Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 548 LEU Chi-restraints excluded: chain K residue 552 PHE Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 436 THR Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 540 ILE Chi-restraints excluded: chain L residue 582 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 30.0000 chunk 250 optimal weight: 0.6980 chunk 671 optimal weight: 10.0000 chunk 549 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 807 optimal weight: 0.0010 chunk 872 optimal weight: 2.9990 chunk 719 optimal weight: 0.9990 chunk 801 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 648 optimal weight: 2.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 ASN ** G 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 HIS H 460 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 71280 Z= 0.163 Angle : 0.596 8.497 96252 Z= 0.296 Chirality : 0.044 0.161 10812 Planarity : 0.004 0.044 12780 Dihedral : 5.206 55.912 9714 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.36 % Allowed : 15.30 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.10 (0.09), residues: 8844 helix: -0.68 (0.09), residues: 3276 sheet: -2.31 (0.14), residues: 1212 loop : -1.61 (0.09), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 454 HIS 0.021 0.000 HIS H 115 PHE 0.019 0.001 PHE E 363 TYR 0.028 0.001 TYR K 244 ARG 0.009 0.000 ARG B 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17688 Ramachandran restraints generated. 8844 Oldfield, 0 Emsley, 8844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 473 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5832 (ttt) cc_final: 0.5608 (ppp) REVERT: A 275 MET cc_start: 0.8191 (mmm) cc_final: 0.7886 (mmm) REVERT: A 404 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7446 (t-90) REVERT: A 757 MET cc_start: 0.7900 (tmm) cc_final: 0.7486 (tmm) REVERT: B 552 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 757 MET cc_start: 0.7955 (tmm) cc_final: 0.7569 (tmm) REVERT: C 158 MET cc_start: 0.5565 (ttt) cc_final: 0.4998 (tmm) REVERT: C 542 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8819 (pt) REVERT: C 757 MET cc_start: 0.7540 (tmm) cc_final: 0.6991 (tmm) REVERT: D 332 MET cc_start: 0.8624 (tpp) cc_final: 0.8303 (tpp) REVERT: D 404 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7304 (t-90) REVERT: D 582 ILE cc_start: 0.9122 (pt) cc_final: 0.8844 (tt) REVERT: D 678 MET cc_start: 0.8502 (tpp) cc_final: 0.8208 (tpp) REVERT: D 757 MET cc_start: 0.7889 (tmm) cc_final: 0.7384 (tmm) REVERT: E 84 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3509 (mmm) REVERT: E 550 MET cc_start: 0.7620 (mtt) cc_final: 0.7355 (mtt) REVERT: E 552 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8334 (t80) REVERT: E 582 ILE cc_start: 0.8782 (pt) cc_final: 0.8541 (tt) REVERT: E 757 MET cc_start: 0.7733 (tmm) cc_final: 0.7345 (tmm) REVERT: F 427 MET cc_start: 0.8195 (tpp) cc_final: 0.7858 (tpp) REVERT: F 542 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8845 (pt) REVERT: F 678 MET cc_start: 0.8297 (tpp) cc_final: 0.7857 (mpp) REVERT: F 757 MET cc_start: 0.7955 (tmm) cc_final: 0.7529 (tmm) REVERT: G 275 MET cc_start: 0.8274 (mmm) cc_final: 0.7974 (mmm) REVERT: G 404 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7405 (t-90) REVERT: G 678 MET cc_start: 0.8306 (tpp) cc_final: 0.8047 (mpp) REVERT: G 757 MET cc_start: 0.8001 (tmm) cc_final: 0.7726 (tmm) REVERT: H 550 MET cc_start: 0.7653 (mtt) cc_final: 0.7305 (mtt) REVERT: H 552 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8497 (t80) REVERT: H 740 MET cc_start: 0.8823 (mmm) cc_final: 0.8567 (mmm) REVERT: I 542 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8883 (pt) REVERT: I 757 MET cc_start: 0.7876 (tmm) cc_final: 0.7494 (tmm) REVERT: J 158 MET cc_start: 0.5217 (ttt) cc_final: 0.4962 (ppp) REVERT: J 275 MET cc_start: 0.8154 (mmm) cc_final: 0.7877 (mmm) REVERT: J 404 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7435 (t-90) REVERT: J 582 ILE cc_start: 0.9089 (pt) cc_final: 0.8861 (tt) REVERT: J 757 MET cc_start: 0.7794 (tmm) cc_final: 0.7160 (tmm) REVERT: J 761 THR cc_start: 0.7722 (m) cc_final: 0.6963 (m) REVERT: K 84 MET cc_start: 0.3690 (mtt) cc_final: 0.3384 (mmm) REVERT: K 552 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8443 (t80) REVERT: K 757 MET cc_start: 0.7915 (tmm) cc_final: 0.7549 (tmm) REVERT: L 542 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8869 (pt) REVERT: L 757 MET cc_start: 0.7865 (tmm) cc_final: 0.7438 (tmm) outliers start: 181 outliers final: 112 residues processed: 637 average time/residue: 0.5609 time to fit residues: 652.6233 Evaluate side-chains 540 residues out of total 7656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 415 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 552 PHE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 552 PHE Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 552 PHE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 540 ILE Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 548 LEU Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 244 TYR Chi-restraints excluded: chain G residue 404 HIS Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 468 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 548 LEU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 617 VAL Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 404 HIS Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 552 PHE Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 407 VAL Chi-restraints excluded: chain I residue 441 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 542 ILE Chi-restraints excluded: chain I residue 548 LEU Chi-restraints excluded: chain I residue 582 ILE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 244 TYR Chi-restraints excluded: chain J residue 404 HIS Chi-restraints excluded: chain J residue 441 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 552 PHE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 404 HIS Chi-restraints excluded: chain K residue 441 VAL Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 552 PHE Chi-restraints excluded: chain K residue 582 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 233 ILE Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 471 VAL Chi-restraints excluded: chain L residue 514 VAL Chi-restraints excluded: chain L residue 542 ILE Chi-restraints excluded: chain L residue 548 LEU Chi-restraints excluded: chain L residue 582 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6151 > 50: distance: 87 - 150: 36.929 distance: 90 - 147: 34.062 distance: 117 - 122: 33.324 distance: 122 - 123: 58.873 distance: 123 - 124: 38.200 distance: 123 - 126: 16.852 distance: 124 - 125: 8.262 distance: 124 - 128: 32.747 distance: 126 - 127: 36.928 distance: 128 - 129: 46.734 distance: 128 - 134: 40.530 distance: 129 - 130: 26.143 distance: 129 - 132: 41.744 distance: 130 - 131: 48.978 distance: 135 - 136: 17.673 distance: 136 - 137: 33.890 distance: 136 - 139: 46.569 distance: 137 - 138: 14.831 distance: 137 - 147: 25.199 distance: 139 - 140: 58.903 distance: 140 - 141: 23.274 distance: 140 - 142: 44.988 distance: 142 - 144: 19.399 distance: 144 - 145: 22.389 distance: 148 - 151: 38.243 distance: 149 - 150: 38.930 distance: 153 - 154: 39.270 distance: 154 - 155: 48.820 distance: 154 - 157: 40.457 distance: 155 - 156: 9.887 distance: 155 - 161: 40.883 distance: 157 - 158: 58.599 distance: 157 - 159: 39.998 distance: 161 - 162: 69.316 distance: 162 - 165: 41.005 distance: 163 - 164: 40.733 distance: 165 - 166: 56.676 distance: 165 - 167: 39.121 distance: 168 - 169: 39.854 distance: 170 - 171: 39.041 distance: 170 - 173: 39.939 distance: 173 - 179: 39.413 distance: 174 - 177: 38.675 distance: 175 - 176: 27.574 distance: 177 - 178: 41.983 distance: 178 - 179: 29.483 distance: 181 - 182: 41.855 distance: 181 - 184: 56.239 distance: 182 - 183: 42.048 distance: 182 - 188: 49.952 distance: 188 - 189: 39.981 distance: 189 - 190: 33.745 distance: 189 - 192: 24.136 distance: 190 - 195: 33.625 distance: 192 - 193: 6.749 distance: 192 - 194: 8.673