Starting phenix.real_space_refine on Mon Mar 25 06:20:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr8_34963/03_2024/8hr8_34963_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 216 5.16 5 C 29577 2.51 5 N 8023 2.21 5 O 8857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "D GLU 789": "OE1" <-> "OE2" Residue "E GLU 789": "OE1" <-> "OE2" Residue "E GLU 800": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "F GLU 529": "OE1" <-> "OE2" Residue "F GLU 789": "OE1" <-> "OE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 471": "OE1" <-> "OE2" Residue "G GLU 534": "OE1" <-> "OE2" Residue "G GLU 800": "OE1" <-> "OE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 277": "OE1" <-> "OE2" Residue "H GLU 714": "OE1" <-> "OE2" Residue "H GLU 790": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "C" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6655 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "D" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6654 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6633 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 809} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6658 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "G" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6617 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 23, 'TRANS': 806} Chain breaks: 5 Chain: "H" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6653 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.27, per 1000 atoms: 0.46 Number of scatterers: 46688 At special positions: 0 Unit cell: (166.4, 179.92, 164.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 P 15 15.00 O 8857 8.00 N 8023 7.00 C 29577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.44 Conformation dependent library (CDL) restraints added in 8.8 seconds 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 267 helices and 20 sheets defined 54.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.67 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.534A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 121 through 139 removed outlier: 3.821A pdb=" N GLY A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.633A pdb=" N SER A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.941A pdb=" N GLU A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.502A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.509A pdb=" N GLN A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.593A pdb=" N GLY A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.630A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.577A pdb=" N MET A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 413 through 432 removed outlier: 5.384A pdb=" N SER A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.628A pdb=" N PHE A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.159A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 504 through 514 removed outlier: 3.953A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 527 through 539 Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 598 through 606 Processing helix chain 'A' and resid 622 through 633 Processing helix chain 'A' and resid 639 through 646 Processing helix chain 'A' and resid 705 through 726 removed outlier: 3.574A pdb=" N ASN A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLY A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.565A pdb=" N ASN A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 792 Processing helix chain 'A' and resid 815 through 830 removed outlier: 3.770A pdb=" N LYS A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 No H-bonds generated for 'chain 'A' and resid 835 through 838' Processing helix chain 'A' and resid 840 through 846 removed outlier: 3.558A pdb=" N LEU A 844 " --> pdb=" O PRO A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Proline residue: A 853 - end of helix No H-bonds generated for 'chain 'A' and resid 849 through 855' Processing helix chain 'A' and resid 865 through 882 removed outlier: 3.988A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 896 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.669A pdb=" N ILE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 121 through 139 removed outlier: 3.932A pdb=" N LYS C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 166 removed outlier: 3.947A pdb=" N LYS C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 180 removed outlier: 4.123A pdb=" N SER C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.615A pdb=" N GLU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 removed outlier: 3.674A pdb=" N ASP C 232 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 235 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 240 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.527A pdb=" N ASN C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.788A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.805A pdb=" N MET C 366 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 394 removed outlier: 3.773A pdb=" N LYS C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.969A pdb=" N GLY C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 443 through 457 removed outlier: 3.834A pdb=" N CYS C 447 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.706A pdb=" N SER C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 505 through 513 removed outlier: 3.640A pdb=" N SER C 509 " --> pdb=" O CYS C 505 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 511 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 512 " --> pdb=" O VAL C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 518 Processing helix chain 'C' and resid 528 through 538 removed outlier: 3.651A pdb=" N ILE C 532 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 536 " --> pdb=" O ILE C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 4.267A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 558 " --> pdb=" O CYS C 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 559 " --> pdb=" O CYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 598 through 607 Processing helix chain 'C' and resid 622 through 632 removed outlier: 3.514A pdb=" N ASP C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 649 removed outlier: 4.432A pdb=" N ASN C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 726 removed outlier: 3.576A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 715 " --> pdb=" O THR C 711 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 751 removed outlier: 4.059A pdb=" N GLY C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 747 " --> pdb=" O PHE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 788 removed outlier: 3.873A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 831 removed outlier: 3.534A pdb=" N ILE C 823 " --> pdb=" O LYS C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 838 No H-bonds generated for 'chain 'C' and resid 835 through 838' Processing helix chain 'C' and resid 840 through 846 Processing helix chain 'C' and resid 849 through 855 Proline residue: C 853 - end of helix No H-bonds generated for 'chain 'C' and resid 849 through 855' Processing helix chain 'C' and resid 867 through 882 removed outlier: 3.561A pdb=" N GLU C 871 " --> pdb=" O ALA C 867 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 896 removed outlier: 3.504A pdb=" N ASP C 893 " --> pdb=" O ASP C 889 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR C 894 " --> pdb=" O GLU C 890 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C 895 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 896 " --> pdb=" O TRP C 892 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 889 through 896' Processing helix chain 'D' and resid 35 through 50 removed outlier: 3.551A pdb=" N SER D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 121 through 139 removed outlier: 3.537A pdb=" N LYS D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 168 removed outlier: 3.875A pdb=" N ARG D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N HIS D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.712A pdb=" N PHE D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 301 removed outlier: 3.505A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 344 through 355 removed outlier: 3.533A pdb=" N GLU D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 removed outlier: 3.582A pdb=" N TYR D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 394 removed outlier: 4.360A pdb=" N LYS D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 432 removed outlier: 3.638A pdb=" N SER D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 429 " --> pdb=" O MET D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 457 removed outlier: 3.546A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.200A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 506 through 514 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 527 through 539 Processing helix chain 'D' and resid 547 through 558 removed outlier: 3.736A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 601 through 607 Processing helix chain 'D' and resid 622 through 633 Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.740A pdb=" N LYS D 648 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 651 " --> pdb=" O ASN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 726 removed outlier: 3.605A pdb=" N ASN D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE D 725 " --> pdb=" O ASN D 721 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 754 removed outlier: 4.056A pdb=" N LYS D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR D 754 " --> pdb=" O ASP D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 792 removed outlier: 3.798A pdb=" N VAL D 779 " --> pdb=" O MET D 775 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 830 removed outlier: 3.575A pdb=" N LYS D 820 " --> pdb=" O GLU D 816 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 838 No H-bonds generated for 'chain 'D' and resid 835 through 838' Processing helix chain 'D' and resid 840 through 846 Processing helix chain 'D' and resid 852 through 855 No H-bonds generated for 'chain 'D' and resid 852 through 855' Processing helix chain 'D' and resid 866 through 882 removed outlier: 3.818A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 896 removed outlier: 3.548A pdb=" N LEU D 895 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 50 removed outlier: 4.246A pdb=" N SER E 36 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA E 50 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 121 through 139 removed outlier: 3.513A pdb=" N GLY E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 167 removed outlier: 3.579A pdb=" N LYS E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.733A pdb=" N SER E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 210 Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.756A pdb=" N TRP E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP E 232 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 235 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG E 238 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 239 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.554A pdb=" N GLN E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 301 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 344 through 355 Processing helix chain 'E' and resid 362 through 372 removed outlier: 4.153A pdb=" N TYR E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 394 removed outlier: 4.130A pdb=" N LYS E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.533A pdb=" N SER E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 457 removed outlier: 3.588A pdb=" N LYS E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 473 through 489 removed outlier: 3.665A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 502 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 529 through 539 Processing helix chain 'E' and resid 547 through 560 Processing helix chain 'E' and resid 564 through 566 No H-bonds generated for 'chain 'E' and resid 564 through 566' Processing helix chain 'E' and resid 593 through 595 No H-bonds generated for 'chain 'E' and resid 593 through 595' Processing helix chain 'E' and resid 598 through 605 Processing helix chain 'E' and resid 622 through 632 Processing helix chain 'E' and resid 639 through 648 removed outlier: 3.990A pdb=" N ASN E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 648 " --> pdb=" O ASN E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 726 removed outlier: 4.012A pdb=" N GLU E 722 " --> pdb=" O LYS E 718 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE E 725 " --> pdb=" O ASN E 721 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY E 726 " --> pdb=" O GLU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 751 Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.851A pdb=" N MET E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 790 " --> pdb=" O VAL E 786 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 830 removed outlier: 3.692A pdb=" N LYS E 820 " --> pdb=" O GLU E 816 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 838 No H-bonds generated for 'chain 'E' and resid 835 through 838' Processing helix chain 'E' and resid 840 through 846 removed outlier: 3.703A pdb=" N LEU E 845 " --> pdb=" O LEU E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 855 No H-bonds generated for 'chain 'E' and resid 852 through 855' Processing helix chain 'E' and resid 867 through 881 removed outlier: 3.914A pdb=" N THR E 872 " --> pdb=" O ASN E 869 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN E 875 " --> pdb=" O THR E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 895 removed outlier: 3.654A pdb=" N LEU E 895 " --> pdb=" O GLU E 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 919 No H-bonds generated for 'chain 'E' and resid 916 through 919' Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.547A pdb=" N ILE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 121 through 139 removed outlier: 3.516A pdb=" N MET F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 162 removed outlier: 3.783A pdb=" N GLN F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 174 through 180 removed outlier: 3.518A pdb=" N SER F 178 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 211 Processing helix chain 'F' and resid 227 through 240 removed outlier: 3.865A pdb=" N TRP F 231 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 235 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER F 236 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE F 240 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.793A pdb=" N GLN F 259 " --> pdb=" O ARG F 255 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU F 267 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.605A pdb=" N GLU F 285 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN F 296 " --> pdb=" O HIS F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 362 through 372 removed outlier: 3.508A pdb=" N TYR F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 394 Processing helix chain 'F' and resid 413 through 432 removed outlier: 3.531A pdb=" N SER F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER F 427 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 457 removed outlier: 3.710A pdb=" N LYS F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP F 449 " --> pdb=" O SER F 445 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 465 No H-bonds generated for 'chain 'F' and resid 463 through 465' Processing helix chain 'F' and resid 473 through 489 removed outlier: 3.817A pdb=" N ILE F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'F' and resid 505 through 512 removed outlier: 3.715A pdb=" N SER F 509 " --> pdb=" O CYS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 527 through 539 Processing helix chain 'F' and resid 547 through 559 Processing helix chain 'F' and resid 564 through 566 No H-bonds generated for 'chain 'F' and resid 564 through 566' Processing helix chain 'F' and resid 593 through 595 No H-bonds generated for 'chain 'F' and resid 593 through 595' Processing helix chain 'F' and resid 599 through 607 Processing helix chain 'F' and resid 622 through 632 Processing helix chain 'F' and resid 639 through 647 removed outlier: 3.593A pdb=" N ASN F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 645 " --> pdb=" O ALA F 641 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN F 647 " --> pdb=" O THR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 726 removed outlier: 3.688A pdb=" N GLU F 722 " --> pdb=" O LYS F 718 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE F 725 " --> pdb=" O ASN F 721 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY F 726 " --> pdb=" O GLU F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 731 through 751 Processing helix chain 'F' and resid 758 through 760 No H-bonds generated for 'chain 'F' and resid 758 through 760' Processing helix chain 'F' and resid 771 through 793 removed outlier: 3.546A pdb=" N PHE F 782 " --> pdb=" O ASN F 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 789 " --> pdb=" O ALA F 785 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER F 791 " --> pdb=" O LEU F 787 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 792 " --> pdb=" O VAL F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 831 removed outlier: 3.717A pdb=" N LYS F 820 " --> pdb=" O GLU F 816 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 825 " --> pdb=" O ILE F 821 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU F 826 " --> pdb=" O LYS F 822 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 829 " --> pdb=" O GLY F 825 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 846 Processing helix chain 'F' and resid 849 through 855 Proline residue: F 853 - end of helix No H-bonds generated for 'chain 'F' and resid 849 through 855' Processing helix chain 'F' and resid 867 through 882 Processing helix chain 'F' and resid 889 through 896 removed outlier: 3.510A pdb=" N TYR F 894 " --> pdb=" O GLU F 890 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 47 removed outlier: 3.506A pdb=" N ASP G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 43 " --> pdb=" O ASP G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 121 through 139 removed outlier: 4.082A pdb=" N GLY G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 168 removed outlier: 3.535A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS G 165 " --> pdb=" O GLN G 161 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.686A pdb=" N LEU G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 229 through 240 Processing helix chain 'G' and resid 254 through 264 Processing helix chain 'G' and resid 271 through 276 removed outlier: 3.520A pdb=" N GLU G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 301 Processing helix chain 'G' and resid 313 through 317 Processing helix chain 'G' and resid 344 through 353 Processing helix chain 'G' and resid 362 through 372 Processing helix chain 'G' and resid 376 through 394 removed outlier: 3.801A pdb=" N TYR G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 432 removed outlier: 5.082A pdb=" N SER G 427 " --> pdb=" O GLY G 423 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER G 428 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 457 removed outlier: 3.650A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE G 451 " --> pdb=" O CYS G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 465 No H-bonds generated for 'chain 'G' and resid 463 through 465' Processing helix chain 'G' and resid 473 through 489 removed outlier: 3.649A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'G' and resid 505 through 514 Processing helix chain 'G' and resid 527 through 539 removed outlier: 3.536A pdb=" N SER G 533 " --> pdb=" O GLU G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 560 removed outlier: 3.571A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G 557 " --> pdb=" O ARG G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 564 through 566 No H-bonds generated for 'chain 'G' and resid 564 through 566' Processing helix chain 'G' and resid 593 through 595 No H-bonds generated for 'chain 'G' and resid 593 through 595' Processing helix chain 'G' and resid 601 through 607 Processing helix chain 'G' and resid 622 through 632 Processing helix chain 'G' and resid 639 through 650 removed outlier: 3.555A pdb=" N LYS G 648 " --> pdb=" O ASN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 726 removed outlier: 3.719A pdb=" N THR G 711 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 713 " --> pdb=" O ALA G 709 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN G 715 " --> pdb=" O THR G 711 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP G 716 " --> pdb=" O LYS G 712 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU G 722 " --> pdb=" O LYS G 718 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE G 725 " --> pdb=" O ASN G 721 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY G 726 " --> pdb=" O GLU G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 731 through 751 removed outlier: 3.638A pdb=" N LEU G 745 " --> pdb=" O PHE G 741 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN G 746 " --> pdb=" O TYR G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 771 through 793 removed outlier: 3.653A pdb=" N MET G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 776 " --> pdb=" O ALA G 772 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER G 791 " --> pdb=" O LEU G 787 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU G 792 " --> pdb=" O VAL G 788 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR G 793 " --> pdb=" O GLU G 789 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 830 removed outlier: 3.617A pdb=" N LYS G 819 " --> pdb=" O ASP G 815 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS G 820 " --> pdb=" O GLU G 816 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 821 " --> pdb=" O PHE G 817 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 823 " --> pdb=" O LYS G 819 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 829 " --> pdb=" O GLY G 825 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 830 " --> pdb=" O GLU G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 835 through 838 No H-bonds generated for 'chain 'G' and resid 835 through 838' Processing helix chain 'G' and resid 840 through 846 Processing helix chain 'G' and resid 849 through 855 Proline residue: G 853 - end of helix No H-bonds generated for 'chain 'G' and resid 849 through 855' Processing helix chain 'G' and resid 865 through 882 removed outlier: 4.619A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE G 874 " --> pdb=" O LYS G 870 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS G 876 " --> pdb=" O THR G 872 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE G 878 " --> pdb=" O PHE G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 889 through 896 Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.506A pdb=" N ASP H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'H' and resid 121 through 138 Processing helix chain 'H' and resid 143 through 168 removed outlier: 3.738A pdb=" N LYS H 148 " --> pdb=" O ASN H 144 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N HIS H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 179 removed outlier: 3.815A pdb=" N SER H 178 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.597A pdb=" N GLU H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'H' and resid 254 through 268 removed outlier: 3.517A pdb=" N ASN H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 280 through 301 Processing helix chain 'H' and resid 313 through 317 Processing helix chain 'H' and resid 344 through 353 Processing helix chain 'H' and resid 362 through 373 removed outlier: 3.557A pdb=" N GLU H 370 " --> pdb=" O MET H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 392 removed outlier: 4.515A pdb=" N THR H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 389 " --> pdb=" O ASP H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 424 removed outlier: 3.981A pdb=" N GLY H 423 " --> pdb=" O ASN H 419 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 432 removed outlier: 3.574A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 457 removed outlier: 3.703A pdb=" N ASP H 449 " --> pdb=" O SER H 445 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 465 No H-bonds generated for 'chain 'H' and resid 463 through 465' Processing helix chain 'H' and resid 473 through 489 removed outlier: 3.589A pdb=" N ILE H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN H 489 " --> pdb=" O GLN H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 502 Processing helix chain 'H' and resid 504 through 514 removed outlier: 4.215A pdb=" N VAL H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 509 " --> pdb=" O CYS H 505 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 513 " --> pdb=" O SER H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 527 through 539 Processing helix chain 'H' and resid 547 through 559 removed outlier: 4.337A pdb=" N ALA H 556 " --> pdb=" O ASN H 552 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 557 " --> pdb=" O ARG H 553 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 558 " --> pdb=" O CYS H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 566 No H-bonds generated for 'chain 'H' and resid 564 through 566' Processing helix chain 'H' and resid 598 through 607 Processing helix chain 'H' and resid 622 through 632 Processing helix chain 'H' and resid 639 through 650 removed outlier: 3.584A pdb=" N ASN H 644 " --> pdb=" O SER H 640 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA H 645 " --> pdb=" O ALA H 641 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 648 " --> pdb=" O ASN H 644 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 649 " --> pdb=" O ALA H 645 " (cutoff:3.500A) Processing helix chain 'H' and resid 706 through 726 removed outlier: 4.293A pdb=" N THR H 711 " --> pdb=" O SER H 707 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN H 719 " --> pdb=" O GLN H 715 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU H 722 " --> pdb=" O LYS H 718 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE H 725 " --> pdb=" O ASN H 721 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY H 726 " --> pdb=" O GLU H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 731 through 754 removed outlier: 3.500A pdb=" N ASN H 746 " --> pdb=" O TYR H 742 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN H 747 " --> pdb=" O PHE H 743 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS H 753 " --> pdb=" O ALA H 749 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR H 754 " --> pdb=" O ASP H 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 771 through 793 removed outlier: 3.723A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER H 791 " --> pdb=" O LEU H 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 830 removed outlier: 3.519A pdb=" N LYS H 820 " --> pdb=" O GLU H 816 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 821 " --> pdb=" O PHE H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 840 through 847 Processing helix chain 'H' and resid 849 through 855 Proline residue: H 853 - end of helix No H-bonds generated for 'chain 'H' and resid 849 through 855' Processing helix chain 'H' and resid 865 through 882 removed outlier: 4.139A pdb=" N ASN H 869 " --> pdb=" O VAL H 865 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS H 870 " --> pdb=" O LYS H 866 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 880 " --> pdb=" O LYS H 876 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE H 881 " --> pdb=" O LEU H 877 " (cutoff:3.500A) Processing helix chain 'H' and resid 889 through 896 removed outlier: 4.378A pdb=" N TYR H 894 " --> pdb=" O GLU H 890 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 307 through 309 removed outlier: 8.291A pdb=" N ILE A 308 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 73 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE A 72 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 248 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL A 74 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 250 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE A 220 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.255A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= E, first strand: chain 'C' and resid 307 through 309 removed outlier: 8.060A pdb=" N ILE C 308 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE C 73 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE C 72 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 248 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL C 74 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 250 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 573 through 576 removed outlier: 3.631A pdb=" N ASP C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 619 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 609 " --> pdb=" O PHE C 619 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 14 through 17 Processing sheet with id= H, first strand: chain 'D' and resid 70 through 74 Processing sheet with id= I, first strand: chain 'D' and resid 616 through 620 Processing sheet with id= J, first strand: chain 'E' and resid 14 through 17 Processing sheet with id= K, first strand: chain 'E' and resid 307 through 309 removed outlier: 7.568A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN E 70 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 252 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 573 through 576 removed outlier: 4.381A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 612 " --> pdb=" O CYS E 655 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 14 through 17 Processing sheet with id= N, first strand: chain 'F' and resid 71 through 75 removed outlier: 8.135A pdb=" N PHE F 72 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL F 248 " --> pdb=" O PHE F 72 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL F 74 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA F 250 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE F 216 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL F 249 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE F 218 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR F 251 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE F 220 " --> pdb=" O THR F 251 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 573 through 575 Processing sheet with id= P, first strand: chain 'G' and resid 14 through 17 Processing sheet with id= Q, first strand: chain 'G' and resid 307 through 309 removed outlier: 8.448A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE G 72 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL G 248 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL G 74 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA G 250 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE G 220 " --> pdb=" O THR G 251 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 610 through 612 removed outlier: 3.589A pdb=" N CYS G 655 " --> pdb=" O THR G 610 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 307 through 309 removed outlier: 8.062A pdb=" N ILE H 308 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE H 73 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE H 72 " --> pdb=" O LEU H 246 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL H 248 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL H 74 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA H 250 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE H 216 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL H 249 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE H 218 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N THR H 251 " --> pdb=" O ILE H 218 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE H 220 " --> pdb=" O THR H 251 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 573 through 576 removed outlier: 4.216A pdb=" N ASP H 618 " --> pdb=" O LEU H 576 " (cutoff:3.500A) 1923 hydrogen bonds defined for protein. 5568 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: 16.22 Time building geometry restraints manager: 19.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13957 1.34 - 1.46: 7499 1.46 - 1.58: 25694 1.58 - 1.70: 25 1.70 - 1.82: 328 Bond restraints: 47503 Sorted by residual: bond pdb=" N THR G 225 " pdb=" CA THR G 225 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.31e+00 bond pdb=" N ASP H 169 " pdb=" CA ASP H 169 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" N TYR G 172 " pdb=" CA TYR G 172 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.32e+00 bond pdb=" N ILE G 223 " pdb=" CA ILE G 223 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.20e+00 bond pdb=" N ASN A 144 " pdb=" CA ASN A 144 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.16e-02 7.43e+03 6.17e+00 ... (remaining 47498 not shown) Histogram of bond angle deviations from ideal: 98.40 - 106.69: 951 106.69 - 114.99: 28952 114.99 - 123.29: 32899 123.29 - 131.58: 1236 131.58 - 139.88: 78 Bond angle restraints: 64116 Sorted by residual: angle pdb=" N ILE D 223 " pdb=" CA ILE D 223 " pdb=" C ILE D 223 " ideal model delta sigma weight residual 111.91 108.15 3.76 8.90e-01 1.26e+00 1.78e+01 angle pdb=" N ILE F 510 " pdb=" CA ILE F 510 " pdb=" C ILE F 510 " ideal model delta sigma weight residual 112.98 108.54 4.44 1.25e+00 6.40e-01 1.26e+01 angle pdb=" C LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 109.85 113.90 -4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" N VAL F 515 " pdb=" CA VAL F 515 " pdb=" C VAL F 515 " ideal model delta sigma weight residual 113.71 110.45 3.26 9.50e-01 1.11e+00 1.18e+01 angle pdb=" N ILE H 339 " pdb=" CA ILE H 339 " pdb=" C ILE H 339 " ideal model delta sigma weight residual 113.20 109.93 3.27 9.60e-01 1.09e+00 1.16e+01 ... (remaining 64111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 25644 17.96 - 35.92: 2664 35.92 - 53.87: 528 53.87 - 71.83: 94 71.83 - 89.79: 53 Dihedral angle restraints: 28983 sinusoidal: 11919 harmonic: 17064 Sorted by residual: dihedral pdb=" C ASP G 224 " pdb=" N ASP G 224 " pdb=" CA ASP G 224 " pdb=" CB ASP G 224 " ideal model delta harmonic sigma weight residual -122.60 -133.43 10.83 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" CA PHE G 227 " pdb=" C PHE G 227 " pdb=" N ASP G 228 " pdb=" CA ASP G 228 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR D 225 " pdb=" C THR D 225 " pdb=" N GLN D 226 " pdb=" CA GLN D 226 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 28980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 6690 0.068 - 0.135: 504 0.135 - 0.203: 11 0.203 - 0.271: 1 0.271 - 0.338: 1 Chirality restraints: 7207 Sorted by residual: chirality pdb=" CA ASP G 224 " pdb=" N ASP G 224 " pdb=" C ASP G 224 " pdb=" CB ASP G 224 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ILE G 223 " pdb=" N ILE G 223 " pdb=" C ILE G 223 " pdb=" CB ILE G 223 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE H 104 " pdb=" CA ILE H 104 " pdb=" CG1 ILE H 104 " pdb=" CG2 ILE H 104 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 7204 not shown) Planarity restraints: 8202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 223 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ILE G 223 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE G 223 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP G 224 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 148 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C LYS A 148 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS A 148 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 149 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 511 " -0.012 2.00e-02 2.50e+03 1.43e-02 3.58e+00 pdb=" CG PHE C 511 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 511 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 511 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 511 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 511 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 511 " 0.003 2.00e-02 2.50e+03 ... (remaining 8199 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 772 2.67 - 3.23: 46517 3.23 - 3.79: 72722 3.79 - 4.34: 105903 4.34 - 4.90: 169079 Nonbonded interactions: 394993 Sorted by model distance: nonbonded pdb=" OG SER D 888 " pdb=" OE1 GLU D 891 " model vdw 2.116 2.440 nonbonded pdb=" OG1 THR G 83 " pdb=" O2G ATP G1001 " model vdw 2.135 2.440 nonbonded pdb=" OG1 THR F 83 " pdb=" O2G ATP F1001 " model vdw 2.166 2.440 nonbonded pdb=" OD1 ASN H 22 " pdb=" O2' ATP H1001 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR H 140 " pdb=" O ILE H 210 " model vdw 2.174 2.440 ... (remaining 394988 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' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'C' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'D' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'E' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or resid 908 through 932)) selection = (chain 'F' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'G' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 634 or (resid 635 and (name N or name \ CA or name C or name O or name CB )) or resid 636 through 897 or (resid 907 and \ (name N or name CA or name C or name O or name CB )) or resid 909 through 932)) \ selection = (chain 'H' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 208 or (resid 209 and \ (name N or name CA or name C or name O or name CB )) or resid 210 through 394 o \ r resid 412 through 517 or resid 527 through 634 or (resid 635 and (name N or na \ me CA or name C or name O or name CB )) or resid 636 through 663 or resid 706 th \ rough 897 or (resid 907 and (name N or name CA or name C or name O or name CB )) \ or resid 909 through 932)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.040 Extract box with map and model: 7.470 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 114.280 Find NCS groups from input model: 3.840 Set up NCS constraints: 0.160 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47503 Z= 0.152 Angle : 0.457 7.333 64116 Z= 0.253 Chirality : 0.038 0.338 7207 Planarity : 0.003 0.045 8202 Dihedral : 15.293 89.790 17919 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.02 % Allowed : 0.49 % Favored : 99.50 % Cbeta Deviations : 0.02 % 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: -0.57 (0.11), residues: 5755 helix: -0.09 (0.09), residues: 3090 sheet: 0.32 (0.34), residues: 270 loop : -0.69 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 892 HIS 0.010 0.001 HIS F 292 PHE 0.032 0.001 PHE C 511 TYR 0.024 0.001 TYR C 538 ARG 0.009 0.000 ARG F 799 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 635 time to evaluate : 5.363 Fit side-chains revert: symmetry clash REVERT: C 498 LEU cc_start: 0.8527 (mt) cc_final: 0.8257 (mt) REVERT: C 500 MET cc_start: 0.8572 (tpt) cc_final: 0.8086 (tpt) REVERT: D 161 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 336 MET cc_start: 0.7584 (mtp) cc_final: 0.7271 (mtp) REVERT: D 527 LYS cc_start: 0.6498 (pttm) cc_final: 0.6210 (pttm) REVERT: E 328 ILE cc_start: 0.7898 (mt) cc_final: 0.7631 (mt) REVERT: F 161 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7555 (tp-100) REVERT: G 604 MET cc_start: 0.7597 (tpp) cc_final: 0.7091 (tpp) outliers start: 1 outliers final: 1 residues processed: 636 average time/residue: 0.6265 time to fit residues: 645.2486 Evaluate side-chains 506 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 505 time to evaluate : 5.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 490 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 297 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 455 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 527 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN C 489 ASN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 47 ASN D 560 ASN E 156 HIS E 346 GLN E 577 ASN E 644 ASN E 898 ASN F 22 ASN G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 GLN H 549 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 47503 Z= 0.404 Angle : 0.583 7.009 64116 Z= 0.308 Chirality : 0.043 0.184 7207 Planarity : 0.004 0.049 8202 Dihedral : 6.849 89.896 6452 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.01 % Allowed : 8.29 % Favored : 90.70 % 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: -0.44 (0.11), residues: 5755 helix: 0.18 (0.09), residues: 3178 sheet: 0.00 (0.34), residues: 264 loop : -0.86 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 738 HIS 0.007 0.001 HIS E 549 PHE 0.029 0.002 PHE C 511 TYR 0.023 0.002 TYR E 266 ARG 0.008 0.000 ARG G 740 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 508 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 370 GLU cc_start: 0.7590 (tp30) cc_final: 0.7345 (tp30) REVERT: A 832 ASN cc_start: 0.7502 (t0) cc_final: 0.7264 (t0) REVERT: C 500 MET cc_start: 0.8595 (tpt) cc_final: 0.8154 (tpt) REVERT: C 710 ILE cc_start: 0.7394 (mt) cc_final: 0.6451 (pt) REVERT: D 161 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 366 MET cc_start: 0.8350 (ttt) cc_final: 0.8004 (ttm) REVERT: E 718 LYS cc_start: 0.7613 (pttm) cc_final: 0.7068 (ttpp) REVERT: G 604 MET cc_start: 0.7449 (tpp) cc_final: 0.6884 (tpp) outliers start: 52 outliers final: 35 residues processed: 540 average time/residue: 0.6335 time to fit residues: 556.3307 Evaluate side-chains 495 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 459 time to evaluate : 5.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 592 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 733 LEU Chi-restraints excluded: chain H residue 747 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 293 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 439 optimal weight: 0.7980 chunk 359 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 528 optimal weight: 8.9990 chunk 570 optimal weight: 9.9990 chunk 470 optimal weight: 9.9990 chunk 524 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS G 87 ASN G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 GLN H 575 GLN ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47503 Z= 0.190 Angle : 0.469 8.370 64116 Z= 0.250 Chirality : 0.038 0.141 7207 Planarity : 0.003 0.043 8202 Dihedral : 6.622 88.700 6452 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.03 % Allowed : 10.64 % Favored : 88.33 % 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: -0.04 (0.11), residues: 5755 helix: 0.55 (0.09), residues: 3194 sheet: 0.20 (0.35), residues: 254 loop : -0.77 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 738 HIS 0.005 0.001 HIS F 292 PHE 0.017 0.001 PHE C 227 TYR 0.029 0.001 TYR C 535 ARG 0.005 0.000 ARG D 807 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 535 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 THR cc_start: 0.9079 (p) cc_final: 0.8843 (p) REVERT: A 291 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 832 ASN cc_start: 0.7443 (t0) cc_final: 0.7176 (t0) REVERT: D 161 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 366 MET cc_start: 0.8244 (ttt) cc_final: 0.7894 (ttm) REVERT: E 309 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6805 (mp-120) REVERT: E 604 MET cc_start: 0.8059 (tpp) cc_final: 0.7710 (tpt) REVERT: E 608 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8003 (mm) REVERT: G 289 MET cc_start: 0.7709 (tpp) cc_final: 0.7333 (tpt) REVERT: G 604 MET cc_start: 0.7438 (tpp) cc_final: 0.6972 (tpp) REVERT: H 224 ASP cc_start: 0.7162 (m-30) cc_final: 0.6933 (m-30) REVERT: H 710 ILE cc_start: 0.7687 (tp) cc_final: 0.7225 (mt) outliers start: 53 outliers final: 34 residues processed: 576 average time/residue: 0.6094 time to fit residues: 569.8191 Evaluate side-chains 524 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 487 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 522 optimal weight: 7.9990 chunk 397 optimal weight: 1.9990 chunk 274 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 354 optimal weight: 3.9990 chunk 530 optimal weight: 7.9990 chunk 561 optimal weight: 8.9990 chunk 277 optimal weight: 0.2980 chunk 502 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 552 ASN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 HIS E 70 ASN E 156 HIS F 435 ASN G 337 GLN G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 GLN H 549 HIS H 575 GLN ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 47503 Z= 0.363 Angle : 0.543 8.834 64116 Z= 0.284 Chirality : 0.041 0.150 7207 Planarity : 0.004 0.043 8202 Dihedral : 6.670 88.244 6452 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.86 % Allowed : 12.46 % Favored : 85.67 % 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: -0.14 (0.11), residues: 5755 helix: 0.52 (0.09), residues: 3202 sheet: 0.05 (0.35), residues: 256 loop : -0.89 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 738 HIS 0.007 0.001 HIS H 762 PHE 0.021 0.002 PHE F 227 TYR 0.022 0.002 TYR C 538 ARG 0.005 0.000 ARG F 799 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 501 time to evaluate : 5.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: A 370 GLU cc_start: 0.7564 (tp30) cc_final: 0.7347 (tp30) REVERT: C 464 PHE cc_start: 0.7567 (p90) cc_final: 0.7298 (p90) REVERT: D 161 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 366 MET cc_start: 0.8299 (ttt) cc_final: 0.7851 (ttm) REVERT: D 560 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8223 (t0) REVERT: E 309 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6915 (mp-120) REVERT: E 608 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8056 (mm) REVERT: F 285 GLU cc_start: 0.7730 (tp30) cc_final: 0.7502 (tp30) REVERT: G 436 TYR cc_start: 0.5925 (p90) cc_final: 0.5237 (p90) REVERT: G 500 MET cc_start: 0.7730 (tpt) cc_final: 0.7162 (tpp) REVERT: G 604 MET cc_start: 0.7526 (tpp) cc_final: 0.6929 (tpp) REVERT: G 793 TYR cc_start: 0.7663 (m-80) cc_final: 0.7435 (m-10) REVERT: H 224 ASP cc_start: 0.7249 (m-30) cc_final: 0.6994 (m-30) REVERT: H 425 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.4550 (mmt) REVERT: H 590 LYS cc_start: 0.6980 (ptmm) cc_final: 0.6627 (mttp) REVERT: H 710 ILE cc_start: 0.7791 (tp) cc_final: 0.7150 (mt) outliers start: 96 outliers final: 73 residues processed: 568 average time/residue: 0.6199 time to fit residues: 574.2574 Evaluate side-chains 552 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 474 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 592 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain E residue 930 ASP Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 435 ASN Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 467 optimal weight: 9.9990 chunk 318 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 418 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 479 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 504 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN C 485 GLN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS E 644 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 ASN F 469 GLN G 337 GLN G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 GLN H 165 HIS H 575 GLN ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 47503 Z= 0.159 Angle : 0.452 11.596 64116 Z= 0.240 Chirality : 0.038 0.141 7207 Planarity : 0.003 0.042 8202 Dihedral : 6.434 89.183 6452 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.49 % Allowed : 13.71 % Favored : 84.80 % 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: 0.21 (0.11), residues: 5755 helix: 0.82 (0.09), residues: 3203 sheet: 0.25 (0.35), residues: 254 loop : -0.76 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 738 HIS 0.005 0.001 HIS F 118 PHE 0.027 0.001 PHE D 646 TYR 0.020 0.001 TYR C 538 ARG 0.004 0.000 ARG F 799 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 547 time to evaluate : 5.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 THR cc_start: 0.9056 (p) cc_final: 0.8820 (p) REVERT: A 291 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: A 473 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7736 (tt0) REVERT: C 254 LEU cc_start: 0.9377 (tp) cc_final: 0.9137 (tp) REVERT: C 376 VAL cc_start: 0.5116 (t) cc_final: 0.4881 (p) REVERT: C 464 PHE cc_start: 0.7465 (p90) cc_final: 0.7139 (p90) REVERT: D 366 MET cc_start: 0.8189 (ttt) cc_final: 0.7837 (ttm) REVERT: D 560 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8158 (t0) REVERT: E 309 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6843 (mp-120) REVERT: E 604 MET cc_start: 0.8082 (tpp) cc_final: 0.7726 (tpt) REVERT: E 608 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7972 (mm) REVERT: G 289 MET cc_start: 0.7809 (tpp) cc_final: 0.7378 (tpt) REVERT: G 425 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.6846 (mmt) REVERT: G 436 TYR cc_start: 0.5803 (p90) cc_final: 0.5147 (p90) REVERT: G 500 MET cc_start: 0.7775 (tpt) cc_final: 0.7145 (tpp) REVERT: G 604 MET cc_start: 0.7399 (tpp) cc_final: 0.6895 (tpp) REVERT: H 224 ASP cc_start: 0.7220 (m-30) cc_final: 0.6977 (m-30) REVERT: H 258 SER cc_start: 0.8687 (p) cc_final: 0.8450 (p) REVERT: H 425 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.4445 (mmt) REVERT: H 500 MET cc_start: 0.7606 (tpp) cc_final: 0.7263 (tpp) REVERT: H 710 ILE cc_start: 0.7876 (tp) cc_final: 0.7444 (mt) outliers start: 77 outliers final: 39 residues processed: 602 average time/residue: 0.6014 time to fit residues: 590.3938 Evaluate side-chains 548 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 503 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 539 MET Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 610 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 188 optimal weight: 10.0000 chunk 505 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 329 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 562 optimal weight: 8.9990 chunk 466 optimal weight: 6.9990 chunk 260 optimal weight: 0.0970 chunk 46 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 513 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 47503 Z= 0.335 Angle : 0.524 12.389 64116 Z= 0.273 Chirality : 0.041 0.215 7207 Planarity : 0.004 0.053 8202 Dihedral : 6.503 89.664 6452 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.10 % Allowed : 13.96 % Favored : 83.94 % 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: 0.08 (0.11), residues: 5755 helix: 0.73 (0.09), residues: 3212 sheet: 0.13 (0.35), residues: 256 loop : -0.85 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 892 HIS 0.008 0.001 HIS H 762 PHE 0.021 0.002 PHE G 227 TYR 0.021 0.001 TYR C 538 ARG 0.011 0.000 ARG H 639 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 498 time to evaluate : 5.164 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8272 (t0) REVERT: A 291 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 473 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7667 (tt0) REVERT: A 751 GLN cc_start: 0.7687 (mp10) cc_final: 0.7410 (mp10) REVERT: C 464 PHE cc_start: 0.7563 (p90) cc_final: 0.7263 (p90) REVERT: D 366 MET cc_start: 0.8261 (ttt) cc_final: 0.7827 (ttm) REVERT: D 560 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8228 (t0) REVERT: E 309 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6922 (mp-120) REVERT: E 604 MET cc_start: 0.8085 (tpp) cc_final: 0.7804 (tpt) REVERT: E 608 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8042 (mm) REVERT: E 764 ARG cc_start: 0.6741 (mtp180) cc_final: 0.6176 (mtp85) REVERT: E 775 MET cc_start: 0.7710 (mmm) cc_final: 0.7460 (mmm) REVERT: G 425 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.6902 (mmt) REVERT: G 436 TYR cc_start: 0.6055 (p90) cc_final: 0.5266 (p90) REVERT: G 500 MET cc_start: 0.7900 (tpt) cc_final: 0.7688 (tpt) REVERT: G 604 MET cc_start: 0.7495 (tpp) cc_final: 0.6917 (tpp) REVERT: G 708 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7099 (t70) REVERT: G 802 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7956 (pt) REVERT: H 224 ASP cc_start: 0.7247 (m-30) cc_final: 0.7005 (m-30) REVERT: H 425 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.4528 (mmt) REVERT: H 500 MET cc_start: 0.7680 (tpp) cc_final: 0.7355 (tpp) outliers start: 108 outliers final: 75 residues processed: 572 average time/residue: 0.6181 time to fit residues: 573.8345 Evaluate side-chains 564 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 480 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 592 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain E residue 930 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 541 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 320 optimal weight: 0.0670 chunk 410 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 473 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 chunk 559 optimal weight: 9.9990 chunk 350 optimal weight: 0.3980 chunk 341 optimal weight: 0.9990 chunk 258 optimal weight: 0.6980 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 GLN G 615 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 47503 Z= 0.136 Angle : 0.449 14.176 64116 Z= 0.237 Chirality : 0.038 0.139 7207 Planarity : 0.003 0.053 8202 Dihedral : 6.284 88.478 6452 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.44 % Allowed : 15.07 % Favored : 83.50 % 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: 0.41 (0.11), residues: 5755 helix: 1.01 (0.09), residues: 3187 sheet: 0.42 (0.36), residues: 244 loop : -0.72 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 892 HIS 0.009 0.001 HIS H 762 PHE 0.028 0.001 PHE D 646 TYR 0.021 0.001 TYR C 535 ARG 0.011 0.000 ARG H 639 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 530 time to evaluate : 5.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 473 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7821 (tt0) REVERT: C 51 TYR cc_start: 0.3586 (m-10) cc_final: 0.3361 (m-10) REVERT: C 254 LEU cc_start: 0.9373 (tp) cc_final: 0.9114 (tp) REVERT: C 466 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7947 (mp) REVERT: C 488 GLU cc_start: 0.7101 (tp30) cc_final: 0.6866 (tp30) REVERT: D 332 THR cc_start: 0.8571 (m) cc_final: 0.8350 (p) REVERT: D 366 MET cc_start: 0.8139 (ttt) cc_final: 0.7797 (ttm) REVERT: D 560 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8071 (t0) REVERT: E 309 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6857 (mp-120) REVERT: E 346 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: E 604 MET cc_start: 0.8110 (tpp) cc_final: 0.7737 (tpt) REVERT: E 608 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8023 (mm) REVERT: E 643 THR cc_start: 0.7797 (p) cc_final: 0.7365 (t) REVERT: E 775 MET cc_start: 0.7569 (mmm) cc_final: 0.7339 (mmm) REVERT: G 289 MET cc_start: 0.7849 (tpp) cc_final: 0.7364 (tpt) REVERT: G 342 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7252 (tp) REVERT: G 425 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: G 436 TYR cc_start: 0.5883 (p90) cc_final: 0.5100 (p90) REVERT: G 500 MET cc_start: 0.7884 (tpt) cc_final: 0.7682 (tpt) REVERT: G 604 MET cc_start: 0.7354 (tpp) cc_final: 0.6863 (tpp) REVERT: H 224 ASP cc_start: 0.7227 (m-30) cc_final: 0.6996 (m-30) REVERT: H 258 SER cc_start: 0.8663 (p) cc_final: 0.8416 (p) REVERT: H 425 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.4367 (mmt) REVERT: H 500 MET cc_start: 0.7648 (tpp) cc_final: 0.7280 (tpp) outliers start: 74 outliers final: 52 residues processed: 581 average time/residue: 0.6441 time to fit residues: 609.8350 Evaluate side-chains 561 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 500 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 610 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 346 optimal weight: 0.0170 chunk 223 optimal weight: 1.9990 chunk 334 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 chunk 276 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 440 optimal weight: 2.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47503 Z= 0.184 Angle : 0.457 13.809 64116 Z= 0.240 Chirality : 0.038 0.144 7207 Planarity : 0.003 0.042 8202 Dihedral : 6.199 86.452 6452 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.79 % Allowed : 15.08 % Favored : 83.13 % 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: 0.45 (0.11), residues: 5755 helix: 1.05 (0.09), residues: 3196 sheet: 0.47 (0.37), residues: 244 loop : -0.73 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 892 HIS 0.009 0.001 HIS H 762 PHE 0.016 0.001 PHE C 227 TYR 0.023 0.001 TYR D 538 ARG 0.009 0.000 ARG F 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 509 time to evaluate : 5.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 THR cc_start: 0.9006 (p) cc_final: 0.8765 (p) REVERT: A 291 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 473 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7815 (tt0) REVERT: C 51 TYR cc_start: 0.3645 (m-10) cc_final: 0.3436 (m-10) REVERT: C 254 LEU cc_start: 0.9381 (tp) cc_final: 0.9128 (tp) REVERT: D 560 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8091 (t0) REVERT: E 309 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6865 (mp-120) REVERT: E 346 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: E 604 MET cc_start: 0.8126 (tpp) cc_final: 0.7769 (tpt) REVERT: E 608 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 643 THR cc_start: 0.7755 (p) cc_final: 0.7307 (t) REVERT: E 775 MET cc_start: 0.7637 (mmm) cc_final: 0.7425 (mmm) REVERT: G 289 MET cc_start: 0.7800 (tpp) cc_final: 0.7340 (tpt) REVERT: G 342 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7254 (tp) REVERT: G 425 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.6971 (mmt) REVERT: G 436 TYR cc_start: 0.5820 (p90) cc_final: 0.5014 (p90) REVERT: G 500 MET cc_start: 0.7893 (tpt) cc_final: 0.7676 (tpt) REVERT: G 604 MET cc_start: 0.7379 (tpp) cc_final: 0.6881 (tpp) REVERT: H 224 ASP cc_start: 0.7245 (m-30) cc_final: 0.7018 (m-30) REVERT: H 258 SER cc_start: 0.8718 (p) cc_final: 0.8464 (p) REVERT: H 425 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.4388 (mmt) REVERT: H 775 MET cc_start: 0.7791 (mmm) cc_final: 0.7428 (mmm) outliers start: 92 outliers final: 66 residues processed: 572 average time/residue: 0.6073 time to fit residues: 565.6262 Evaluate side-chains 570 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 496 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 294 GLU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 509 optimal weight: 0.0470 chunk 536 optimal weight: 6.9990 chunk 489 optimal weight: 0.0870 chunk 521 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 409 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 471 optimal weight: 7.9990 chunk 493 optimal weight: 7.9990 chunk 520 optimal weight: 4.9990 overall best weight: 3.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47503 Z= 0.280 Angle : 0.503 13.163 64116 Z= 0.262 Chirality : 0.040 0.225 7207 Planarity : 0.003 0.042 8202 Dihedral : 6.273 86.518 6452 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.86 % Allowed : 15.38 % Favored : 82.76 % 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: 0.31 (0.11), residues: 5755 helix: 0.95 (0.09), residues: 3210 sheet: 0.27 (0.35), residues: 256 loop : -0.80 (0.13), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 892 HIS 0.010 0.001 HIS H 762 PHE 0.027 0.001 PHE D 646 TYR 0.024 0.001 TYR H 146 ARG 0.010 0.000 ARG H 639 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 492 time to evaluate : 5.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 425 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7778 (mmt) REVERT: A 473 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7903 (tt0) REVERT: C 254 LEU cc_start: 0.9408 (tp) cc_final: 0.9140 (tp) REVERT: C 466 LEU cc_start: 0.8104 (mp) cc_final: 0.7736 (mt) REVERT: D 560 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8210 (t0) REVERT: E 309 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6930 (mp-120) REVERT: E 346 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: E 604 MET cc_start: 0.8145 (tpp) cc_final: 0.7826 (tpt) REVERT: E 608 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8027 (mm) REVERT: G 342 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7259 (tp) REVERT: G 425 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.6957 (mmt) REVERT: G 436 TYR cc_start: 0.5866 (p90) cc_final: 0.4989 (p90) REVERT: G 500 MET cc_start: 0.7935 (tpt) cc_final: 0.7693 (tpt) REVERT: G 604 MET cc_start: 0.7459 (tpp) cc_final: 0.6979 (tpp) REVERT: H 224 ASP cc_start: 0.7216 (m-30) cc_final: 0.6998 (m-30) REVERT: H 425 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.4458 (mmt) outliers start: 96 outliers final: 74 residues processed: 559 average time/residue: 0.6086 time to fit residues: 552.7289 Evaluate side-chains 566 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 483 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 272 THR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 342 optimal weight: 0.8980 chunk 551 optimal weight: 0.4980 chunk 336 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 383 optimal weight: 0.6980 chunk 578 optimal weight: 0.4980 chunk 532 optimal weight: 10.0000 chunk 460 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 356 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 512 ASN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN G 292 HIS ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 47503 Z= 0.140 Angle : 0.456 14.041 64116 Z= 0.239 Chirality : 0.038 0.202 7207 Planarity : 0.003 0.043 8202 Dihedral : 6.086 84.088 6452 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.40 % Allowed : 15.96 % Favored : 82.64 % 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: 0.53 (0.11), residues: 5755 helix: 1.13 (0.09), residues: 3192 sheet: 0.54 (0.37), residues: 244 loop : -0.72 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 892 HIS 0.011 0.001 HIS H 762 PHE 0.016 0.001 PHE C 227 TYR 0.026 0.001 TYR C 535 ARG 0.008 0.000 ARG H 639 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 534 time to evaluate : 5.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 473 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7795 (tt0) REVERT: C 254 LEU cc_start: 0.9374 (tp) cc_final: 0.9121 (tp) REVERT: D 366 MET cc_start: 0.7958 (ttm) cc_final: 0.7521 (ttm) REVERT: D 560 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8102 (t0) REVERT: E 346 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: E 604 MET cc_start: 0.8163 (tpp) cc_final: 0.7756 (tpt) REVERT: E 608 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8012 (mm) REVERT: E 643 THR cc_start: 0.7753 (p) cc_final: 0.7293 (t) REVERT: E 710 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (mp) REVERT: G 289 MET cc_start: 0.7762 (tpp) cc_final: 0.7223 (tpt) REVERT: G 295 GLN cc_start: 0.7966 (tt0) cc_final: 0.7720 (tt0) REVERT: G 342 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7254 (tp) REVERT: G 436 TYR cc_start: 0.5714 (p90) cc_final: 0.4851 (p90) REVERT: G 500 MET cc_start: 0.7886 (tpt) cc_final: 0.7665 (tpt) REVERT: G 604 MET cc_start: 0.7301 (tpp) cc_final: 0.6844 (tpp) REVERT: G 758 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7430 (ttp80) REVERT: G 780 LEU cc_start: 0.8751 (mt) cc_final: 0.8546 (mt) REVERT: H 75 ASP cc_start: 0.8343 (t0) cc_final: 0.8094 (t0) REVERT: H 224 ASP cc_start: 0.7230 (m-30) cc_final: 0.6989 (m-30) REVERT: H 258 SER cc_start: 0.8671 (p) cc_final: 0.8423 (p) REVERT: H 425 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.4268 (mmt) outliers start: 72 outliers final: 54 residues processed: 583 average time/residue: 0.6651 time to fit residues: 639.1988 Evaluate side-chains 564 residues out of total 5156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 503 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 543 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain D residue 921 THR Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 710 ILE Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 610 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 366 optimal weight: 4.9990 chunk 490 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 424 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 461 optimal weight: 10.0000 chunk 193 optimal weight: 0.1980 chunk 474 optimal weight: 6.9990 chunk 58 optimal weight: 0.0670 chunk 85 optimal weight: 8.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN A 560 ASN C 512 ASN ** C 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN G 292 HIS ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117768 restraints weight = 70248.680| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.98 r_work: 0.3198 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 47503 Z= 0.178 Angle : 0.471 13.766 64116 Z= 0.245 Chirality : 0.039 0.285 7207 Planarity : 0.003 0.043 8202 Dihedral : 6.025 81.738 6452 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.40 % Allowed : 16.39 % Favored : 82.22 % 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: 0.55 (0.11), residues: 5755 helix: 1.15 (0.09), residues: 3195 sheet: 0.57 (0.37), residues: 244 loop : -0.72 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 892 HIS 0.007 0.001 HIS H 762 PHE 0.020 0.001 PHE C 646 TYR 0.063 0.001 TYR C 535 ARG 0.010 0.000 ARG H 639 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10785.03 seconds wall clock time: 195 minutes 59.65 seconds (11759.65 seconds total)