Starting phenix.real_space_refine on Tue Nov 21 19:02:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rld_24526/11_2023/7rld_24526_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 21852 2.51 5 N 6150 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 635": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 34854 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 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: 18.44, per 1000 atoms: 0.53 Number of scatterers: 34854 At special positions: 0 Unit cell: (173.262, 179.488, 101.675, 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 6648 8.00 N 6150 7.00 C 21852 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 - 3.50 Amino acid : False - 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: 13.46 Conformation dependent library (CDL) restraints added in 6.4 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... running ksdssp... Secondary structure from input PDB file: 180 helices and 36 sheets defined 38.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.09 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.575A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 49' Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.851A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 4.085A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.476A 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 227 through 232 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.647A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.609A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.643A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.621A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 402' Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.740A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.632A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.608A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.702A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.755A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.084A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.866A pdb=" N VAL A 559 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 561 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.185A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.565A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.889A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.659A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 706 removed outlier: 4.577A pdb=" N GLU A 689 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 690 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 704 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.653A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.070A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.574A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 49' Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.852A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 4.085A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 4.476A 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 227 through 232 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.648A pdb=" N MET B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.607A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.642A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.622A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 402' Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.740A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 458 removed outlier: 3.634A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.608A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.702A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.755A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 4.085A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.866A pdb=" N VAL B 559 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 561 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.186A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.566A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.888A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.657A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 706 removed outlier: 4.578A pdb=" N GLU B 689 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 690 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 704 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.653A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.072A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.574A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 49' Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.852A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 4.086A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 4.477A 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 227 through 232 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.647A pdb=" N MET C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.608A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.643A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 removed outlier: 3.621A pdb=" N ALA C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 402' Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.741A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 458 removed outlier: 3.633A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 490 removed outlier: 3.609A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.701A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.755A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 553 removed outlier: 4.085A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.865A pdb=" N VAL C 559 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 561 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.186A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 removed outlier: 3.564A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.888A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 662 " --> pdb=" O LYS C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.659A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 706 removed outlier: 4.578A pdb=" N GLU C 689 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 690 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 704 " --> pdb=" O GLU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.652A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 4.071A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 removed outlier: 3.574A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 49' Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.852A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 4.085A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.476A 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 227 through 232 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.648A pdb=" N MET D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 275' Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.609A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.642A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 removed outlier: 3.622A pdb=" N ALA D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 402' Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.741A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.633A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 490 removed outlier: 3.608A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.704A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.756A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 removed outlier: 4.085A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.865A pdb=" N VAL D 559 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 561 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.186A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 removed outlier: 3.565A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.888A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.658A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 706 removed outlier: 4.578A pdb=" N GLU D 689 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 690 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 704 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.653A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.071A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 removed outlier: 3.575A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 49' Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.852A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 4.085A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 4.477A 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 227 through 232 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 275 removed outlier: 3.648A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 271 through 275' Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.608A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.641A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 removed outlier: 3.622A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 402' Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.740A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.631A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 490 removed outlier: 3.608A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.702A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.755A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 553 removed outlier: 4.085A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.866A pdb=" N VAL E 559 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.185A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 610 removed outlier: 3.564A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.889A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.657A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 706 removed outlier: 4.577A pdb=" N GLU E 689 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 690 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 704 " --> pdb=" O GLU E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.653A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 763 removed outlier: 4.071A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.574A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 49' Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.850A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 4.086A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.476A 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 227 through 232 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 271 through 275 removed outlier: 3.647A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 271 through 275' Processing helix chain 'F' and resid 281 through 295 removed outlier: 3.608A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.642A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 removed outlier: 3.622A pdb=" N ALA F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 402' Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.740A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.632A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 490 removed outlier: 3.609A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.703A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.754A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 553 removed outlier: 4.085A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.866A pdb=" N VAL F 559 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 561 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.187A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 removed outlier: 3.565A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 662 removed outlier: 3.888A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.658A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 706 removed outlier: 4.578A pdb=" N GLU F 689 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 690 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 704 " --> pdb=" O GLU F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.654A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 763 removed outlier: 4.071A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.649A pdb=" N ILE A 82 " --> pdb=" O ASP A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 39 through 42 removed outlier: 3.527A pdb=" N LEU A 41 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 156 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.739A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.967A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= H, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.647A pdb=" N ILE B 82 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.526A pdb=" N LEU B 41 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.682A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 156 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.739A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.968A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= N, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.648A pdb=" N ILE C 82 " --> pdb=" O ASP C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 39 through 42 removed outlier: 3.527A pdb=" N LEU C 41 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 156 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.740A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.969A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= T, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.648A pdb=" N ILE D 82 " --> pdb=" O ASP D 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.527A pdb=" N LEU D 41 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 156 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.739A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.969A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= Z, first strand: chain 'E' and resid 28 through 30 removed outlier: 6.648A pdb=" N ILE E 82 " --> pdb=" O ASP E 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.526A pdb=" N LEU E 41 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY E 156 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.740A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.968A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= AF, first strand: chain 'F' and resid 28 through 30 removed outlier: 6.648A pdb=" N ILE F 82 " --> pdb=" O ASP F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.526A pdb=" N LEU F 41 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY F 156 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.740A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.969A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2142 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: 12.49 Time building geometry restraints manager: 14.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11877 1.34 - 1.46: 6598 1.46 - 1.58: 16655 1.58 - 1.70: 36 1.70 - 1.81: 288 Bond restraints: 35454 Sorted by residual: bond pdb=" C ARG C 635 " pdb=" N PRO C 636 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.75e+00 bond pdb=" C ARG F 635 " pdb=" N PRO F 636 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.75e+00 bond pdb=" C ARG D 635 " pdb=" N PRO D 636 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.59e+00 bond pdb=" C ARG E 635 " pdb=" N PRO E 636 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.12e-02 7.97e+03 2.33e+00 bond pdb=" C ARG B 635 " pdb=" N PRO B 636 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.12e-02 7.97e+03 2.29e+00 ... (remaining 35449 not shown) Histogram of bond angle deviations from ideal: 99.78 - 107.06: 1233 107.06 - 114.34: 20988 114.34 - 121.62: 17254 121.62 - 128.91: 8315 128.91 - 136.19: 150 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C MET E 508 " pdb=" N THR E 509 " pdb=" CA THR E 509 " ideal model delta sigma weight residual 120.68 126.30 -5.62 1.52e+00 4.33e-01 1.37e+01 angle pdb=" C MET C 508 " pdb=" N THR C 509 " pdb=" CA THR C 509 " ideal model delta sigma weight residual 120.68 126.28 -5.60 1.52e+00 4.33e-01 1.36e+01 angle pdb=" C MET F 508 " pdb=" N THR F 509 " pdb=" CA THR F 509 " ideal model delta sigma weight residual 120.68 126.28 -5.60 1.52e+00 4.33e-01 1.36e+01 angle pdb=" C MET D 508 " pdb=" N THR D 509 " pdb=" CA THR D 509 " ideal model delta sigma weight residual 120.68 126.27 -5.59 1.52e+00 4.33e-01 1.35e+01 angle pdb=" C MET B 508 " pdb=" N THR B 509 " pdb=" CA THR B 509 " ideal model delta sigma weight residual 120.68 126.25 -5.57 1.52e+00 4.33e-01 1.34e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 21065 27.34 - 54.69: 769 54.69 - 82.03: 48 82.03 - 109.37: 0 109.37 - 136.71: 36 Dihedral angle restraints: 21918 sinusoidal: 9234 harmonic: 12684 Sorted by residual: dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.72 -136.71 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP C1001 " pdb=" O5' ADP C1001 " pdb=" PA ADP C1001 " pdb=" O2A ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.71 -136.71 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.69 -136.68 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 21915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3391 0.035 - 0.070: 1414 0.070 - 0.105: 388 0.105 - 0.140: 177 0.140 - 0.175: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CG LEU E 135 " pdb=" CB LEU E 135 " pdb=" CD1 LEU E 135 " pdb=" CD2 LEU E 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CG LEU B 135 " pdb=" CB LEU B 135 " pdb=" CD1 LEU B 135 " pdb=" CD2 LEU B 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CG LEU F 135 " pdb=" CB LEU F 135 " pdb=" CD1 LEU F 135 " pdb=" CD2 LEU F 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO F 188 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 188 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO E 188 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 188 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO C 188 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " -0.031 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 32 2.33 - 2.98: 16596 2.98 - 3.62: 50077 3.62 - 4.26: 78064 4.26 - 4.90: 124151 Nonbonded interactions: 268920 Sorted by model distance: nonbonded pdb=" OD2 ASP F 368 " pdb=" NE2 GLN F 568 " model vdw 1.692 2.520 nonbonded pdb=" OD2 ASP A 368 " pdb=" NE2 GLN A 568 " model vdw 1.693 2.520 nonbonded pdb=" OD2 ASP E 368 " pdb=" NE2 GLN E 568 " model vdw 1.693 2.520 nonbonded pdb=" OD2 ASP D 368 " pdb=" NE2 GLN D 568 " model vdw 1.694 2.520 nonbonded pdb=" OD2 ASP C 368 " pdb=" NE2 GLN C 568 " model vdw 1.694 2.520 ... (remaining 268915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.620 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 90.200 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.002 0.044 35454 Z= 0.164 Angle : 0.664 10.366 47940 Z= 0.361 Chirality : 0.043 0.175 5376 Planarity : 0.003 0.056 6300 Dihedral : 14.568 136.715 13698 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4386 helix: -0.68 (0.13), residues: 1428 sheet: 0.79 (0.22), residues: 648 loop : -1.56 (0.13), residues: 2310 *********************** 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 190 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 4.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.4676 time to fit residues: 149.1566 Evaluate side-chains 140 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 0.0470 chunk 208 optimal weight: 0.7980 chunk 255 optimal weight: 0.6980 chunk 397 optimal weight: 6.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35454 Z= 0.175 Angle : 0.573 6.882 47940 Z= 0.267 Chirality : 0.043 0.132 5376 Planarity : 0.004 0.048 6300 Dihedral : 10.711 134.575 4920 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.04 % Favored : 95.83 % Rotamer: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4386 helix: -0.57 (0.13), residues: 1476 sheet: 0.69 (0.22), residues: 648 loop : -1.59 (0.13), residues: 2262 *********************** 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 160 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 3.714 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 159 average time/residue: 0.4337 time to fit residues: 120.3582 Evaluate side-chains 137 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 3.939 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3438 time to fit residues: 6.8651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 398 optimal weight: 0.8980 chunk 430 optimal weight: 10.0000 chunk 354 optimal weight: 0.7980 chunk 395 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 319 optimal weight: 0.0980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 494 GLN C 494 GLN D 494 GLN E 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35454 Z= 0.196 Angle : 0.564 7.999 47940 Z= 0.261 Chirality : 0.043 0.143 5376 Planarity : 0.004 0.062 6300 Dihedral : 9.985 130.299 4920 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 0.51 % Allowed : 6.59 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4386 helix: -0.47 (0.13), residues: 1572 sheet: 0.63 (0.22), residues: 654 loop : -1.31 (0.14), residues: 2160 *********************** 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 165 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 4.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 162 average time/residue: 0.4425 time to fit residues: 125.0713 Evaluate side-chains 141 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 4.299 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3518 time to fit residues: 11.5378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 190 optimal weight: 0.0470 chunk 267 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 423 optimal weight: 0.1980 chunk 208 optimal weight: 0.7980 chunk 379 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 35454 Z= 0.143 Angle : 0.530 8.042 47940 Z= 0.239 Chirality : 0.042 0.143 5376 Planarity : 0.004 0.050 6300 Dihedral : 9.596 128.195 4920 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 0.40 % Allowed : 7.65 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4386 helix: -0.32 (0.13), residues: 1602 sheet: 0.68 (0.22), residues: 642 loop : -1.19 (0.14), residues: 2142 *********************** 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 160 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 3.970 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 157 average time/residue: 0.4626 time to fit residues: 125.6885 Evaluate side-chains 142 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 4.194 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3425 time to fit residues: 11.9443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 361 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 216 optimal weight: 0.0980 chunk 380 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35454 Z= 0.364 Angle : 0.705 10.144 47940 Z= 0.333 Chirality : 0.047 0.154 5376 Planarity : 0.005 0.045 6300 Dihedral : 10.197 135.407 4920 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 0.72 % Allowed : 9.55 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4386 helix: -0.71 (0.12), residues: 1686 sheet: 0.50 (0.22), residues: 660 loop : -1.06 (0.15), residues: 2040 *********************** 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 189 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 4.108 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 186 average time/residue: 0.4761 time to fit residues: 148.9617 Evaluate side-chains 160 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 4.533 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3361 time to fit residues: 17.2588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 423 optimal weight: 0.9990 chunk 351 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35454 Z= 0.176 Angle : 0.566 8.584 47940 Z= 0.258 Chirality : 0.043 0.165 5376 Planarity : 0.004 0.044 6300 Dihedral : 9.717 137.600 4920 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 0.72 % Allowed : 10.40 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4386 helix: -0.39 (0.13), residues: 1698 sheet: 0.48 (0.21), residues: 642 loop : -0.93 (0.15), residues: 2046 *********************** 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 188 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 4.213 Fit side-chains outliers start: 27 outliers final: 8 residues processed: 183 average time/residue: 0.4454 time to fit residues: 139.8960 Evaluate side-chains 152 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 3.988 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3164 time to fit residues: 9.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 241 optimal weight: 0.0980 chunk 309 optimal weight: 1.9990 chunk 239 optimal weight: 0.0070 chunk 356 optimal weight: 0.5980 chunk 236 optimal weight: 9.9990 chunk 422 optimal weight: 7.9990 chunk 264 optimal weight: 0.0370 chunk 257 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35454 Z= 0.150 Angle : 0.560 11.616 47940 Z= 0.254 Chirality : 0.042 0.157 5376 Planarity : 0.004 0.042 6300 Dihedral : 9.091 140.268 4920 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.40 % Allowed : 11.41 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4386 helix: -0.15 (0.13), residues: 1716 sheet: 0.61 (0.21), residues: 642 loop : -1.01 (0.14), residues: 2028 *********************** 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 163 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 161 average time/residue: 0.4608 time to fit residues: 127.1702 Evaluate side-chains 146 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 3.723 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4355 time to fit residues: 7.5698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 252 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 268 optimal weight: 0.6980 chunk 287 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35454 Z= 0.236 Angle : 0.600 14.188 47940 Z= 0.273 Chirality : 0.043 0.167 5376 Planarity : 0.004 0.043 6300 Dihedral : 9.024 143.246 4920 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.21 % Allowed : 11.97 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 4386 helix: -0.04 (0.13), residues: 1716 sheet: 0.71 (0.21), residues: 642 loop : -0.80 (0.15), residues: 2028 *********************** 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 157 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 4.580 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 154 average time/residue: 0.4936 time to fit residues: 128.0594 Evaluate side-chains 145 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3175 time to fit residues: 6.7462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 1.9990 chunk 404 optimal weight: 0.9990 chunk 368 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 308 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 355 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 392 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35454 Z= 0.189 Angle : 0.573 11.995 47940 Z= 0.259 Chirality : 0.043 0.165 5376 Planarity : 0.004 0.043 6300 Dihedral : 8.699 141.453 4920 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.29 % Allowed : 12.11 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4386 helix: 0.03 (0.13), residues: 1758 sheet: 0.75 (0.21), residues: 642 loop : -0.85 (0.15), residues: 1986 *********************** 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 158 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 4.228 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 158 average time/residue: 0.4701 time to fit residues: 126.8160 Evaluate side-chains 147 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.857 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3059 time to fit residues: 5.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 6.9990 chunk 415 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 289 optimal weight: 6.9990 chunk 436 optimal weight: 3.9990 chunk 401 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35454 Z= 0.193 Angle : 0.578 11.750 47940 Z= 0.261 Chirality : 0.043 0.164 5376 Planarity : 0.004 0.046 6300 Dihedral : 8.498 140.048 4920 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 12.29 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4386 helix: 0.10 (0.13), residues: 1758 sheet: 0.83 (0.21), residues: 642 loop : -0.83 (0.15), residues: 1986 ********************** 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 151 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 3.959 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.4779 time to fit residues: 123.5561 Evaluate side-chains 143 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3449 time to fit residues: 6.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 320 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 384 HIS E 494 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.081039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054832 restraints weight = 107806.303| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.48 r_work: 0.2720 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 35454 Z= 0.411 Angle : 0.714 12.255 47940 Z= 0.335 Chirality : 0.046 0.178 5376 Planarity : 0.004 0.045 6300 Dihedral : 9.403 151.946 4920 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.21 % Allowed : 12.29 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4386 helix: -0.20 (0.13), residues: 1770 sheet: 0.58 (0.20), residues: 672 loop : -0.80 (0.15), residues: 1944 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5467.83 seconds wall clock time: 102 minutes 45.46 seconds (6165.46 seconds total)