Starting phenix.real_space_refine on Fri Mar 6 22:42:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.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/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.map" model { file = "/net/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlg_24529/03_2026/7rlg_24529.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21858 2.51 5 N 6156 2.21 5 O 6642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.35, per 1000 atoms: 0.21 Number of scatterers: 34860 At special positions: 0 Unit cell: (174.96, 176.256, 101.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6642 8.00 N 6156 7.00 C 21858 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: 2.75 Conformation dependent library (CDL) restraints added in 1.6 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 47.9% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 5.162A 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 232 removed outlier: 4.117A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.749A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.030A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.803A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.544A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.581A pdb=" N LEU A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 431 removed outlier: 3.700A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.109A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.635A pdb=" N ALA A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.676A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.826A pdb=" N LYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.952A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.954A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.623A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.502A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.634A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.550A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.680A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.383A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.699A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 5.161A 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 232 removed outlier: 4.117A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.750A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 4.031A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.802A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.544A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.580A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 431 removed outlier: 3.702A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.109A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.634A pdb=" N ALA B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.676A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.826A pdb=" N LYS B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.954A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.956A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.623A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 removed outlier: 3.502A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.632A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.549A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.680A pdb=" N LEU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 4.383A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 764 removed outlier: 3.698A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 5.161A 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 232 removed outlier: 4.118A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.750A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.031A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.802A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.544A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.580A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.700A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 4.109A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.634A pdb=" N ALA C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.676A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.827A pdb=" N LYS C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.954A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.955A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.622A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 610 removed outlier: 3.501A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.633A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 656 " --> pdb=" O SER C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.549A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.679A pdb=" N LEU C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 4.383A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 764 removed outlier: 3.698A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 5.160A 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 232 removed outlier: 4.119A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.749A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 4.031A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.802A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.543A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.580A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.702A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 4.108A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 443' Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.634A pdb=" N ALA D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 493 removed outlier: 3.676A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.827A pdb=" N LYS D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.952A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.954A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.623A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 removed outlier: 3.502A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.633A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 656 " --> pdb=" O SER D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.550A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.679A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 4.383A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 764 removed outlier: 3.698A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 5.161A 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 232 removed outlier: 4.118A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.749A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 4.032A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.804A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.544A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 removed outlier: 3.580A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 3.701A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 4.109A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 438 through 443' Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.635A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 493 removed outlier: 3.677A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 493 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.827A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.954A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.954A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.622A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 610 removed outlier: 3.502A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.633A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.548A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.680A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 4.381A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 764 removed outlier: 3.698A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 5.161A 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 232 removed outlier: 4.118A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.749A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 4.032A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.586A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.803A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.544A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 removed outlier: 3.581A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 3.700A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 4.108A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 438 through 443' Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.634A pdb=" N ALA F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 493 removed outlier: 3.676A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 500 through 505 removed outlier: 3.826A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.954A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.954A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 Processing helix chain 'F' and resid 580 through 585 removed outlier: 3.623A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 610 removed outlier: 3.501A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.634A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.549A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.680A pdb=" N LEU F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 4.384A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 764 removed outlier: 3.697A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.434A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 83 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 40 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.607A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.826A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.435A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 83 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 40 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.606A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.826A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.435A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 83 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.608A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.825A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.435A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D 83 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 40 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.607A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.827A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 29 removed outlier: 7.434A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 83 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 116 through 117 removed outlier: 3.607A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.827A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.434A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER F 40 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 116 through 117 removed outlier: 3.607A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.641A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.826A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9371 1.33 - 1.45: 5282 1.45 - 1.57: 20483 1.57 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35460 Sorted by residual: bond pdb=" C LYS C 136 " pdb=" N PRO C 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.20e+01 bond pdb=" C LYS D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.20e+01 bond pdb=" C LYS F 136 " pdb=" N PRO F 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C LYS A 136 " pdb=" N PRO A 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C LYS B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 1.334 1.372 -0.039 8.40e-03 1.42e+04 2.12e+01 ... (remaining 35455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 47742 4.08 - 8.15: 184 8.15 - 12.23: 14 12.23 - 16.31: 0 16.31 - 20.39: 6 Bond angle restraints: 47946 Sorted by residual: angle pdb=" C VAL C 471 " pdb=" N PRO C 472 " pdb=" CA PRO C 472 " ideal model delta sigma weight residual 119.89 131.52 -11.63 1.02e+00 9.61e-01 1.30e+02 angle pdb=" C VAL A 471 " pdb=" N PRO A 472 " pdb=" CA PRO A 472 " ideal model delta sigma weight residual 119.89 130.33 -10.44 1.02e+00 9.61e-01 1.05e+02 angle pdb=" C VAL B 471 " pdb=" N PRO B 472 " pdb=" CA PRO B 472 " ideal model delta sigma weight residual 119.78 130.00 -10.22 1.03e+00 9.43e-01 9.85e+01 angle pdb=" C VAL E 471 " pdb=" N PRO E 472 " pdb=" CA PRO E 472 " ideal model delta sigma weight residual 119.78 129.97 -10.19 1.03e+00 9.43e-01 9.78e+01 angle pdb=" N VAL B 471 " pdb=" CA VAL B 471 " pdb=" C VAL B 471 " ideal model delta sigma weight residual 108.88 88.49 20.39 2.16e+00 2.14e-01 8.91e+01 ... (remaining 47941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19803 17.88 - 35.76: 1764 35.76 - 53.64: 287 53.64 - 71.52: 40 71.52 - 89.39: 30 Dihedral angle restraints: 21924 sinusoidal: 9240 harmonic: 12684 Sorted by residual: dihedral pdb=" C VAL D 471 " pdb=" N VAL D 471 " pdb=" CA VAL D 471 " pdb=" CB VAL D 471 " ideal model delta harmonic sigma weight residual -122.00 -108.47 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" C VAL A 471 " pdb=" N VAL A 471 " pdb=" CA VAL A 471 " pdb=" CB VAL A 471 " ideal model delta harmonic sigma weight residual -122.00 -108.51 -13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" C VAL E 471 " pdb=" N VAL E 471 " pdb=" CA VAL E 471 " pdb=" CB VAL E 471 " ideal model delta harmonic sigma weight residual -122.00 -108.88 -13.12 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 21921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4951 0.085 - 0.171: 419 0.171 - 0.256: 0 0.256 - 0.342: 0 0.342 - 0.427: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CA VAL A 471 " pdb=" N VAL A 471 " pdb=" C VAL A 471 " pdb=" CB VAL A 471 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA VAL D 471 " pdb=" N VAL D 471 " pdb=" C VAL D 471 " pdb=" CB VAL D 471 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA VAL E 471 " pdb=" N VAL E 471 " pdb=" C VAL E 471 " pdb=" CB VAL E 471 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 630 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 631 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 631 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 631 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 630 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 631 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 631 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 631 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 630 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO F 631 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 631 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 631 " -0.028 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8046 2.79 - 3.32: 32544 3.32 - 3.84: 56940 3.84 - 4.37: 66111 4.37 - 4.90: 111486 Nonbonded interactions: 275127 Sorted by model distance: nonbonded pdb=" OG SER E 748 " pdb=" OD1 ASN E 750 " model vdw 2.261 3.040 nonbonded pdb=" OG SER C 748 " pdb=" OD1 ASN C 750 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 748 " pdb=" OD1 ASN A 750 " model vdw 2.261 3.040 nonbonded pdb=" OG SER D 748 " pdb=" OD1 ASN D 750 " model vdw 2.262 3.040 nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.262 3.040 ... (remaining 275122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.810 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.003 0.052 35460 Z= 0.156 Angle : 0.734 20.387 47946 Z= 0.409 Chirality : 0.045 0.427 5376 Planarity : 0.004 0.051 6300 Dihedral : 13.671 89.394 13704 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.16 % Allowed : 0.27 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4386 helix: -0.20 (0.13), residues: 1566 sheet: -0.34 (0.20), residues: 666 loop : -1.59 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.016 0.001 TYR D 244 PHE 0.011 0.001 PHE F 52 TRP 0.006 0.001 TRP F 454 HIS 0.003 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00273 (35460) covalent geometry : angle 0.73363 (47946) hydrogen bonds : bond 0.25987 ( 1224) hydrogen bonds : angle 6.99531 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 309 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8582 (pt0) cc_final: 0.8082 (pp30) REVERT: A 52 PHE cc_start: 0.8221 (m-80) cc_final: 0.7993 (m-80) REVERT: A 332 MET cc_start: 0.9133 (tpt) cc_final: 0.8815 (tpp) REVERT: A 427 MET cc_start: 0.7224 (tpt) cc_final: 0.6472 (tpt) REVERT: A 504 LEU cc_start: 0.8840 (pt) cc_final: 0.7983 (tt) REVERT: B 50 GLN cc_start: 0.8330 (pt0) cc_final: 0.8099 (pp30) REVERT: B 193 ASP cc_start: 0.8906 (t0) cc_final: 0.8465 (p0) REVERT: B 332 MET cc_start: 0.9212 (tpt) cc_final: 0.8990 (tpt) REVERT: B 344 MET cc_start: 0.8884 (mtp) cc_final: 0.8668 (mtp) REVERT: B 427 MET cc_start: 0.7620 (tpt) cc_final: 0.7223 (tpt) REVERT: B 442 MET cc_start: 0.9171 (mmm) cc_final: 0.8937 (mpp) REVERT: B 504 LEU cc_start: 0.8852 (pt) cc_final: 0.8133 (tt) REVERT: C 50 GLN cc_start: 0.8529 (pt0) cc_final: 0.8191 (pp30) REVERT: C 52 PHE cc_start: 0.8359 (m-80) cc_final: 0.8129 (m-80) REVERT: C 79 ASP cc_start: 0.8469 (p0) cc_final: 0.8045 (t0) REVERT: C 193 ASP cc_start: 0.8966 (t0) cc_final: 0.8356 (p0) REVERT: C 275 MET cc_start: 0.8947 (mmm) cc_final: 0.8565 (mmp) REVERT: C 504 LEU cc_start: 0.8857 (pt) cc_final: 0.8287 (tt) REVERT: D 50 GLN cc_start: 0.8435 (pt0) cc_final: 0.8045 (pp30) REVERT: D 52 PHE cc_start: 0.8258 (m-80) cc_final: 0.7969 (m-80) REVERT: D 193 ASP cc_start: 0.8859 (t0) cc_final: 0.8381 (p0) REVERT: D 275 MET cc_start: 0.9103 (mmm) cc_final: 0.8829 (mmm) REVERT: D 427 MET cc_start: 0.7644 (tpt) cc_final: 0.7179 (tpt) REVERT: D 504 LEU cc_start: 0.8830 (pt) cc_final: 0.7996 (tt) REVERT: E 50 GLN cc_start: 0.8316 (pt0) cc_final: 0.8070 (pp30) REVERT: E 193 ASP cc_start: 0.8891 (t0) cc_final: 0.8329 (p0) REVERT: E 324 ILE cc_start: 0.8361 (mt) cc_final: 0.7984 (mm) REVERT: E 344 MET cc_start: 0.8905 (mtp) cc_final: 0.8641 (mtp) REVERT: E 427 MET cc_start: 0.7597 (tpt) cc_final: 0.7209 (tpt) REVERT: E 442 MET cc_start: 0.9311 (mmm) cc_final: 0.9019 (mpp) REVERT: E 504 LEU cc_start: 0.8876 (pt) cc_final: 0.8106 (tt) REVERT: F 50 GLN cc_start: 0.8481 (pt0) cc_final: 0.8244 (pp30) REVERT: F 64 ARG cc_start: 0.9174 (mmm160) cc_final: 0.8931 (mmm160) REVERT: F 79 ASP cc_start: 0.8523 (p0) cc_final: 0.8261 (t0) REVERT: F 193 ASP cc_start: 0.9028 (t0) cc_final: 0.8602 (p0) REVERT: F 219 MET cc_start: 0.8446 (ttm) cc_final: 0.8195 (ttp) REVERT: F 342 ILE cc_start: 0.8752 (mt) cc_final: 0.8530 (mt) REVERT: F 427 MET cc_start: 0.7839 (tpt) cc_final: 0.7384 (tpt) REVERT: F 442 MET cc_start: 0.9169 (mmm) cc_final: 0.8914 (mpp) REVERT: F 504 LEU cc_start: 0.8894 (pt) cc_final: 0.8222 (tt) outliers start: 6 outliers final: 0 residues processed: 315 average time/residue: 0.2098 time to fit residues: 106.6959 Evaluate side-chains 210 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.2980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 384 HIS D 602 ASN F 602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.086394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064364 restraints weight = 97373.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064391 restraints weight = 75821.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065066 restraints weight = 59255.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065608 restraints weight = 49490.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065728 restraints weight = 44754.117| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35460 Z= 0.156 Angle : 0.634 7.739 47946 Z= 0.304 Chirality : 0.045 0.208 5376 Planarity : 0.004 0.049 6300 Dihedral : 3.753 23.925 4920 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.53 % Allowed : 6.53 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4386 helix: -0.06 (0.12), residues: 1788 sheet: -0.36 (0.21), residues: 654 loop : -1.48 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 25 TYR 0.009 0.001 TYR D 173 PHE 0.008 0.001 PHE D 360 TRP 0.012 0.001 TRP B 454 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00361 (35460) covalent geometry : angle 0.63394 (47946) hydrogen bonds : bond 0.04324 ( 1224) hydrogen bonds : angle 4.98469 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8159 (pt) cc_final: 0.7622 (tt) REVERT: B 427 MET cc_start: 0.6546 (tpt) cc_final: 0.6320 (tpp) REVERT: B 504 LEU cc_start: 0.8317 (pt) cc_final: 0.7666 (tt) REVERT: C 427 MET cc_start: 0.6620 (tpt) cc_final: 0.6268 (tpt) REVERT: C 504 LEU cc_start: 0.8454 (pt) cc_final: 0.7858 (tp) REVERT: D 504 LEU cc_start: 0.8206 (pt) cc_final: 0.7701 (tt) REVERT: D 574 LEU cc_start: 0.9363 (tp) cc_final: 0.9159 (tp) REVERT: E 193 ASP cc_start: 0.8058 (t0) cc_final: 0.7853 (p0) REVERT: E 324 ILE cc_start: 0.9303 (mt) cc_final: 0.8962 (mm) REVERT: E 344 MET cc_start: 0.8849 (mtp) cc_final: 0.8622 (mtm) REVERT: E 504 LEU cc_start: 0.8372 (pt) cc_final: 0.7717 (tt) REVERT: F 112 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7434 (pttp) REVERT: F 504 LEU cc_start: 0.8455 (pt) cc_final: 0.7870 (tp) outliers start: 20 outliers final: 9 residues processed: 221 average time/residue: 0.2058 time to fit residues: 74.9734 Evaluate side-chains 195 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 358 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 378 optimal weight: 8.9990 chunk 312 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 314 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN B 226 HIS C 226 HIS C 384 HIS E 398 GLN F 226 HIS F 384 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062149 restraints weight = 97181.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.063035 restraints weight = 61544.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063555 restraints weight = 46663.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063857 restraints weight = 44862.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063935 restraints weight = 41442.460| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35460 Z= 0.129 Angle : 0.583 7.168 47946 Z= 0.274 Chirality : 0.044 0.160 5376 Planarity : 0.004 0.095 6300 Dihedral : 3.835 25.482 4920 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.96 % Allowed : 9.28 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4386 helix: 0.35 (0.13), residues: 1800 sheet: -0.28 (0.21), residues: 636 loop : -1.34 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 753 TYR 0.013 0.001 TYR D 110 PHE 0.008 0.001 PHE D 360 TRP 0.011 0.001 TRP E 454 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00299 (35460) covalent geometry : angle 0.58347 (47946) hydrogen bonds : bond 0.03000 ( 1224) hydrogen bonds : angle 4.40046 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.8753 (mmm) cc_final: 0.8417 (mmm) REVERT: A 504 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7731 (tt) REVERT: B 504 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7882 (tt) REVERT: C 427 MET cc_start: 0.6875 (tpt) cc_final: 0.6483 (tpt) REVERT: C 504 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.7995 (tp) REVERT: D 383 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (mm) REVERT: D 504 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7745 (tt) REVERT: E 324 ILE cc_start: 0.9378 (mt) cc_final: 0.9062 (mm) REVERT: E 427 MET cc_start: 0.6895 (tpp) cc_final: 0.6679 (tpp) REVERT: E 504 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7854 (tt) REVERT: F 504 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8127 (tt) outliers start: 36 outliers final: 17 residues processed: 218 average time/residue: 0.1881 time to fit residues: 69.5632 Evaluate side-chains 207 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 412 optimal weight: 0.0020 chunk 357 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 372 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053944 restraints weight = 98324.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.055048 restraints weight = 60409.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055870 restraints weight = 47627.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.056101 restraints weight = 46683.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.056182 restraints weight = 42145.021| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 35460 Z= 0.291 Angle : 0.724 10.147 47946 Z= 0.349 Chirality : 0.048 0.213 5376 Planarity : 0.005 0.047 6300 Dihedral : 5.223 43.564 4920 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.84 % Allowed : 11.28 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4386 helix: 0.20 (0.12), residues: 1842 sheet: -0.38 (0.21), residues: 660 loop : -1.39 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 89 TYR 0.017 0.002 TYR D 110 PHE 0.018 0.002 PHE B 360 TRP 0.019 0.002 TRP D 454 HIS 0.005 0.002 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00679 (35460) covalent geometry : angle 0.72424 (47946) hydrogen bonds : bond 0.03420 ( 1224) hydrogen bonds : angle 4.52864 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 1.357 Fit side-chains REVERT: A 158 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8860 (mtp) REVERT: A 193 ASP cc_start: 0.8362 (t0) cc_final: 0.8144 (t70) REVERT: A 442 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8710 (mmm) REVERT: A 608 MET cc_start: 0.8641 (ttm) cc_final: 0.8349 (mtp) REVERT: B 427 MET cc_start: 0.7472 (tpp) cc_final: 0.7243 (tpp) REVERT: B 608 MET cc_start: 0.8677 (ttm) cc_final: 0.8317 (ttm) REVERT: D 110 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6557 (t80) REVERT: E 324 ILE cc_start: 0.9483 (mt) cc_final: 0.9190 (mm) REVERT: E 427 MET cc_start: 0.7223 (tpp) cc_final: 0.7009 (tpp) REVERT: E 608 MET cc_start: 0.8611 (ttm) cc_final: 0.8189 (ttm) REVERT: F 112 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8096 (pttp) outliers start: 69 outliers final: 38 residues processed: 251 average time/residue: 0.1840 time to fit residues: 78.1933 Evaluate side-chains 222 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 228 optimal weight: 0.0470 chunk 216 optimal weight: 0.0570 chunk 33 optimal weight: 0.3980 chunk 414 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 356 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 90 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 36 ASN E 226 HIS F 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056942 restraints weight = 96614.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.058340 restraints weight = 59331.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059601 restraints weight = 44148.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059782 restraints weight = 41903.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059763 restraints weight = 37476.242| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35460 Z= 0.107 Angle : 0.588 10.060 47946 Z= 0.276 Chirality : 0.044 0.155 5376 Planarity : 0.004 0.044 6300 Dihedral : 4.693 34.123 4920 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.85 % Allowed : 13.41 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4386 helix: 0.66 (0.13), residues: 1794 sheet: -0.43 (0.20), residues: 642 loop : -1.14 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.011 0.001 TYR D 110 PHE 0.008 0.001 PHE A 139 TRP 0.009 0.001 TRP C 454 HIS 0.005 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00252 (35460) covalent geometry : angle 0.58779 (47946) hydrogen bonds : bond 0.02594 ( 1224) hydrogen bonds : angle 4.34151 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.283 Fit side-chains REVERT: A 193 ASP cc_start: 0.8233 (t0) cc_final: 0.8028 (t70) REVERT: A 504 LEU cc_start: 0.8642 (pt) cc_final: 0.7615 (tt) REVERT: A 608 MET cc_start: 0.8472 (ttm) cc_final: 0.8270 (ttm) REVERT: B 84 MET cc_start: 0.7850 (mtp) cc_final: 0.7508 (mtp) REVERT: B 189 ILE cc_start: 0.8439 (pt) cc_final: 0.8222 (pt) REVERT: B 504 LEU cc_start: 0.8668 (pt) cc_final: 0.7636 (tt) REVERT: B 608 MET cc_start: 0.8481 (ttm) cc_final: 0.8051 (ttm) REVERT: C 79 ASP cc_start: 0.7315 (t0) cc_final: 0.7032 (t0) REVERT: C 504 LEU cc_start: 0.8795 (pt) cc_final: 0.7828 (tt) REVERT: D 110 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6621 (t80) REVERT: D 449 MET cc_start: 0.8107 (tpp) cc_final: 0.7886 (tpp) REVERT: D 504 LEU cc_start: 0.8529 (pt) cc_final: 0.7526 (tt) REVERT: E 427 MET cc_start: 0.7117 (tpp) cc_final: 0.6914 (tpp) REVERT: E 504 LEU cc_start: 0.8629 (pt) cc_final: 0.7521 (tt) REVERT: E 608 MET cc_start: 0.8419 (ttm) cc_final: 0.7971 (ttm) REVERT: F 427 MET cc_start: 0.7250 (tpt) cc_final: 0.7036 (tpp) outliers start: 32 outliers final: 16 residues processed: 211 average time/residue: 0.1911 time to fit residues: 68.3775 Evaluate side-chains 194 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 232 optimal weight: 0.9980 chunk 396 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 311 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 432 optimal weight: 7.9990 chunk 329 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055811 restraints weight = 96633.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057758 restraints weight = 61552.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059010 restraints weight = 46659.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059698 restraints weight = 39426.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.060257 restraints weight = 35777.354| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35460 Z= 0.114 Angle : 0.586 10.447 47946 Z= 0.274 Chirality : 0.044 0.176 5376 Planarity : 0.004 0.044 6300 Dihedral : 4.552 32.871 4920 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.96 % Allowed : 14.00 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 4386 helix: 0.82 (0.13), residues: 1788 sheet: -0.35 (0.20), residues: 642 loop : -1.03 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 89 TYR 0.011 0.001 TYR D 110 PHE 0.007 0.001 PHE C 758 TRP 0.009 0.001 TRP D 454 HIS 0.005 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00272 (35460) covalent geometry : angle 0.58627 (47946) hydrogen bonds : bond 0.02470 ( 1224) hydrogen bonds : angle 4.24548 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.9101 (ttp) cc_final: 0.8691 (mtp) REVERT: A 442 MET cc_start: 0.8458 (mmm) cc_final: 0.8224 (mmm) REVERT: B 84 MET cc_start: 0.7897 (mtp) cc_final: 0.7585 (mtp) REVERT: B 189 ILE cc_start: 0.8486 (pt) cc_final: 0.8232 (pt) REVERT: B 504 LEU cc_start: 0.8729 (pt) cc_final: 0.7565 (tt) REVERT: B 608 MET cc_start: 0.8571 (ttm) cc_final: 0.8138 (ttm) REVERT: D 110 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6764 (t80) REVERT: E 504 LEU cc_start: 0.8778 (pt) cc_final: 0.7585 (tt) REVERT: E 550 MET cc_start: 0.8937 (mtm) cc_final: 0.8253 (ptp) REVERT: E 608 MET cc_start: 0.8507 (ttm) cc_final: 0.8050 (ttm) outliers start: 36 outliers final: 23 residues processed: 208 average time/residue: 0.1907 time to fit residues: 66.4406 Evaluate side-chains 201 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 191 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 341 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 434 optimal weight: 9.9990 chunk 423 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 410 optimal weight: 0.8980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 90 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053990 restraints weight = 97516.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.055142 restraints weight = 62166.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056330 restraints weight = 46147.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056546 restraints weight = 43191.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056564 restraints weight = 39228.768| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35460 Z= 0.211 Angle : 0.650 11.950 47946 Z= 0.307 Chirality : 0.045 0.207 5376 Planarity : 0.004 0.050 6300 Dihedral : 4.839 37.944 4920 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 1.52 % Allowed : 14.08 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4386 helix: 0.63 (0.13), residues: 1824 sheet: -0.15 (0.22), residues: 576 loop : -0.95 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 64 TYR 0.014 0.001 TYR D 110 PHE 0.012 0.001 PHE B 360 TRP 0.011 0.001 TRP E 454 HIS 0.004 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00497 (35460) covalent geometry : angle 0.65050 (47946) hydrogen bonds : bond 0.02755 ( 1224) hydrogen bonds : angle 4.34364 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 1.158 Fit side-chains REVERT: A 449 MET cc_start: 0.8201 (tpp) cc_final: 0.7990 (tpp) REVERT: A 504 LEU cc_start: 0.8715 (pt) cc_final: 0.7636 (tt) REVERT: B 84 MET cc_start: 0.8141 (mtp) cc_final: 0.7878 (mtp) REVERT: B 158 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8764 (ttm) REVERT: B 189 ILE cc_start: 0.8649 (pt) cc_final: 0.8443 (pt) REVERT: B 608 MET cc_start: 0.8627 (ttm) cc_final: 0.8175 (ttm) REVERT: D 110 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6910 (t80) REVERT: D 158 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8849 (mtp) REVERT: E 608 MET cc_start: 0.8524 (ttm) cc_final: 0.8043 (ttm) REVERT: F 64 ARG cc_start: 0.7533 (mmm160) cc_final: 0.7247 (tpm170) REVERT: F 427 MET cc_start: 0.7782 (tpt) cc_final: 0.7385 (tpp) outliers start: 57 outliers final: 31 residues processed: 222 average time/residue: 0.1863 time to fit residues: 70.0424 Evaluate side-chains 203 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 151 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054608 restraints weight = 96681.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056647 restraints weight = 59740.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057942 restraints weight = 44574.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058705 restraints weight = 37302.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059225 restraints weight = 33610.435| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35460 Z= 0.119 Angle : 0.609 11.741 47946 Z= 0.283 Chirality : 0.044 0.196 5376 Planarity : 0.004 0.050 6300 Dihedral : 4.673 33.471 4920 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.17 % Allowed : 14.77 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4386 helix: 0.85 (0.13), residues: 1788 sheet: -0.28 (0.20), residues: 648 loop : -0.83 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 64 TYR 0.011 0.001 TYR D 110 PHE 0.012 0.001 PHE A 758 TRP 0.009 0.001 TRP C 454 HIS 0.005 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00285 (35460) covalent geometry : angle 0.60924 (47946) hydrogen bonds : bond 0.02478 ( 1224) hydrogen bonds : angle 4.28760 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.228 Fit side-chains REVERT: A 168 THR cc_start: 0.3110 (OUTLIER) cc_final: 0.2810 (m) REVERT: B 84 MET cc_start: 0.7939 (mtp) cc_final: 0.7698 (mtp) REVERT: B 158 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8737 (ttm) REVERT: B 189 ILE cc_start: 0.8646 (pt) cc_final: 0.8431 (pt) REVERT: B 608 MET cc_start: 0.8576 (ttm) cc_final: 0.8113 (ttm) REVERT: C 427 MET cc_start: 0.7707 (tpp) cc_final: 0.7404 (tpp) REVERT: D 110 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7114 (t80) REVERT: D 158 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8724 (mtp) REVERT: D 168 THR cc_start: 0.3227 (OUTLIER) cc_final: 0.2999 (m) REVERT: D 442 MET cc_start: 0.8922 (mmm) cc_final: 0.8685 (mmm) REVERT: E 504 LEU cc_start: 0.8715 (pt) cc_final: 0.7531 (tt) REVERT: E 550 MET cc_start: 0.8957 (mtm) cc_final: 0.8730 (ptp) REVERT: E 608 MET cc_start: 0.8478 (ttm) cc_final: 0.8006 (ttm) REVERT: F 64 ARG cc_start: 0.7566 (mmm160) cc_final: 0.7292 (tpm170) REVERT: F 275 MET cc_start: 0.9072 (mmp) cc_final: 0.8783 (mmp) REVERT: F 427 MET cc_start: 0.7470 (tpt) cc_final: 0.7251 (tpp) REVERT: F 762 LEU cc_start: 0.7965 (mm) cc_final: 0.7746 (mm) outliers start: 44 outliers final: 30 residues processed: 207 average time/residue: 0.1825 time to fit residues: 65.3240 Evaluate side-chains 204 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 177 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 408 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 90 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051202 restraints weight = 98185.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.053054 restraints weight = 62733.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054234 restraints weight = 48041.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054967 restraints weight = 40774.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055357 restraints weight = 36954.424| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 35460 Z= 0.319 Angle : 0.746 11.141 47946 Z= 0.353 Chirality : 0.048 0.181 5376 Planarity : 0.005 0.047 6300 Dihedral : 5.239 44.689 4920 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.28 % Allowed : 15.09 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4386 helix: 0.48 (0.12), residues: 1812 sheet: -0.10 (0.22), residues: 552 loop : -0.80 (0.15), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 64 TYR 0.015 0.002 TYR C 110 PHE 0.017 0.002 PHE B 360 TRP 0.015 0.002 TRP A 454 HIS 0.005 0.002 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00739 (35460) covalent geometry : angle 0.74576 (47946) hydrogen bonds : bond 0.03134 ( 1224) hydrogen bonds : angle 4.54729 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.419 Fit side-chains REVERT: A 158 MET cc_start: 0.9074 (ttp) cc_final: 0.8851 (mtp) REVERT: A 168 THR cc_start: 0.3835 (OUTLIER) cc_final: 0.3567 (m) REVERT: B 158 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8778 (ttm) REVERT: C 275 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8859 (mmp) REVERT: D 110 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6641 (t80) REVERT: D 158 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8773 (mtp) REVERT: E 608 MET cc_start: 0.8605 (ttm) cc_final: 0.8217 (ttm) REVERT: F 757 MET cc_start: 0.8343 (ppp) cc_final: 0.8114 (ppp) REVERT: F 762 LEU cc_start: 0.8083 (mm) cc_final: 0.7866 (mm) outliers start: 48 outliers final: 33 residues processed: 198 average time/residue: 0.1870 time to fit residues: 63.4907 Evaluate side-chains 198 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 108 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 430 optimal weight: 9.9990 chunk 354 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053770 restraints weight = 97303.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055814 restraints weight = 59668.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057127 restraints weight = 44528.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057941 restraints weight = 37209.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058350 restraints weight = 33428.136| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 35460 Z= 0.123 Angle : 0.644 13.138 47946 Z= 0.298 Chirality : 0.045 0.204 5376 Planarity : 0.004 0.046 6300 Dihedral : 4.959 36.004 4920 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.96 % Allowed : 15.55 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4386 helix: 0.68 (0.13), residues: 1836 sheet: -0.35 (0.21), residues: 636 loop : -0.54 (0.16), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 64 TYR 0.011 0.001 TYR D 110 PHE 0.020 0.001 PHE D 52 TRP 0.010 0.001 TRP C 454 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00292 (35460) covalent geometry : angle 0.64413 (47946) hydrogen bonds : bond 0.02572 ( 1224) hydrogen bonds : angle 4.36193 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.242 Fit side-chains REVERT: A 158 MET cc_start: 0.8931 (ttp) cc_final: 0.8716 (mtp) REVERT: A 162 GLU cc_start: 0.8066 (pp20) cc_final: 0.7779 (pt0) REVERT: A 168 THR cc_start: 0.3770 (OUTLIER) cc_final: 0.3482 (m) REVERT: A 568 GLN cc_start: 0.8491 (pp30) cc_final: 0.7864 (tm-30) REVERT: B 84 MET cc_start: 0.8089 (mtp) cc_final: 0.7772 (mtp) REVERT: B 158 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8722 (ttm) REVERT: B 608 MET cc_start: 0.8497 (ttm) cc_final: 0.8014 (ttm) REVERT: D 110 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6486 (t80) REVERT: D 158 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8696 (mtp) REVERT: E 550 MET cc_start: 0.8952 (mtm) cc_final: 0.8627 (ptp) REVERT: E 608 MET cc_start: 0.8566 (ttm) cc_final: 0.8101 (ttm) REVERT: F 757 MET cc_start: 0.8408 (ppp) cc_final: 0.8206 (ppp) outliers start: 36 outliers final: 26 residues processed: 200 average time/residue: 0.1815 time to fit residues: 62.4025 Evaluate side-chains 194 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 21 optimal weight: 0.6980 chunk 378 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 218 optimal weight: 0.1980 chunk 328 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 0.6980 chunk 274 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054548 restraints weight = 96668.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056604 restraints weight = 59773.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057882 restraints weight = 44696.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058710 restraints weight = 37486.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059209 restraints weight = 33654.116| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35460 Z= 0.111 Angle : 0.621 12.642 47946 Z= 0.286 Chirality : 0.044 0.197 5376 Planarity : 0.004 0.080 6300 Dihedral : 4.681 33.994 4920 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.91 % Allowed : 15.57 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.13), residues: 4386 helix: 0.83 (0.13), residues: 1824 sheet: -0.18 (0.21), residues: 630 loop : -0.48 (0.16), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG D 64 TYR 0.011 0.001 TYR D 110 PHE 0.011 0.001 PHE C 758 TRP 0.011 0.001 TRP A 454 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00264 (35460) covalent geometry : angle 0.62090 (47946) hydrogen bonds : bond 0.02455 ( 1224) hydrogen bonds : angle 4.23600 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4077.78 seconds wall clock time: 71 minutes 56.95 seconds (4316.95 seconds total)