Starting phenix.real_space_refine on Fri Mar 22 01:47:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/03_2024/7ykr_33895.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/03_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_33895/03_2024/7ykr_33895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/03_2024/7ykr_33895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/03_2024/7ykr_33895.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykr_33895/03_2024/7ykr_33895.pdb" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.22, per 1000 atoms: 0.48 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: 10.45 Conformation dependent library (CDL) restraints added in 5.6 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: 3.55 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: 11.49 Time building geometry restraints manager: 11.57 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 2.440 ... (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 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: 0.720 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: 0.020 Extract box with map and model: 5.330 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 77.180 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.180 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.990 ------------------------------------------------------------------------------- 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 : 3.410 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: 0.4553 time to fit residues: 476.0612 Evaluate side-chains 431 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 3.228 ------------------------------------------------------------------------------- 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: 0.8980 chunk 312 optimal weight: 0.0040 chunk 173 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 210 optimal weight: 50.0000 chunk 166 optimal weight: 0.7980 chunk 322 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 374 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 342 HIS A 370 HIS A 456 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 842 ASN ** A 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1037 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS D 235 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 370 HIS D 495 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 HIS D 667 GLN D 734 HIS D 738 GLN D 746 ASN D 753 HIS ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 991 ASN D1021 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** 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 667 GLN B 721 ASN B 738 GLN ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 296 GLN C 336 GLN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2932 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32540 Z= 0.177 Angle : 0.639 12.882 44108 Z= 0.337 Chirality : 0.041 0.254 5144 Planarity : 0.005 0.056 5616 Dihedral : 5.873 54.712 4453 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.28 % Allowed : 8.16 % Favored : 90.55 % 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: -2.89 (0.08), residues: 2552 sheet: 3.13 (0.56), residues: 40 loop : -2.75 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 383 HIS 0.008 0.001 HIS D 342 PHE 0.029 0.002 PHE C 261 TYR 0.020 0.001 TYR B 201 ARG 0.006 0.001 ARG C 905 *********************** 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 537 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 494 time to evaluate : 3.269 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: A 175 MET cc_start: 0.2212 (mtt) cc_final: 0.1794 (mtm) REVERT: A 388 LEU cc_start: 0.1452 (tp) cc_final: 0.0810 (pp) REVERT: A 412 MET cc_start: 0.1545 (tpp) cc_final: 0.1008 (ppp) REVERT: A 568 HIS cc_start: 0.4260 (m90) cc_final: 0.3775 (m170) REVERT: A 585 LEU cc_start: 0.5177 (mt) cc_final: 0.4762 (mt) REVERT: A 617 TYR cc_start: 0.5286 (m-80) cc_final: 0.4664 (m-80) REVERT: A 726 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.4687 (m-70) REVERT: A 844 MET cc_start: 0.6903 (mmt) cc_final: 0.6164 (ppp) REVERT: A 865 ILE cc_start: 0.5844 (mm) cc_final: 0.5120 (tt) REVERT: A 1064 ARG cc_start: 0.5867 (ptm-80) cc_final: 0.5387 (ttp80) REVERT: D 312 ILE cc_start: 0.2626 (tp) cc_final: 0.2088 (tt) REVERT: D 840 LEU cc_start: 0.3399 (OUTLIER) cc_final: 0.3016 (tt) REVERT: D 921 VAL cc_start: 0.2439 (t) cc_final: 0.2164 (t) REVERT: D 991 ASN cc_start: 0.2746 (m110) cc_final: 0.2439 (m110) REVERT: D 1002 MET cc_start: 0.3628 (ppp) cc_final: 0.3300 (ppp) REVERT: D 1083 PHE cc_start: 0.4320 (p90) cc_final: 0.3120 (m-80) REVERT: B 321 MET cc_start: 0.7433 (mmt) cc_final: 0.6151 (mmt) REVERT: B 339 THR cc_start: 0.5408 (m) cc_final: 0.4761 (p) REVERT: B 412 MET cc_start: 0.6361 (ppp) cc_final: 0.5963 (ppp) REVERT: B 775 MET cc_start: 0.3850 (mmm) cc_final: 0.3594 (mmp) REVERT: B 842 ASN cc_start: 0.6061 (t0) cc_final: 0.5761 (m-40) REVERT: B 870 TYR cc_start: 0.6303 (m-10) cc_final: 0.5588 (m-10) REVERT: C 245 PHE cc_start: 0.4377 (m-10) cc_final: 0.4080 (m-10) REVERT: C 338 MET cc_start: -0.0116 (OUTLIER) cc_final: -0.0390 (ptm) REVERT: C 1041 LYS cc_start: 0.2641 (mmtp) cc_final: 0.2071 (mtmm) outliers start: 43 outliers final: 15 residues processed: 519 average time/residue: 0.3952 time to fit residues: 336.8867 Evaluate side-chains 384 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 366 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 632 THR 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 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 648 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 338 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 374 optimal weight: 0.9980 chunk 404 optimal weight: 0.9990 chunk 333 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 300 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 309 GLN A 349 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 721 ASN A 746 ASN A 842 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 530 GLN D 534 ASN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN ** D 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 ASN ** 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** ** B 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN C 336 GLN C 349 HIS C 364 ASN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 495 GLN C 543 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** C 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN C1021 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4517 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32540 Z= 0.231 Angle : 0.700 10.723 44108 Z= 0.364 Chirality : 0.043 0.219 5144 Planarity : 0.005 0.061 5616 Dihedral : 5.295 27.729 4440 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.94 % Allowed : 10.31 % Favored : 87.75 % 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: -3.05 (0.12), residues: 4108 helix: -1.70 (0.09), residues: 2496 sheet: 3.35 (0.54), residues: 40 loop : -2.56 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 383 HIS 0.016 0.002 HIS C 962 PHE 0.029 0.002 PHE D 944 TYR 0.031 0.002 TYR D 994 ARG 0.006 0.001 ARG C 179 *********************** 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 583 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 518 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 ASN cc_start: 0.7021 (m110) cc_final: 0.6795 (m110) REVERT: A 844 MET cc_start: 0.6861 (mmt) cc_final: 0.6431 (ppp) REVERT: A 918 ILE cc_start: 0.7283 (tp) cc_final: 0.5795 (pt) REVERT: D 161 HIS cc_start: 0.1016 (m90) cc_final: 0.0615 (m-70) REVERT: D 201 TYR cc_start: 0.6030 (m-80) cc_final: 0.5546 (m-80) REVERT: D 258 MET cc_start: 0.3839 (ptp) cc_final: 0.0446 (tmm) REVERT: D 312 ILE cc_start: 0.3229 (OUTLIER) cc_final: 0.2504 (mm) REVERT: D 775 MET cc_start: 0.5129 (mmt) cc_final: 0.4869 (mmt) REVERT: D 906 LEU cc_start: 0.7616 (tp) cc_final: 0.7408 (mm) REVERT: D 935 MET cc_start: 0.5115 (ttt) cc_final: 0.4909 (ttp) REVERT: D 1053 LEU cc_start: 0.6129 (tp) cc_final: 0.5595 (tp) REVERT: B 200 ILE cc_start: 0.4459 (mt) cc_final: 0.4247 (tt) REVERT: B 321 MET cc_start: 0.7196 (mmt) cc_final: 0.6930 (mmp) REVERT: B 412 MET cc_start: 0.6676 (ppp) cc_final: 0.6320 (ppp) REVERT: B 775 MET cc_start: 0.5663 (mmm) cc_final: 0.5427 (mmp) REVERT: C 196 HIS cc_start: 0.3595 (OUTLIER) cc_final: 0.3360 (t70) REVERT: C 324 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4383 (tpt) REVERT: C 1146 MET cc_start: 0.1137 (mmm) cc_final: 0.0814 (mmm) outliers start: 65 outliers final: 20 residues processed: 566 average time/residue: 0.3939 time to fit residues: 366.0935 Evaluate side-chains 409 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 386 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain D residue 599 MET Chi-restraints excluded: chain D residue 962 HIS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 978 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 178 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 376 optimal weight: 4.9990 chunk 398 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 530 GLN A 534 ASN A 540 HIS ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN D 547 ASN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 GLN ** D 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN D 738 GLN D 746 ASN ** D 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS ** D1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN ** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 738 GLN C 842 ASN C 849 GLN C 852 GLN C 991 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 1.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32540 Z= 0.395 Angle : 0.952 15.458 44108 Z= 0.492 Chirality : 0.052 0.302 5144 Planarity : 0.006 0.084 5616 Dihedral : 6.431 38.144 4440 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.30 % Favored : 90.63 % Rotamer: Outliers : 3.43 % Allowed : 12.01 % Favored : 84.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.25 (0.12), residues: 4108 helix: -1.91 (0.09), residues: 2414 sheet: 2.69 (0.73), residues: 40 loop : -2.51 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 383 HIS 0.054 0.003 HIS D 962 PHE 0.040 0.003 PHE B 261 TYR 0.035 0.003 TYR D 623 ARG 0.013 0.001 ARG A 541 *********************** 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 832 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 717 time to evaluate : 3.465 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 255 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5463 (mtt180) REVERT: A 318 MET cc_start: 0.3850 (OUTLIER) cc_final: 0.3427 (mmm) REVERT: A 428 GLN cc_start: 0.6776 (mp10) cc_final: 0.6486 (tp40) REVERT: A 844 MET cc_start: 0.7102 (mmt) cc_final: 0.6786 (ppp) REVERT: A 1092 PHE cc_start: 0.7384 (m-80) cc_final: 0.7086 (m-10) REVERT: D 175 MET cc_start: 0.5461 (ptp) cc_final: 0.4891 (pmm) REVERT: D 678 LYS cc_start: 0.7316 (mmtm) cc_final: 0.7051 (tttp) REVERT: D 845 ARG cc_start: 0.6208 (mtp-110) cc_final: 0.5484 (mpt180) REVERT: D 1046 GLN cc_start: 0.7196 (mt0) cc_final: 0.6984 (mt0) REVERT: D 1131 MET cc_start: 0.5538 (ttt) cc_final: 0.4929 (tpt) REVERT: B 258 MET cc_start: 0.6789 (tmm) cc_final: 0.6528 (ttp) REVERT: B 321 MET cc_start: 0.7144 (mmt) cc_final: 0.6399 (mmt) REVERT: B 383 TRP cc_start: 0.7532 (m-90) cc_final: 0.7189 (m-90) REVERT: B 483 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8271 (m-10) REVERT: B 612 MET cc_start: 0.8361 (tpp) cc_final: 0.8104 (tpp) REVERT: B 984 ASP cc_start: 0.8385 (t0) cc_final: 0.8147 (t0) REVERT: B 1131 MET cc_start: 0.6453 (tpt) cc_final: 0.5856 (tmm) REVERT: C 324 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5777 (tpp) REVERT: C 608 ASN cc_start: 0.7814 (t0) cc_final: 0.7550 (t0) REVERT: C 723 MET cc_start: 0.6411 (mmm) cc_final: 0.5964 (mmt) REVERT: C 905 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8338 (tpt-90) REVERT: C 996 ASP cc_start: 0.7249 (t70) cc_final: 0.6878 (t0) REVERT: C 1146 MET cc_start: 0.1497 (mmm) cc_final: 0.0785 (mmt) outliers start: 115 outliers final: 30 residues processed: 788 average time/residue: 0.4089 time to fit residues: 517.8008 Evaluate side-chains 518 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 483 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1119 GLU 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 429 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 888 ASN Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 268 VAL 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 842 ASN Chi-restraints excluded: chain C residue 905 ARG Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1059 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 296 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 0 optimal weight: 70.0000 chunk 203 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 456 HIS A 534 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 777 ASN ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 915 GLN D1021 ASN D1094 ASN B 161 HIS ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 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** B 997 GLN B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 224 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN C 309 GLN C 387 HIS ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 ASN C 842 ASN C 849 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 1.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32540 Z= 0.181 Angle : 0.622 10.996 44108 Z= 0.323 Chirality : 0.042 0.214 5144 Planarity : 0.004 0.059 5616 Dihedral : 5.054 25.599 4440 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.03 % Allowed : 16.48 % Favored : 81.50 % 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: -2.20 (0.12), residues: 4108 helix: -0.89 (0.10), residues: 2437 sheet: 2.96 (0.73), residues: 40 loop : -2.40 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 247 HIS 0.013 0.001 HIS B 648 PHE 0.026 0.001 PHE B 261 TYR 0.029 0.001 TYR C 620 ARG 0.006 0.000 ARG D 453 *********************** 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 622 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 554 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5271 (ptp) cc_final: 0.4787 (ptp) REVERT: A 428 GLN cc_start: 0.7077 (mp10) cc_final: 0.6440 (tp40) REVERT: A 844 MET cc_start: 0.7216 (mmt) cc_final: 0.6815 (ppp) REVERT: A 1131 MET cc_start: 0.3699 (ptm) cc_final: 0.3023 (ptp) REVERT: D 175 MET cc_start: 0.5560 (ptp) cc_final: 0.5100 (ptm) REVERT: D 241 MET cc_start: 0.6211 (tmm) cc_final: 0.5359 (ptm) REVERT: D 845 ARG cc_start: 0.6588 (mtp-110) cc_final: 0.5668 (mtt-85) REVERT: D 1131 MET cc_start: 0.4858 (ttt) cc_final: 0.4151 (tpt) REVERT: B 321 MET cc_start: 0.7219 (mmt) cc_final: 0.6583 (mmt) REVERT: B 984 ASP cc_start: 0.8438 (t0) cc_final: 0.8124 (t0) REVERT: B 1032 GLU cc_start: 0.7599 (tp30) cc_final: 0.7330 (tp30) REVERT: B 1131 MET cc_start: 0.6835 (tpt) cc_final: 0.5268 (ptp) REVERT: C 416 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7436 (ttm170) REVERT: C 450 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.5785 (m-10) REVERT: C 634 GLU cc_start: 0.7504 (pp20) cc_final: 0.7224 (pm20) REVERT: C 746 ASN cc_start: 0.8094 (t0) cc_final: 0.7874 (t0) REVERT: C 984 ASP cc_start: 0.8311 (t0) cc_final: 0.8034 (t0) REVERT: C 996 ASP cc_start: 0.7260 (t70) cc_final: 0.6938 (t0) REVERT: C 1146 MET cc_start: 0.1271 (mmm) cc_final: 0.0691 (mmt) outliers start: 68 outliers final: 31 residues processed: 603 average time/residue: 0.3897 time to fit residues: 391.2204 Evaluate side-chains 490 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 458 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 992 THR Chi-restraints excluded: chain B residue 197 LEU 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 979 MET 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 386 VAL Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 0.0770 chunk 209 optimal weight: 20.0000 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 777 ASN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 HIS ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN D 849 GLN D1021 ASN D1046 GLN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 275 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 ASN B1037 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 HIS C 157 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN C 309 GLN ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 GLN C 856 HIS C 962 HIS C1021 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 1.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32540 Z= 0.190 Angle : 0.647 15.514 44108 Z= 0.329 Chirality : 0.043 0.263 5144 Planarity : 0.004 0.055 5616 Dihedral : 4.860 26.987 4440 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.18 % Allowed : 17.37 % Favored : 80.45 % 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: -1.73 (0.13), residues: 4108 helix: -0.49 (0.10), residues: 2459 sheet: 1.34 (0.78), residues: 55 loop : -2.21 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 867 HIS 0.014 0.001 HIS C 856 PHE 0.021 0.001 PHE B 261 TYR 0.016 0.001 TYR C 892 ARG 0.006 0.000 ARG D 208 *********************** 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 635 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 562 time to evaluate : 4.665 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 241 MET cc_start: 0.2187 (mmt) cc_final: 0.1541 (mtm) REVERT: A 258 MET cc_start: 0.5790 (ptp) cc_final: 0.5373 (ptp) REVERT: A 428 GLN cc_start: 0.7415 (mp10) cc_final: 0.7025 (tp40) REVERT: A 450 TYR cc_start: 0.8050 (m-10) cc_final: 0.7832 (m-10) REVERT: A 470 ILE cc_start: 0.7688 (mm) cc_final: 0.7273 (mt) REVERT: A 991 ASN cc_start: 0.7334 (m110) cc_final: 0.7122 (m-40) REVERT: A 1045 MET cc_start: 0.7876 (mmm) cc_final: 0.7675 (mmt) REVERT: A 1131 MET cc_start: 0.3704 (ptm) cc_final: 0.2968 (ptp) REVERT: D 175 MET cc_start: 0.5931 (ptp) cc_final: 0.5564 (ptm) REVERT: D 241 MET cc_start: 0.6385 (tmm) cc_final: 0.6173 (ptm) REVERT: D 432 GLN cc_start: 0.3027 (tp40) cc_final: 0.2668 (tm-30) REVERT: D 470 ILE cc_start: 0.7833 (mm) cc_final: 0.7545 (mm) REVERT: D 845 ARG cc_start: 0.6718 (mtp-110) cc_final: 0.5803 (mtt-85) REVERT: D 1131 MET cc_start: 0.5848 (ttt) cc_final: 0.5112 (tpt) REVERT: B 321 MET cc_start: 0.7184 (mmt) cc_final: 0.6719 (mmt) REVERT: B 578 ASP cc_start: 0.7807 (t0) cc_final: 0.7525 (t0) REVERT: B 678 LYS cc_start: 0.8030 (tttp) cc_final: 0.7738 (tmtt) REVERT: B 1032 GLU cc_start: 0.7789 (tp30) cc_final: 0.7515 (tp30) REVERT: C 154 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7440 (tp30) REVERT: C 196 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.6630 (t-90) REVERT: C 416 ARG cc_start: 0.8035 (tpp80) cc_final: 0.6976 (ttt180) REVERT: C 450 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6930 (m-10) REVERT: C 746 ASN cc_start: 0.8305 (t0) cc_final: 0.8078 (t0) REVERT: C 842 ASN cc_start: 0.7793 (m-40) cc_final: 0.7365 (m110) REVERT: C 843 SER cc_start: 0.8394 (t) cc_final: 0.8176 (p) REVERT: C 844 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6723 (mmm) REVERT: C 867 TRP cc_start: 0.7026 (m100) cc_final: 0.6805 (m100) REVERT: C 984 ASP cc_start: 0.8271 (t0) cc_final: 0.8045 (t0) REVERT: C 996 ASP cc_start: 0.7332 (t70) cc_final: 0.7065 (t0) REVERT: C 1146 MET cc_start: 0.1396 (mmm) cc_final: 0.0941 (mmt) outliers start: 73 outliers final: 35 residues processed: 609 average time/residue: 0.4076 time to fit residues: 405.9974 Evaluate side-chains 497 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 459 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 MET 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 299 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain B residue 197 LEU 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 343 CYS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 641 MET Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain C residue 914 ASP Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 983 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 291 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 335 optimal weight: 0.1980 chunk 222 optimal weight: 9.9990 chunk 397 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 183 optimal weight: 0.0470 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 HIS ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1046 GLN ** D1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** 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 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 ASN B1037 ASN C 223 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 ASN C1046 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 1.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32540 Z= 0.174 Angle : 0.603 12.663 44108 Z= 0.307 Chirality : 0.041 0.211 5144 Planarity : 0.004 0.054 5616 Dihedral : 4.704 24.877 4440 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.12 % Allowed : 18.77 % Favored : 79.11 % 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: -1.32 (0.13), residues: 4108 helix: -0.20 (0.11), residues: 2440 sheet: 3.64 (0.72), residues: 40 loop : -1.99 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1091 HIS 0.012 0.001 HIS C 196 PHE 0.024 0.001 PHE B 261 TYR 0.016 0.001 TYR A 857 ARG 0.013 0.000 ARG A 995 *********************** 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 581 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 510 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.3119 (mmt) cc_final: 0.2599 (mtm) REVERT: A 275 HIS cc_start: 0.8025 (m90) cc_final: 0.7512 (m90) REVERT: A 324 MET cc_start: 0.6317 (mmp) cc_final: 0.6042 (mmt) REVERT: A 363 ILE cc_start: 0.6196 (mp) cc_final: 0.5891 (mt) REVERT: A 470 ILE cc_start: 0.8064 (mm) cc_final: 0.7622 (mt) REVERT: A 844 MET cc_start: 0.7290 (mmt) cc_final: 0.6888 (ppp) REVERT: A 1045 MET cc_start: 0.7932 (mmm) cc_final: 0.7719 (mmm) REVERT: A 1131 MET cc_start: 0.3868 (ptm) cc_final: 0.3161 (ptp) REVERT: D 175 MET cc_start: 0.6109 (ptp) cc_final: 0.5677 (ptm) REVERT: D 299 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7387 (tt) REVERT: D 324 MET cc_start: 0.5892 (mmp) cc_final: 0.5401 (mmm) REVERT: D 338 MET cc_start: 0.5878 (tpp) cc_final: 0.5573 (tpp) REVERT: D 432 GLN cc_start: 0.4784 (tp40) cc_final: 0.4347 (tm-30) REVERT: D 470 ILE cc_start: 0.8472 (mm) cc_final: 0.8130 (mm) REVERT: D 509 SER cc_start: 0.8908 (p) cc_final: 0.8664 (m) REVERT: D 845 ARG cc_start: 0.7145 (mtp-110) cc_final: 0.6021 (mtt-85) REVERT: D 864 LEU cc_start: 0.8245 (mm) cc_final: 0.8022 (mp) REVERT: D 989 TYR cc_start: 0.8263 (m-80) cc_final: 0.7932 (m-80) REVERT: D 1067 LYS cc_start: 0.7248 (tppt) cc_final: 0.7043 (tppt) REVERT: D 1131 MET cc_start: 0.5626 (ttt) cc_final: 0.5022 (tpt) REVERT: B 318 MET cc_start: 0.8667 (mpp) cc_final: 0.8315 (mtt) REVERT: B 321 MET cc_start: 0.7105 (mmt) cc_final: 0.6683 (mmt) REVERT: B 501 LYS cc_start: 0.7595 (mttm) cc_final: 0.7371 (mtmt) REVERT: B 678 LYS cc_start: 0.8135 (tttp) cc_final: 0.7918 (tmtt) REVERT: B 1032 GLU cc_start: 0.7781 (tp30) cc_final: 0.7566 (tp30) REVERT: C 154 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7493 (tp30) REVERT: C 258 MET cc_start: 0.7199 (ppp) cc_final: 0.6978 (tmm) REVERT: C 416 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7169 (ttt-90) REVERT: C 450 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: C 593 HIS cc_start: 0.7665 (m-70) cc_final: 0.7446 (m-70) REVERT: C 746 ASN cc_start: 0.8224 (t0) cc_final: 0.7835 (m-40) REVERT: C 844 MET cc_start: 0.7411 (tmm) cc_final: 0.6971 (mmt) REVERT: C 984 ASP cc_start: 0.8267 (t0) cc_final: 0.8000 (t0) REVERT: C 996 ASP cc_start: 0.7278 (t70) cc_final: 0.7024 (t0) REVERT: C 1138 LEU cc_start: 0.2588 (OUTLIER) cc_final: 0.2249 (pp) outliers start: 71 outliers final: 35 residues processed: 549 average time/residue: 0.3969 time to fit residues: 360.5519 Evaluate side-chains 477 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 439 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain B residue 259 ILE 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 381 SER Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain B residue 1037 ASN Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 353 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 507 ASN Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1065 VAL 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: 3.9990 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 312 optimal weight: 50.0000 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN B 525 HIS B 543 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 1.8373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32540 Z= 0.186 Angle : 0.617 11.574 44108 Z= 0.315 Chirality : 0.042 0.251 5144 Planarity : 0.004 0.056 5616 Dihedral : 4.648 22.024 4440 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.06 % Allowed : 19.34 % Favored : 78.61 % 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: -1.11 (0.13), residues: 4108 helix: -0.00 (0.11), residues: 2427 sheet: 1.87 (0.79), residues: 55 loop : -1.93 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1091 HIS 0.008 0.001 HIS D 753 PHE 0.043 0.001 PHE A 261 TYR 0.016 0.001 TYR A 355 ARG 0.016 0.001 ARG B1035 *********************** REFINEMENT MACRO_CYCLE 8 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 546 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 477 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6005 (mm-30) cc_final: 0.5505 (mt-10) REVERT: A 241 MET cc_start: 0.4226 (mmt) cc_final: 0.3673 (mtm) REVERT: A 318 MET cc_start: 0.6811 (mmm) cc_final: 0.6052 (mmm) REVERT: A 383 TRP cc_start: 0.8225 (m100) cc_final: 0.7688 (m100) REVERT: A 458 ARG cc_start: 0.8373 (ptt180) cc_final: 0.8034 (ptt-90) REVERT: A 507 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8846 (p0) REVERT: A 844 MET cc_start: 0.7353 (mmt) cc_final: 0.6943 (ppp) REVERT: A 910 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 1045 MET cc_start: 0.7983 (mmm) cc_final: 0.7770 (mmm) REVERT: A 1131 MET cc_start: 0.3895 (ptm) cc_final: 0.3207 (ptp) REVERT: D 175 MET cc_start: 0.6154 (ptp) cc_final: 0.5654 (ptm) REVERT: D 235 ASN cc_start: 0.7833 (m110) cc_final: 0.7516 (m-40) REVERT: D 321 MET cc_start: 0.7234 (tpp) cc_final: 0.6916 (mmm) REVERT: D 392 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7383 (tt) REVERT: D 845 ARG cc_start: 0.7149 (mtp-110) cc_final: 0.5996 (mtt-85) REVERT: D 864 LEU cc_start: 0.8356 (mm) cc_final: 0.7941 (mp) REVERT: D 1067 LYS cc_start: 0.7385 (tppt) cc_final: 0.7059 (mmtp) REVERT: D 1131 MET cc_start: 0.5771 (ttt) cc_final: 0.5246 (tpt) REVERT: B 318 MET cc_start: 0.8768 (mpp) cc_final: 0.8484 (mtt) REVERT: B 321 MET cc_start: 0.7239 (mmt) cc_final: 0.6995 (mmt) REVERT: B 678 LYS cc_start: 0.8314 (tttp) cc_final: 0.8109 (tmtt) REVERT: B 764 LEU cc_start: 0.7872 (tp) cc_final: 0.7587 (tp) REVERT: B 1032 GLU cc_start: 0.7867 (tp30) cc_final: 0.7601 (tp30) REVERT: C 154 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7621 (tp30) REVERT: C 355 TYR cc_start: 0.6971 (t80) cc_final: 0.6762 (t80) REVERT: C 450 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: C 746 ASN cc_start: 0.8233 (t0) cc_final: 0.7986 (m-40) REVERT: C 844 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: C 984 ASP cc_start: 0.8279 (t0) cc_final: 0.7992 (t0) REVERT: C 996 ASP cc_start: 0.7368 (t70) cc_final: 0.7106 (t0) outliers start: 69 outliers final: 47 residues processed: 513 average time/residue: 0.3798 time to fit residues: 324.4072 Evaluate side-chains 471 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 419 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 590 ASN Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 1054 GLU Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 259 ILE 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 429 THR Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 353 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 466 LEU Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 347 optimal weight: 0.9980 chunk 370 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 290 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 349 optimal weight: 8.9990 chunk 368 optimal weight: 0.0270 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 295 GLN A 491 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 267 ASN D 309 GLN D 349 HIS ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 HIS ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN D 991 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS C 408 HIS C 570 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 1.9227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32540 Z= 0.208 Angle : 0.623 12.374 44108 Z= 0.317 Chirality : 0.042 0.187 5144 Planarity : 0.004 0.055 5616 Dihedral : 4.700 23.885 4440 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.85 % Allowed : 19.79 % Favored : 78.37 % 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: -1.08 (0.13), residues: 4108 helix: 0.01 (0.11), residues: 2469 sheet: 2.03 (0.79), residues: 55 loop : -1.95 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 247 HIS 0.011 0.001 HIS D 593 PHE 0.028 0.001 PHE B 261 TYR 0.019 0.001 TYR A 857 ARG 0.007 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 9 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 559 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 497 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7429 (mmm) cc_final: 0.7019 (mmm) REVERT: A 363 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6933 (mp) REVERT: A 458 ARG cc_start: 0.8384 (ptt180) cc_final: 0.8105 (ptt-90) REVERT: A 507 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.8871 (p0) REVERT: A 677 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7384 (ttpt) REVERT: A 910 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8910 (tt) REVERT: A 1053 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 1131 MET cc_start: 0.3788 (ptm) cc_final: 0.3157 (ptp) REVERT: D 175 MET cc_start: 0.6344 (ptp) cc_final: 0.5705 (ptm) REVERT: D 321 MET cc_start: 0.7819 (tpp) cc_final: 0.7551 (mmm) REVERT: D 392 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7715 (tt) REVERT: D 450 TYR cc_start: 0.7377 (m-10) cc_final: 0.6948 (m-10) REVERT: D 845 ARG cc_start: 0.7194 (mtp-110) cc_final: 0.6065 (mtt-85) REVERT: D 989 TYR cc_start: 0.8298 (m-80) cc_final: 0.8036 (m-80) REVERT: D 1131 MET cc_start: 0.5847 (ttt) cc_final: 0.5296 (tpt) REVERT: B 156 LYS cc_start: 0.7415 (mtpm) cc_final: 0.7051 (mppt) REVERT: B 321 MET cc_start: 0.7381 (mmt) cc_final: 0.7176 (mmt) REVERT: B 355 TYR cc_start: 0.7505 (t80) cc_final: 0.7271 (t80) REVERT: B 388 LEU cc_start: 0.8494 (mp) cc_final: 0.8173 (tt) REVERT: B 501 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7820 (ptmt) REVERT: B 764 LEU cc_start: 0.7945 (tp) cc_final: 0.7683 (tp) REVERT: B 1032 GLU cc_start: 0.7727 (tp30) cc_final: 0.7454 (tp30) REVERT: B 1086 PHE cc_start: 0.8491 (t80) cc_final: 0.8283 (t80) REVERT: C 295 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: C 450 TYR cc_start: 0.8577 (m-10) cc_final: 0.8120 (m-80) REVERT: C 620 TYR cc_start: 0.8207 (t80) cc_final: 0.7972 (t80) REVERT: C 746 ASN cc_start: 0.8337 (t0) cc_final: 0.8134 (m-40) REVERT: C 984 ASP cc_start: 0.8293 (t0) cc_final: 0.8049 (t0) REVERT: C 996 ASP cc_start: 0.7416 (t70) cc_final: 0.7146 (t0) outliers start: 62 outliers final: 41 residues processed: 531 average time/residue: 0.3859 time to fit residues: 339.5559 Evaluate side-chains 474 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 427 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 1054 GLU 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 429 THR Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 979 MET Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 7.9990 chunk 391 optimal weight: 0.5980 chunk 238 optimal weight: 0.0370 chunk 185 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 GLN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 962 HIS D 991 ASN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 530 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 1.9454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 32540 Z= 0.156 Angle : 0.587 10.413 44108 Z= 0.297 Chirality : 0.040 0.197 5144 Planarity : 0.004 0.056 5616 Dihedral : 4.454 21.279 4440 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.43 % Allowed : 20.92 % Favored : 77.65 % 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: -0.87 (0.13), residues: 4108 helix: 0.20 (0.11), residues: 2494 sheet: 2.17 (0.81), residues: 55 loop : -1.94 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C1061 HIS 0.009 0.001 HIS A 370 PHE 0.026 0.001 PHE B 261 TYR 0.021 0.001 TYR D 355 ARG 0.007 0.000 ARG D 453 ********************** REFINEMENT MACRO_CYCLE 10 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 512 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 464 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7096 (mp) REVERT: A 458 ARG cc_start: 0.8370 (ptt180) cc_final: 0.8108 (ptt-90) REVERT: A 507 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8904 (p0) REVERT: A 677 LYS cc_start: 0.7642 (mtpt) cc_final: 0.7406 (ttpt) REVERT: A 730 GLU cc_start: 0.7992 (pt0) cc_final: 0.7780 (pt0) REVERT: A 1131 MET cc_start: 0.3266 (ptm) cc_final: 0.2659 (ptp) REVERT: D 175 MET cc_start: 0.6323 (ptp) cc_final: 0.5682 (ptm) REVERT: D 321 MET cc_start: 0.7918 (tpp) cc_final: 0.7429 (mmm) REVERT: D 392 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7642 (tt) REVERT: D 842 ASN cc_start: 0.7705 (t0) cc_final: 0.7358 (t0) REVERT: D 845 ARG cc_start: 0.7111 (mtp-110) cc_final: 0.6168 (mtt180) REVERT: D 864 LEU cc_start: 0.8425 (mt) cc_final: 0.8162 (tp) REVERT: D 989 TYR cc_start: 0.8331 (m-80) cc_final: 0.7957 (m-80) REVERT: D 1131 MET cc_start: 0.5825 (ttt) cc_final: 0.5387 (tpt) REVERT: D 1134 GLN cc_start: 0.5210 (tp-100) cc_final: 0.4981 (tp-100) REVERT: B 156 LYS cc_start: 0.7489 (mtpm) cc_final: 0.7096 (mppt) REVERT: B 324 MET cc_start: 0.7321 (mmt) cc_final: 0.7095 (mpp) REVERT: B 355 TYR cc_start: 0.7488 (t80) cc_final: 0.7241 (t80) REVERT: B 388 LEU cc_start: 0.8389 (mp) cc_final: 0.8080 (tt) REVERT: B 501 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7809 (ptmt) REVERT: B 1032 GLU cc_start: 0.7794 (tp30) cc_final: 0.7502 (tp30) REVERT: B 1131 MET cc_start: 0.5765 (mmm) cc_final: 0.4039 (ptp) REVERT: C 245 PHE cc_start: 0.7822 (m-10) cc_final: 0.7572 (m-10) REVERT: C 450 TYR cc_start: 0.8504 (m-10) cc_final: 0.8125 (m-80) REVERT: C 833 VAL cc_start: 0.8996 (p) cc_final: 0.8700 (m) REVERT: C 842 ASN cc_start: 0.8543 (m-40) cc_final: 0.8329 (t0) REVERT: C 872 SER cc_start: 0.9057 (m) cc_final: 0.8762 (p) REVERT: C 984 ASP cc_start: 0.8210 (t0) cc_final: 0.7890 (t0) REVERT: C 989 TYR cc_start: 0.8186 (m-80) cc_final: 0.7841 (m-80) REVERT: C 996 ASP cc_start: 0.7344 (t70) cc_final: 0.7056 (t0) outliers start: 48 outliers final: 34 residues processed: 490 average time/residue: 0.3974 time to fit residues: 326.3509 Evaluate side-chains 459 residues out of total 3616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 422 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 1054 GLU 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 429 THR Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 856 HIS Chi-restraints excluded: chain B residue 982 GLU Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 507 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 599 MET Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 982 GLU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 0.0170 chunk 348 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 296 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 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.162659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106897 restraints weight = 44232.376| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.92 r_work: 0.3156 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 1.9655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 32540 Z= 0.152 Angle : 0.581 11.405 44108 Z= 0.294 Chirality : 0.040 0.188 5144 Planarity : 0.004 0.055 5616 Dihedral : 4.313 20.314 4440 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.28 % Allowed : 21.25 % Favored : 77.47 % 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: -0.59 (0.13), residues: 4108 helix: 0.40 (0.11), residues: 2483 sheet: 4.22 (0.72), residues: 40 loop : -1.78 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 383 HIS 0.007 0.001 HIS A 370 PHE 0.025 0.001 PHE B 261 TYR 0.016 0.001 TYR C 748 ARG 0.008 0.000 ARG D 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7954.84 seconds wall clock time: 143 minutes 38.94 seconds (8618.94 seconds total)