Starting phenix.real_space_refine on Sun Aug 11 08:19:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/08_2024/7ykr_33895.cif" } resolution = 3.2 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= 0.006 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 236 5.16 5 C 20384 2.51 5 N 5544 2.21 5 O 5760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 527": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 974": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1055": "NH1" <-> "NH2" Residue "A ARG 1064": "NH1" <-> "NH2" Residue "A ARG 1120": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "D ARG 974": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1055": "NH1" <-> "NH2" Residue "D ARG 1064": "NH1" <-> "NH2" Residue "D ARG 1120": "NH1" <-> "NH2" Residue "D ARG 1122": "NH1" <-> "NH2" Residue "D ARG 1130": "NH1" <-> "NH2" Residue "D ARG 1140": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B ARG 974": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1055": "NH1" <-> "NH2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1140": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 527": "NH1" <-> "NH2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C ARG 1055": "NH1" <-> "NH2" Residue "C ARG 1064": "NH1" <-> "NH2" Residue "C ARG 1120": "NH1" <-> "NH2" Residue "C ARG 1122": "NH1" <-> "NH2" Residue "C ARG 1130": "NH1" <-> "NH2" Residue "C ARG 1140": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7981 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 998} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 162 Chain: "D" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7981 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 998} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7981 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 998} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 7981 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 36, 'TRANS': 998} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 162 Time building chain proxies: 18.10, per 1000 atoms: 0.57 Number of scatterers: 31924 At special positions: 0 Unit cell: (154.53, 154.53, 149.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 236 16.00 O 5760 8.00 N 5544 7.00 C 20384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS D 217 " - pdb=" SG CYS D 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 253 " distance=2.03 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: 13.02 Conformation dependent library (CDL) restraints added in 5.9 seconds 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7904 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 4 sheets defined 61.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.379A pdb=" N GLU A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.605A pdb=" N ARG A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.651A pdb=" N LEU A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.544A pdb=" N LYS A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.397A pdb=" N LEU A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET A 338 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL A 353 " --> pdb=" O HIS A 349 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 3.684A pdb=" N LEU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA A 431 " --> pdb=" O GLN A 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 432 " --> pdb=" O THR A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 432' Processing helix chain 'A' and resid 446 through 454 removed outlier: 3.616A pdb=" N ASP A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU A 551 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE A 561 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 573 " --> pdb=" O HIS A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.555A pdb=" N LEU A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE A 595 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU A 639 " --> pdb=" O ARG A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 659 through 668 removed outlier: 3.771A pdb=" N PHE A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR A 722 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS A 739 " --> pdb=" O PRO A 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR A 770 " --> pdb=" O PHE A 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 840 " --> pdb=" O VAL A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.727A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 853 " --> pdb=" O GLN A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 877 removed outlier: 4.117A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.624A pdb=" N TRP A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 913 removed outlier: 4.124A pdb=" N GLN A 911 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 913 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 937 removed outlier: 3.512A pdb=" N LEU A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 932 " --> pdb=" O GLN A 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA A 947 " --> pdb=" O ALA A 943 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 953 " --> pdb=" O TYR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 966 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR A 989 " --> pdb=" O PHE A 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 990 " --> pdb=" O VAL A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE A1005 " --> pdb=" O PRO A1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A1031 " --> pdb=" O ALA A1027 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1033 " --> pdb=" O GLY A1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A1034 " --> pdb=" O ASP A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 removed outlier: 3.539A pdb=" N LYS A1041 " --> pdb=" O ASN A1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A1045 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1046 " --> pdb=" O ARG A1042 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1052 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP A1061 " --> pdb=" O PRO A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU A1119 " --> pdb=" O ALA A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1129 removed outlier: 3.791A pdb=" N ASP A1127 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP A1154 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A1155 " --> pdb=" O ALA A1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1151 through 1155' Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.618A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.604A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR D 141 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 165 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.651A pdb=" N LEU D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.875A pdb=" N VAL D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS D 316 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 319 " --> pdb=" O VAL D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.397A pdb=" N LEU D 328 " --> pdb=" O MET D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET D 338 " --> pdb=" O VAL D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE D 347 " --> pdb=" O CYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL D 353 " --> pdb=" O HIS D 349 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 355 " --> pdb=" O ASP D 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 3.692A pdb=" N PHE D 409 " --> pdb=" O ASN D 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA D 431 " --> pdb=" O GLN D 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 432 " --> pdb=" O THR D 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 428 through 432' Processing helix chain 'D' and resid 446 through 454 removed outlier: 3.615A pdb=" N ASP D 454 " --> pdb=" O TYR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 463 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 487 Processing helix chain 'D' and resid 489 through 498 removed outlier: 3.680A pdb=" N ASP D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 525 through 535 Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU D 551 " --> pdb=" O ASN D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE D 561 " --> pdb=" O TYR D 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 562 " --> pdb=" O THR D 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 566 " --> pdb=" O GLU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU D 572 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP D 573 " --> pdb=" O HIS D 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 569 through 573' Processing helix chain 'D' and resid 581 through 589 removed outlier: 3.555A pdb=" N LEU D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE D 595 " --> pdb=" O PRO D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR D 617 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 629 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU D 639 " --> pdb=" O ARG D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 Processing helix chain 'D' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR D 722 " --> pdb=" O PRO D 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS D 739 " --> pdb=" O PRO D 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 744 " --> pdb=" O TYR D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU D 754 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN D 756 " --> pdb=" O PHE D 752 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE D 759 " --> pdb=" O ALA D 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 762 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 763 " --> pdb=" O ILE D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 777 removed outlier: 3.847A pdb=" N TYR D 770 " --> pdb=" O PHE D 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL D 833 " --> pdb=" O LEU D 829 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 840 " --> pdb=" O VAL D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 853 removed outlier: 3.726A pdb=" N GLN D 852 " --> pdb=" O ILE D 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 853 " --> pdb=" O GLN D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 877 removed outlier: 4.116A pdb=" N LEU D 864 " --> pdb=" O GLU D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 881 Processing helix chain 'D' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 913 removed outlier: 4.124A pdb=" N GLN D 911 " --> pdb=" O LEU D 908 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG D 912 " --> pdb=" O PHE D 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE D 913 " --> pdb=" O LEU D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 937 removed outlier: 3.512A pdb=" N LEU D 930 " --> pdb=" O ILE D 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 932 " --> pdb=" O GLN D 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA D 947 " --> pdb=" O ALA D 943 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 951 " --> pdb=" O ALA D 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER D 953 " --> pdb=" O TYR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 966 Processing helix chain 'D' and resid 969 through 977 Processing helix chain 'D' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR D 989 " --> pdb=" O PHE D 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE D1005 " --> pdb=" O PRO D1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D1006 " --> pdb=" O MET D1002 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY D1029 " --> pdb=" O GLY D1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE D1031 " --> pdb=" O ALA D1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D1033 " --> pdb=" O GLY D1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL D1034 " --> pdb=" O ASP D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1037 through 1057 removed outlier: 3.539A pdb=" N LYS D1041 " --> pdb=" O ASN D1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D1046 " --> pdb=" O ARG D1042 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D1052 " --> pdb=" O VAL D1048 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D1056 " --> pdb=" O GLU D1052 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP D1061 " --> pdb=" O PRO D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1082 through 1089 Processing helix chain 'D' and resid 1116 through 1121 removed outlier: 3.713A pdb=" N GLU D1119 " --> pdb=" O ALA D1116 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP D1127 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D1128 " --> pdb=" O LYS D1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D1129 " --> pdb=" O LEU D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1143 removed outlier: 3.768A pdb=" N HIS D1137 " --> pdb=" O GLU D1133 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP D1154 " --> pdb=" O GLU D1151 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D1155 " --> pdb=" O ALA D1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1151 through 1155' Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.618A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.604A pdb=" N ARG B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 164 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.652A pdb=" N LEU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.871A pdb=" N THR B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 removed outlier: 4.398A pdb=" N LEU B 328 " --> pdb=" O MET B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET B 338 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.603A pdb=" N ALA B 344 " --> pdb=" O PRO B 340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL B 353 " --> pdb=" O HIS B 349 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.005A pdb=" N ALA B 431 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 432 " --> pdb=" O THR B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 432' Processing helix chain 'B' and resid 446 through 454 removed outlier: 3.617A pdb=" N ASP B 454 " --> pdb=" O TYR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.563A pdb=" N GLU B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 525 through 535 Processing helix chain 'B' and resid 547 through 555 removed outlier: 3.635A pdb=" N LEU B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE B 561 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.855A pdb=" N LEU B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 573 " --> pdb=" O HIS B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 573' Processing helix chain 'B' and resid 581 through 589 removed outlier: 3.554A pdb=" N LEU B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE B 595 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU B 639 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 Processing helix chain 'B' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR B 722 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 723 " --> pdb=" O ALA B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS B 739 " --> pdb=" O PRO B 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 744 " --> pdb=" O TYR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 763 " --> pdb=" O ILE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.727A pdb=" N GLN B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 853 " --> pdb=" O GLN B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 877 removed outlier: 4.117A pdb=" N LEU B 864 " --> pdb=" O GLU B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 881 Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 913 removed outlier: 4.125A pdb=" N GLN B 911 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 912 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 913 " --> pdb=" O LEU B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.556A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 937 removed outlier: 3.511A pdb=" N LEU B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 953 removed outlier: 3.516A pdb=" N ALA B 947 " --> pdb=" O ALA B 943 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 951 " --> pdb=" O ALA B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 953 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 966 Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 984 through 990 removed outlier: 3.530A pdb=" N TYR B 989 " --> pdb=" O PHE B 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 3.513A pdb=" N PHE B1005 " --> pdb=" O PRO B1001 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B1006 " --> pdb=" O MET B1002 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B1031 " --> pdb=" O ALA B1027 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B1033 " --> pdb=" O GLY B1029 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B1034 " --> pdb=" O ASP B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1057 removed outlier: 3.538A pdb=" N LYS B1041 " --> pdb=" O ASN B1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B1045 " --> pdb=" O LYS B1041 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B1046 " --> pdb=" O ARG B1042 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B1052 " --> pdb=" O VAL B1048 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B1056 " --> pdb=" O GLU B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1062 removed outlier: 3.585A pdb=" N TRP B1061 " --> pdb=" O PRO B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1089 Processing helix chain 'B' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU B1119 " --> pdb=" O ALA B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP B1127 " --> pdb=" O ARG B1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B1128 " --> pdb=" O LYS B1124 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B1129 " --> pdb=" O LEU B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS B1137 " --> pdb=" O GLU B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1155 removed outlier: 4.190A pdb=" N ASP B1154 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B1155 " --> pdb=" O ALA B1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1151 through 1155' Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.617A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 83 Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.605A pdb=" N ARG C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 125 through 133 removed outlier: 3.725A pdb=" N SER C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 145 removed outlier: 3.820A pdb=" N ASP C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 removed outlier: 3.687A pdb=" N ALA C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.650A pdb=" N LEU C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 173 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.673A pdb=" N TYR C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.872A pdb=" N THR C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 239 through 246 removed outlier: 3.876A pdb=" N VAL C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.570A pdb=" N GLU C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.545A pdb=" N LYS C 316 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 317 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 319 " --> pdb=" O VAL C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 329 removed outlier: 4.398A pdb=" N LEU C 328 " --> pdb=" O MET C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.259A pdb=" N MET C 338 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.602A pdb=" N ALA C 344 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 removed outlier: 3.560A pdb=" N VAL C 353 " --> pdb=" O HIS C 349 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 removed outlier: 3.509A pdb=" N ARG C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 removed outlier: 3.683A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 3.691A pdb=" N PHE C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 428 through 432 removed outlier: 4.004A pdb=" N ALA C 431 " --> pdb=" O GLN C 428 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 432 " --> pdb=" O THR C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 428 through 432' Processing helix chain 'C' and resid 446 through 454 removed outlier: 3.615A pdb=" N ASP C 454 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.564A pdb=" N GLU C 461 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 Processing helix chain 'C' and resid 489 through 498 removed outlier: 3.681A pdb=" N ASP C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.634A pdb=" N LEU C 551 " --> pdb=" O ASN C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.639A pdb=" N ILE C 561 " --> pdb=" O TYR C 557 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.854A pdb=" N LEU C 572 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 573 " --> pdb=" O HIS C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 569 through 573' Processing helix chain 'C' and resid 581 through 589 removed outlier: 3.554A pdb=" N LEU C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.540A pdb=" N ILE C 595 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 621 removed outlier: 3.749A pdb=" N TYR C 617 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 629 Processing helix chain 'C' and resid 636 through 640 removed outlier: 3.940A pdb=" N GLU C 639 " --> pdb=" O ARG C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 Processing helix chain 'C' and resid 659 through 668 removed outlier: 3.770A pdb=" N PHE C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 727 removed outlier: 3.674A pdb=" N THR C 722 " --> pdb=" O PRO C 718 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET C 723 " --> pdb=" O ALA C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 748 removed outlier: 3.621A pdb=" N LYS C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 744 " --> pdb=" O TYR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 764 removed outlier: 4.104A pdb=" N LEU C 754 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN C 756 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 763 " --> pdb=" O ILE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 777 removed outlier: 3.846A pdb=" N TYR C 770 " --> pdb=" O PHE C 766 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 842 removed outlier: 3.505A pdb=" N VAL C 833 " --> pdb=" O LEU C 829 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 840 " --> pdb=" O VAL C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.726A pdb=" N GLN C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 853 " --> pdb=" O GLN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 877 removed outlier: 4.116A pdb=" N LEU C 864 " --> pdb=" O GLU C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 881 Processing helix chain 'C' and resid 888 through 905 removed outlier: 3.623A pdb=" N TRP C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 913 removed outlier: 4.125A pdb=" N GLN C 911 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 912 " --> pdb=" O PHE C 909 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 913 " --> pdb=" O LEU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 922 removed outlier: 3.557A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 937 removed outlier: 3.511A pdb=" N LEU C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 953 removed outlier: 3.517A pdb=" N ALA C 947 " --> pdb=" O ALA C 943 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 951 " --> pdb=" O ALA C 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 953 " --> pdb=" O TYR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 966 Processing helix chain 'C' and resid 969 through 977 Processing helix chain 'C' and resid 984 through 990 removed outlier: 3.529A pdb=" N TYR C 989 " --> pdb=" O PHE C 985 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1015 removed outlier: 3.514A pdb=" N PHE C1005 " --> pdb=" O PRO C1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C1006 " --> pdb=" O MET C1002 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 removed outlier: 3.783A pdb=" N GLY C1029 " --> pdb=" O GLY C1025 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C1033 " --> pdb=" O GLY C1029 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL C1034 " --> pdb=" O ASP C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1057 removed outlier: 3.538A pdb=" N LYS C1041 " --> pdb=" O ASN C1037 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C1046 " --> pdb=" O ARG C1042 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C1052 " --> pdb=" O VAL C1048 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C1056 " --> pdb=" O GLU C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1062 removed outlier: 3.586A pdb=" N TRP C1061 " --> pdb=" O PRO C1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1089 Processing helix chain 'C' and resid 1116 through 1121 removed outlier: 3.712A pdb=" N GLU C1119 " --> pdb=" O ALA C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1129 removed outlier: 3.790A pdb=" N ASP C1127 " --> pdb=" O ARG C1123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1128 " --> pdb=" O LYS C1124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C1129 " --> pdb=" O LEU C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1131 through 1143 removed outlier: 3.767A pdb=" N HIS C1137 " --> pdb=" O GLU C1133 " (cutoff:3.500A) Processing helix chain 'C' and resid 1151 through 1155 removed outlier: 4.191A pdb=" N ASP C1154 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1155 " --> pdb=" O ALA C1152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1151 through 1155' Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 672 Processing sheet with id=AA2, first strand: chain 'D' and resid 671 through 672 Processing sheet with id=AA3, first strand: chain 'B' and resid 671 through 672 Processing sheet with id=AA4, first strand: chain 'C' and resid 671 through 672 1140 hydrogen bonds defined for protein. 3276 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: 10.67 Time building geometry restraints manager: 14.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7403 1.33 - 1.45: 6661 1.45 - 1.57: 18088 1.57 - 1.70: 0 1.70 - 1.82: 388 Bond restraints: 32540 Sorted by residual: bond pdb=" CA LYS D 368 " pdb=" C LYS D 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.06e+01 bond pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.05e+01 bond pdb=" CA LYS B 368 " pdb=" C LYS B 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" CA LYS C 368 " pdb=" C LYS C 368 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.03e+01 bond pdb=" N GLN C 336 " pdb=" CA GLN C 336 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.05e+01 ... (remaining 32535 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.63: 655 105.63 - 112.75: 17151 112.75 - 119.87: 12049 119.87 - 126.99: 13876 126.99 - 134.11: 377 Bond angle restraints: 44108 Sorted by residual: angle pdb=" N LEU B 855 " pdb=" CA LEU B 855 " pdb=" C LEU B 855 " ideal model delta sigma weight residual 109.62 121.48 -11.86 1.50e+00 4.44e-01 6.25e+01 angle pdb=" N LEU D 855 " pdb=" CA LEU D 855 " pdb=" C LEU D 855 " ideal model delta sigma weight residual 109.62 121.46 -11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" N LEU C 855 " pdb=" CA LEU C 855 " pdb=" C LEU C 855 " ideal model delta sigma weight residual 109.62 121.45 -11.83 1.50e+00 4.44e-01 6.22e+01 angle pdb=" N LEU A 855 " pdb=" CA LEU A 855 " pdb=" C LEU A 855 " ideal model delta sigma weight residual 109.62 121.42 -11.80 1.50e+00 4.44e-01 6.19e+01 angle pdb=" N LYS D 854 " pdb=" CA LYS D 854 " pdb=" C LYS D 854 " ideal model delta sigma weight residual 111.11 119.31 -8.20 1.20e+00 6.94e-01 4.67e+01 ... (remaining 44103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 18492 15.20 - 30.40: 920 30.40 - 45.60: 252 45.60 - 60.80: 29 60.80 - 75.99: 31 Dihedral angle restraints: 19724 sinusoidal: 7560 harmonic: 12164 Sorted by residual: dihedral pdb=" CA ALA C 431 " pdb=" C ALA C 431 " pdb=" N GLN C 432 " pdb=" CA GLN C 432 " ideal model delta harmonic sigma weight residual 180.00 146.22 33.78 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA ALA B 431 " pdb=" C ALA B 431 " pdb=" N GLN B 432 " pdb=" CA GLN B 432 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA ALA A 431 " pdb=" C ALA A 431 " pdb=" N GLN A 432 " pdb=" CA GLN A 432 " ideal model delta harmonic sigma weight residual 180.00 146.27 33.73 0 5.00e+00 4.00e-02 4.55e+01 ... (remaining 19721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4717 0.100 - 0.199: 379 0.199 - 0.299: 32 0.299 - 0.399: 12 0.399 - 0.498: 4 Chirality restraints: 5144 Sorted by residual: chirality pdb=" CA LEU D 855 " pdb=" N LEU D 855 " pdb=" C LEU D 855 " pdb=" CB LEU D 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA LEU B 855 " pdb=" N LEU B 855 " pdb=" C LEU B 855 " pdb=" CB LEU B 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA LEU A 855 " pdb=" N LEU A 855 " pdb=" C LEU A 855 " pdb=" CB LEU A 855 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.16e+00 ... (remaining 5141 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 367 " 0.020 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ASP B 367 " -0.073 2.00e-02 2.50e+03 pdb=" O ASP B 367 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS B 368 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 367 " 0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ASP C 367 " -0.073 2.00e-02 2.50e+03 pdb=" O ASP C 367 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS C 368 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 367 " -0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ASP A 367 " 0.073 2.00e-02 2.50e+03 pdb=" O ASP A 367 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS A 368 " -0.024 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5231 2.75 - 3.29: 29389 3.29 - 3.83: 49245 3.83 - 4.36: 62940 4.36 - 4.90: 105076 Nonbonded interactions: 251881 Sorted by model distance: nonbonded pdb=" O ASP C 298 " pdb=" OD1 ASP C 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP D 298 " pdb=" OD1 ASP D 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP A 298 " pdb=" OD1 ASP A 298 " model vdw 2.215 3.040 nonbonded pdb=" O ASP B 298 " pdb=" OD1 ASP B 298 " model vdw 2.216 3.040 nonbonded pdb=" O ASP A 140 " pdb=" OH TYR A 178 " model vdw 2.326 3.040 ... (remaining 251876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.870 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: 1.450 Check model and map are aligned: 0.280 Set scattering table: 0.330 Process input model: 86.450 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1962 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 : 0.008 0.107 32540 Z= 0.547 Angle : 1.017 14.778 44108 Z= 0.555 Chirality : 0.063 0.498 5144 Planarity : 0.007 0.066 5616 Dihedral : 10.921 75.995 11808 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.83 % Allowed : 2.83 % Favored : 96.33 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -6.34 (0.08), residues: 4108 helix: -4.56 (0.04), residues: 2520 sheet: -0.73 (0.63), residues: 60 loop : -3.36 (0.12), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B1061 HIS 0.009 0.002 HIS C 482 PHE 0.024 0.003 PHE B 689 TYR 0.029 0.003 TYR B 857 ARG 0.006 0.001 ARG B 974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 643 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.1680 (mtt) cc_final: 0.1329 (mtm) REVERT: A 388 LEU cc_start: 0.0745 (tp) cc_final: 0.0185 (tt) REVERT: A 568 HIS cc_start: 0.4186 (m90) cc_final: 0.3569 (m90) REVERT: A 648 HIS cc_start: 0.4221 (m90) cc_final: 0.3050 (m90) REVERT: A 889 THR cc_start: 0.3885 (m) cc_final: 0.3362 (p) REVERT: A 913 PHE cc_start: 0.4738 (m-10) cc_final: 0.4504 (m-10) REVERT: A 985 PHE cc_start: 0.4742 (t80) cc_final: 0.4142 (t80) REVERT: D 244 PHE cc_start: 0.4780 (m-80) cc_final: 0.4459 (m-80) REVERT: D 245 PHE cc_start: 0.3997 (m-10) cc_final: 0.3661 (m-10) REVERT: D 978 MET cc_start: -0.3443 (ptt) cc_final: -0.4128 (ttt) REVERT: D 991 ASN cc_start: 0.2106 (m-40) cc_final: 0.1582 (m-40) REVERT: D 1040 LEU cc_start: 0.3353 (tp) cc_final: 0.2316 (mp) REVERT: D 1119 GLU cc_start: 0.5597 (mp0) cc_final: 0.5177 (tt0) REVERT: B 854 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5472 (ttmt) REVERT: B 870 TYR cc_start: 0.5631 (m-10) cc_final: 0.3380 (m-10) REVERT: B 1131 MET cc_start: 0.6781 (mmt) cc_final: 0.6335 (mtm) REVERT: C 172 LEU cc_start: 0.6465 (mt) cc_final: 0.6244 (mt) outliers start: 28 outliers final: 5 residues processed: 666 average time/residue: 0.4424 time to fit residues: 461.2193 Evaluate side-chains 431 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain D residue 1000 VAL Chi-restraints excluded: chain B residue 678 LYS Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1000 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 0.9990 chunk 312 optimal weight: 0.0030 chunk 173 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 210 optimal weight: 50.0000 chunk 166 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 374 optimal weight: 0.0020 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS A 370 HIS A 456 HIS ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN A 633 HIS A 734 HIS A 738 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1037 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS D 235 ASN D 246 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS D 462 ASN D 495 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 633 HIS D 667 GLN D 734 HIS D 738 GLN D 746 ASN D 753 HIS ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D1021 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN B 342 HIS B 370 HIS B 462 ASN B 530 GLN B 584 HIS B 734 HIS B 738 GLN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 246 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 364 ASN C 370 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 ASN ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN C 633 HIS ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 753 HIS ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 891 HIS C 991 ASN C1021 ASN C1050 HIS ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2864 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32540 Z= 0.178 Angle : 0.649 11.856 44108 Z= 0.342 Chirality : 0.042 0.253 5144 Planarity : 0.005 0.063 5616 Dihedral : 5.858 38.576 4453 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.07 % Allowed : 8.08 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.10), residues: 4108 helix: -2.90 (0.08), residues: 2540 sheet: 3.11 (0.57), residues: 40 loop : -2.74 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 383 HIS 0.011 0.001 HIS D 342 PHE 0.028 0.002 PHE C 261 TYR 0.020 0.002 TYR B 201 ARG 0.006 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 487 time to evaluate : 3.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.2252 (mtt) cc_final: 0.1830 (mtm) REVERT: A 318 MET cc_start: 0.1530 (mpp) cc_final: 0.0685 (ptt) REVERT: A 388 LEU cc_start: 0.1410 (tp) cc_final: 0.0780 (pp) REVERT: A 412 MET cc_start: 0.1680 (tpp) cc_final: 0.1085 (ppp) REVERT: A 568 HIS cc_start: 0.4196 (m90) cc_final: 0.3735 (m170) REVERT: A 585 LEU cc_start: 0.5125 (mt) cc_final: 0.4725 (mt) REVERT: A 617 TYR cc_start: 0.5559 (m-80) cc_final: 0.4823 (m-80) REVERT: A 630 MET cc_start: 0.2305 (mtt) cc_final: 0.2093 (mtt) REVERT: A 726 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5407 (m-70) REVERT: A 844 MET cc_start: 0.6898 (mmt) cc_final: 0.6167 (ppp) REVERT: A 865 ILE cc_start: 0.5743 (mm) cc_final: 0.4982 (tt) REVERT: A 926 ILE cc_start: 0.3949 (pt) cc_final: 0.3743 (pt) REVERT: A 1064 ARG cc_start: 0.5824 (ptm-80) cc_final: 0.5340 (ttp80) REVERT: D 312 ILE cc_start: 0.3000 (tp) cc_final: 0.2398 (tt) REVERT: D 775 MET cc_start: 0.5207 (mmt) cc_final: 0.4718 (mmt) REVERT: D 840 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.3156 (tt) REVERT: D 921 VAL cc_start: 0.2227 (t) cc_final: 0.1946 (t) REVERT: D 991 ASN cc_start: 0.2831 (m-40) cc_final: 0.2295 (m-40) REVERT: D 1083 PHE cc_start: 0.4256 (p90) cc_final: 0.3079 (m-80) REVERT: B 321 MET cc_start: 0.7487 (mmt) cc_final: 0.6333 (mmt) REVERT: B 412 MET cc_start: 0.6319 (ppp) cc_final: 0.5922 (ppp) REVERT: B 775 MET cc_start: 0.3725 (mmm) cc_final: 0.3457 (mmp) REVERT: B 870 TYR cc_start: 0.6337 (m-10) cc_final: 0.5734 (m-10) REVERT: B 1016 PRO cc_start: 0.4680 (Cg_endo) cc_final: 0.4470 (Cg_exo) REVERT: C 491 ASN cc_start: 0.3532 (m-40) cc_final: 0.3040 (m-40) REVERT: C 1000 VAL cc_start: 0.3518 (p) cc_final: 0.2134 (t) REVERT: C 1041 LYS cc_start: 0.2513 (mmtp) cc_final: 0.1944 (mtmm) outliers start: 36 outliers final: 14 residues processed: 508 average time/residue: 0.4121 time to fit residues: 343.5606 Evaluate side-chains 388 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 372 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 942 ILE Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1084 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 324 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 103 optimal weight: 50.0000 chunk 374 optimal weight: 1.9990 chunk 404 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 371 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 271 HIS A 275 HIS A 387 HIS A 430 GLN A 491 ASN A 530 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 246 GLN D 275 HIS D 296 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 543 HIS ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN D 738 GLN D 746 ASN D 753 HIS D 849 GLN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 HIS ** B 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 HIS B1037 ASN B1050 HIS B1075 ASN C 161 HIS C 186 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 HIS C 721 ASN ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 GLN C 852 GLN C 962 HIS C 991 ASN ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 1.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 32540 Z= 0.407 Angle : 1.009 15.398 44108 Z= 0.526 Chirality : 0.053 0.369 5144 Planarity : 0.007 0.090 5616 Dihedral : 6.551 30.708 4440 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.96 % Favored : 90.97 % Rotamer: Outliers : 2.65 % Allowed : 10.04 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.54 (0.11), residues: 4108 helix: -2.23 (0.09), residues: 2383 sheet: 2.64 (0.60), residues: 40 loop : -2.50 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 745 HIS 0.062 0.003 HIS D 962 PHE 0.043 0.004 PHE B 261 TYR 0.035 0.003 TYR C 751 ARG 0.014 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 702 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.3132 (mtt) cc_final: 0.2890 (mtm) REVERT: A 417 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5844 (tt) REVERT: A 554 MET cc_start: 0.7718 (ptm) cc_final: 0.7491 (ptm) REVERT: A 655 LEU cc_start: 0.7980 (mp) cc_final: 0.7743 (mt) REVERT: A 844 MET cc_start: 0.6989 (mmt) cc_final: 0.6623 (ppp) REVERT: A 869 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7157 (mp) REVERT: A 984 ASP cc_start: 0.7725 (t0) cc_final: 0.7406 (t0) REVERT: D 292 ILE cc_start: 0.2648 (OUTLIER) cc_final: 0.2037 (tt) REVERT: D 677 LYS cc_start: 0.4814 (OUTLIER) cc_final: 0.4118 (mtpt) REVERT: D 678 LYS cc_start: 0.6551 (mmtm) cc_final: 0.5685 (tttm) REVERT: D 845 ARG cc_start: 0.6031 (mtp-110) cc_final: 0.5370 (mpt180) REVERT: D 915 GLN cc_start: 0.6625 (tp-100) cc_final: 0.6043 (mp10) REVERT: D 956 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6002 (pt) REVERT: B 321 MET cc_start: 0.7469 (mmt) cc_final: 0.6671 (mmt) REVERT: B 352 ILE cc_start: 0.5803 (mp) cc_final: 0.5553 (mp) REVERT: B 355 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: B 878 THR cc_start: 0.8253 (p) cc_final: 0.7983 (p) REVERT: B 984 ASP cc_start: 0.8345 (t0) cc_final: 0.7973 (t0) REVERT: B 1012 MET cc_start: 0.8522 (ttp) cc_final: 0.8113 (ttp) REVERT: C 196 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6435 (t70) REVERT: C 258 MET cc_start: 0.6431 (ppp) cc_final: 0.6136 (tmm) REVERT: C 324 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5512 (tpt) REVERT: C 368 LYS cc_start: 0.7420 (ttmt) cc_final: 0.7103 (tttp) REVERT: C 996 ASP cc_start: 0.6547 (t70) cc_final: 0.6167 (t0) REVERT: C 1146 MET cc_start: 0.1289 (mmm) cc_final: 0.0321 (mmt) outliers start: 89 outliers final: 22 residues processed: 760 average time/residue: 0.4631 time to fit residues: 581.5728 Evaluate side-chains 505 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 475 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 831 CYS Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 355 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 1065 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 376 optimal weight: 3.9990 chunk 398 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 356 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS A 387 HIS A 522 GLN A 540 HIS A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 853 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN D 309 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 721 ASN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS B 196 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 GLN B 753 HIS ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 223 ASN C 224 ASN C 271 HIS C 309 GLN C 336 GLN ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN ** C 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 734 HIS C 777 ASN C 852 GLN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32540 Z= 0.236 Angle : 0.689 11.489 44108 Z= 0.358 Chirality : 0.044 0.241 5144 Planarity : 0.005 0.065 5616 Dihedral : 5.317 24.822 4440 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.06 % Allowed : 14.54 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 4108 helix: -1.41 (0.10), residues: 2498 sheet: 3.22 (0.67), residues: 40 loop : -2.33 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1091 HIS 0.014 0.001 HIS D 565 PHE 0.031 0.002 PHE A 504 TYR 0.028 0.002 TYR C 851 ARG 0.009 0.001 ARG D1035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 627 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.4368 (mtt) cc_final: 0.4149 (mtm) REVERT: A 321 MET cc_start: 0.3322 (tpp) cc_final: 0.2809 (tpp) REVERT: A 387 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5822 (m170) REVERT: A 428 GLN cc_start: 0.7182 (mp10) cc_final: 0.6433 (tp40) REVERT: A 457 ILE cc_start: 0.7037 (mt) cc_final: 0.6815 (mt) REVERT: A 541 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7085 (mmm-85) REVERT: A 844 MET cc_start: 0.7163 (mmt) cc_final: 0.6744 (ppp) REVERT: A 984 ASP cc_start: 0.7986 (t0) cc_final: 0.7694 (t0) REVERT: A 1053 LEU cc_start: 0.8182 (tp) cc_final: 0.7946 (mm) REVERT: D 175 MET cc_start: 0.5772 (ptp) cc_final: 0.4956 (ptp) REVERT: D 338 MET cc_start: 0.0792 (tpp) cc_final: 0.0174 (ptm) REVERT: D 678 LYS cc_start: 0.7012 (mmtm) cc_final: 0.6766 (tmtt) REVERT: D 746 ASN cc_start: 0.7741 (m-40) cc_final: 0.7536 (m-40) REVERT: D 845 ARG cc_start: 0.6328 (mtp-110) cc_final: 0.5685 (mpt90) REVERT: D 1131 MET cc_start: 0.5168 (ttt) cc_final: 0.4543 (tpt) REVERT: B 321 MET cc_start: 0.7314 (mmt) cc_final: 0.6697 (mmt) REVERT: B 599 MET cc_start: 0.8312 (ptm) cc_final: 0.7953 (ttp) REVERT: B 1131 MET cc_start: 0.7246 (mmt) cc_final: 0.6402 (ptm) REVERT: B 1146 MET cc_start: 0.5445 (mmm) cc_final: 0.4015 (ppp) REVERT: C 237 SER cc_start: 0.8133 (m) cc_final: 0.7437 (p) REVERT: C 321 MET cc_start: 0.7704 (mpp) cc_final: 0.7435 (mpp) REVERT: C 338 MET cc_start: 0.7032 (tpp) cc_final: 0.6759 (tpp) REVERT: C 580 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7795 (m-40) REVERT: C 590 ASN cc_start: 0.6818 (t0) cc_final: 0.6138 (t0) REVERT: C 867 TRP cc_start: 0.6975 (m100) cc_final: 0.6705 (m100) REVERT: C 896 SER cc_start: 0.9163 (p) cc_final: 0.8949 (p) REVERT: C 996 ASP cc_start: 0.7088 (t70) cc_final: 0.6668 (t0) REVERT: C 1146 MET cc_start: 0.1412 (mmm) cc_final: 0.1109 (mmm) outliers start: 69 outliers final: 24 residues processed: 666 average time/residue: 0.3894 time to fit residues: 426.7945 Evaluate side-chains 507 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 481 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 580 ASN Chi-restraints excluded: chain C residue 1049 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 296 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 339 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 0 optimal weight: 60.0000 chunk 203 optimal weight: 6.9990 chunk 357 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 HIS A1075 ASN D 309 GLN D 342 HIS D 432 GLN D 525 HIS D 540 HIS D 574 GLN D 753 HIS ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN B 235 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS B 721 ASN B 962 HIS B1037 ASN B1050 HIS ** B1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 230 HIS C 271 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 1.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32540 Z= 0.258 Angle : 0.729 22.235 44108 Z= 0.375 Chirality : 0.045 0.300 5144 Planarity : 0.005 0.067 5616 Dihedral : 5.196 23.498 4440 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.74 % Allowed : 16.78 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4108 helix: -0.99 (0.10), residues: 2478 sheet: 3.23 (0.68), residues: 40 loop : -2.33 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1061 HIS 0.042 0.002 HIS A 387 PHE 0.020 0.002 PHE A 483 TYR 0.026 0.002 TYR C 851 ARG 0.015 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 622 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.2182 (mmt) cc_final: 0.1953 (mmt) REVERT: A 275 HIS cc_start: 0.8167 (m90) cc_final: 0.7787 (m-70) REVERT: A 428 GLN cc_start: 0.7288 (mp10) cc_final: 0.6564 (tp40) REVERT: A 458 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7907 (ptt180) REVERT: A 730 GLU cc_start: 0.7859 (pt0) cc_final: 0.7602 (pt0) REVERT: A 844 MET cc_start: 0.7323 (mmt) cc_final: 0.6966 (ppp) REVERT: A 984 ASP cc_start: 0.8328 (t0) cc_final: 0.7864 (t0) REVERT: A 1037 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7853 (p0) REVERT: D 175 MET cc_start: 0.6190 (ptp) cc_final: 0.5851 (ptm) REVERT: D 346 MET cc_start: 0.6607 (mmm) cc_final: 0.6186 (mmm) REVERT: D 845 ARG cc_start: 0.6747 (mtp-110) cc_final: 0.5721 (mtt-85) REVERT: D 1131 MET cc_start: 0.4886 (ttt) cc_final: 0.4203 (tpt) REVERT: B 166 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7648 (mt) REVERT: B 321 MET cc_start: 0.7106 (mmt) cc_final: 0.6630 (mmt) REVERT: B 450 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: B 659 MET cc_start: 0.8437 (ptt) cc_final: 0.8163 (ptt) REVERT: B 760 TYR cc_start: 0.8076 (t80) cc_final: 0.7644 (t80) REVERT: B 1146 MET cc_start: 0.5421 (mmm) cc_final: 0.4149 (ppp) REVERT: C 154 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7240 (tp30) REVERT: C 237 SER cc_start: 0.8801 (m) cc_final: 0.8311 (p) REVERT: C 441 ASP cc_start: 0.7848 (p0) cc_final: 0.7401 (p0) REVERT: C 450 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7104 (m-10) REVERT: C 835 ILE cc_start: 0.8772 (mm) cc_final: 0.8508 (mt) REVERT: C 996 ASP cc_start: 0.7340 (t70) cc_final: 0.7034 (t0) outliers start: 92 outliers final: 38 residues processed: 678 average time/residue: 0.4111 time to fit residues: 454.5216 Evaluate side-chains 502 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 459 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 979 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 652 THR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 997 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 343 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 450 TYR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 345 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 936 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 0.0270 chunk 358 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 398 optimal weight: 0.9990 chunk 330 optimal weight: 0.0770 chunk 184 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 408 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 HIS A 891 HIS D 267 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 HIS D 525 HIS ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D1046 GLN B 235 ASN B 304 HIS B 408 HIS B 543 HIS ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 HIS B1037 ASN B1136 HIS C 387 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 1.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32540 Z= 0.152 Angle : 0.606 15.407 44108 Z= 0.309 Chirality : 0.041 0.245 5144 Planarity : 0.004 0.072 5616 Dihedral : 4.711 21.862 4440 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.97 % Allowed : 19.52 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.13), residues: 4108 helix: -0.43 (0.10), residues: 2502 sheet: 3.54 (0.69), residues: 40 loop : -2.13 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 247 HIS 0.010 0.001 HIS A 387 PHE 0.015 0.001 PHE C 420 TYR 0.029 0.001 TYR A 620 ARG 0.009 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 512 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.8082 (m90) cc_final: 0.7627 (m-70) REVERT: A 324 MET cc_start: 0.5740 (mmp) cc_final: 0.5426 (mmt) REVERT: A 428 GLN cc_start: 0.7293 (mp10) cc_final: 0.6734 (tp40) REVERT: A 730 GLU cc_start: 0.7988 (pt0) cc_final: 0.7712 (pt0) REVERT: A 984 ASP cc_start: 0.8275 (t0) cc_final: 0.7844 (t0) REVERT: D 175 MET cc_start: 0.6315 (ptp) cc_final: 0.6046 (ptm) REVERT: D 432 GLN cc_start: 0.4930 (tp-100) cc_final: 0.4314 (tm-30) REVERT: D 470 ILE cc_start: 0.7676 (mm) cc_final: 0.7294 (mm) REVERT: D 845 ARG cc_start: 0.6825 (mtp-110) cc_final: 0.5898 (mtt-85) REVERT: D 1131 MET cc_start: 0.5481 (ttt) cc_final: 0.4923 (tpt) REVERT: B 226 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6918 (t80) REVERT: B 321 MET cc_start: 0.7035 (mmt) cc_final: 0.6799 (mmt) REVERT: B 760 TYR cc_start: 0.7943 (t80) cc_final: 0.7591 (t80) REVERT: B 1146 MET cc_start: 0.5496 (mmm) cc_final: 0.4315 (ppp) REVERT: C 154 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7374 (tp30) REVERT: C 237 SER cc_start: 0.8828 (m) cc_final: 0.8286 (p) REVERT: C 321 MET cc_start: 0.8147 (tpp) cc_final: 0.7941 (mmm) REVERT: C 441 ASP cc_start: 0.7824 (p0) cc_final: 0.7321 (p0) REVERT: C 450 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6896 (m-10) REVERT: C 743 MET cc_start: 0.7249 (tmm) cc_final: 0.7029 (ttp) REVERT: C 835 ILE cc_start: 0.8705 (mm) cc_final: 0.8453 (mt) REVERT: C 996 ASP cc_start: 0.7230 (t70) cc_final: 0.6933 (t0) outliers start: 66 outliers final: 28 residues processed: 550 average time/residue: 0.3972 time to fit residues: 363.3853 Evaluate side-chains 483 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 453 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 979 MET Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 896 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain C residue 978 MET Chi-restraints excluded: chain C residue 1046 GLN Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 291 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 397 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 183 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 387 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** D 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 476 ASN D 547 ASN D 550 GLN D 590 ASN ** D 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN D1046 GLN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 235 ASN B 349 HIS B 525 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN C 157 GLN C 408 HIS ** C 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 1.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32540 Z= 0.197 Angle : 0.638 11.386 44108 Z= 0.329 Chirality : 0.042 0.200 5144 Planarity : 0.005 0.079 5616 Dihedral : 4.708 20.471 4440 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.29 % Allowed : 19.22 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.13), residues: 4108 helix: -0.29 (0.10), residues: 2543 sheet: 3.83 (0.66), residues: 40 loop : -2.09 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 867 HIS 0.010 0.001 HIS D 408 PHE 0.022 0.001 PHE D 830 TYR 0.032 0.001 TYR A 620 ARG 0.011 0.001 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 515 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7680 (ptt180) REVERT: A 730 GLU cc_start: 0.8059 (pt0) cc_final: 0.7856 (pt0) REVERT: A 984 ASP cc_start: 0.8276 (t0) cc_final: 0.7946 (t0) REVERT: A 989 TYR cc_start: 0.8267 (m-80) cc_final: 0.7947 (m-80) REVERT: D 175 MET cc_start: 0.6401 (ptp) cc_final: 0.5858 (ptm) REVERT: D 381 SER cc_start: 0.8881 (t) cc_final: 0.8531 (p) REVERT: D 845 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6088 (mtt-85) REVERT: D 1032 GLU cc_start: 0.7639 (tp30) cc_final: 0.7421 (tm-30) REVERT: D 1052 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7973 (mm-30) REVERT: D 1067 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7033 (mmtm) REVERT: B 156 LYS cc_start: 0.7409 (mtpm) cc_final: 0.6918 (mppt) REVERT: B 321 MET cc_start: 0.7223 (mmt) cc_final: 0.6960 (mmt) REVERT: B 355 TYR cc_start: 0.7570 (t80) cc_final: 0.7224 (t80) REVERT: B 483 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: B 588 MET cc_start: 0.7752 (ptp) cc_final: 0.7552 (ptp) REVERT: B 612 MET cc_start: 0.8291 (tpp) cc_final: 0.7971 (tpp) REVERT: B 760 TYR cc_start: 0.8213 (t80) cc_final: 0.7731 (t80) REVERT: B 1131 MET cc_start: 0.5536 (tmm) cc_final: 0.4717 (ttt) REVERT: C 154 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7554 (tp30) REVERT: C 321 MET cc_start: 0.8191 (tpp) cc_final: 0.7877 (mmm) REVERT: C 441 ASP cc_start: 0.8088 (p0) cc_final: 0.7852 (p0) REVERT: C 450 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: C 472 LEU cc_start: 0.8498 (mt) cc_final: 0.8288 (mp) REVERT: C 842 ASN cc_start: 0.8282 (t0) cc_final: 0.7859 (t0) REVERT: C 984 ASP cc_start: 0.8276 (t0) cc_final: 0.7894 (t0) REVERT: C 996 ASP cc_start: 0.7385 (t70) cc_final: 0.7058 (t0) REVERT: C 1146 MET cc_start: 0.1449 (mmt) cc_final: 0.1077 (mmp) outliers start: 77 outliers final: 29 residues processed: 553 average time/residue: 0.4157 time to fit residues: 373.9711 Evaluate side-chains 464 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 1067 LYS Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 0.3980 chunk 119 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 270 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 312 optimal weight: 40.0000 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: