Starting phenix.real_space_refine on Fri Mar 22 10:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pnq_13550/03_2024/7pnq_13550.pdb" } resolution = 3.7 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 201 5.16 5 C 20931 2.51 5 N 5418 2.21 5 O 6375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 530": "OD1" <-> "OD2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32925 Number of models: 1 Model: "" Number of chains: 12 Chain: "X" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "Y" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.15, per 1000 atoms: 0.49 Number of scatterers: 32925 At special positions: 0 Unit cell: (150.165, 152.295, 198.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 201 16.00 O 6375 8.00 N 5418 7.00 C 20931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 606 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 568 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 570 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 622 " - pdb=" SG CYS C 675 " distance=2.03 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 725 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 930 " - pdb=" SG CYS C 941 " distance=2.03 Simple disulfide: pdb=" SG CYS C1118 " - pdb=" SG CYS C1129 " distance=2.04 Simple disulfide: pdb=" SG CYS C1168 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 675 " distance=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 930 " - pdb=" SG CYS A 941 " distance=2.03 Simple disulfide: pdb=" SG CYS A1118 " - pdb=" SG CYS A1129 " distance=2.04 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 675 " distance=2.04 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 930 " - pdb=" SG CYS B 941 " distance=2.03 Simple disulfide: pdb=" SG CYS B1118 " - pdb=" SG CYS B1129 " distance=2.04 Simple disulfide: pdb=" SG CYS B1168 " - pdb=" SG CYS B1213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1401 " - " ASN A 59 " " NAG A1402 " - " ASN A 146 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 687 " " NAG A1405 " - " ASN A 706 " " NAG B1401 " - " ASN B 59 " " NAG B1402 " - " ASN B 146 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 687 " " NAG B1405 " - " ASN B 706 " " NAG C1401 " - " ASN C 59 " " NAG C1402 " - " ASN C 146 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 687 " " NAG C1405 " - " ASN C 706 " Time building additional restraints: 12.02 Conformation dependent library (CDL) restraints added in 5.6 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 75 sheets defined 22.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'X' and resid 60 through 64 removed outlier: 3.734A pdb=" N LYS X 64 " --> pdb=" O PRO X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 90 removed outlier: 3.711A pdb=" N THR X 90 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 83 removed outlier: 4.172A pdb=" N PHE Y 83 " --> pdb=" O SER Y 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.601A pdb=" N LYS C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.556A pdb=" N ASN C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.016A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 removed outlier: 3.845A pdb=" N GLY C 388 " --> pdb=" O LYS C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.502A pdb=" N ASP C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.515A pdb=" N PHE C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 561 No H-bonds generated for 'chain 'C' and resid 559 through 561' Processing helix chain 'C' and resid 565 through 568 Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.595A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 877 Processing helix chain 'C' and resid 906 through 915 removed outlier: 4.229A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 938 through 946 Processing helix chain 'C' and resid 956 through 970 Processing helix chain 'C' and resid 976 through 980 Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.051A pdb=" N GLN C1004 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1051 Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1119 removed outlier: 3.618A pdb=" N ALA C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.723A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.699A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.181A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.599A pdb=" N LYS A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.990A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 removed outlier: 3.838A pdb=" N GLY A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.641A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 572 through 575 removed outlier: 3.744A pdb=" N PHE A 575 " --> pdb=" O PRO A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 575' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.600A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 877 Processing helix chain 'A' and resid 906 through 916 removed outlier: 4.215A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 938 through 946 Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.054A pdb=" N GLN A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1051 Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1119 removed outlier: 3.581A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.727A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.697A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.170A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.608A pdb=" N LYS B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.076A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 removed outlier: 3.896A pdb=" N GLY B 388 " --> pdb=" O LYS B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.500A pdb=" N ASP B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.506A pdb=" N PHE B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 572 through 575 removed outlier: 3.757A pdb=" N PHE B 575 " --> pdb=" O PRO B 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 575' Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.584A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 906 through 915 removed outlier: 4.207A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 938 through 946 Processing helix chain 'B' and resid 956 through 970 Processing helix chain 'B' and resid 976 through 980 Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 999 through 1004 removed outlier: 4.034A pdb=" N GLN B1004 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1051 Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1119 removed outlier: 3.626A pdb=" N ALA B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.712A pdb=" N TRP X 7 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR X 21 " --> pdb=" O TRP X 7 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU X 16 " --> pdb=" O SER X 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 50 through 51 removed outlier: 4.070A pdb=" N TYR X 33 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.640A pdb=" N THR Y 5 " --> pdb=" O ARG Y 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER Y 7 " --> pdb=" O SER Y 22 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER Y 22 " --> pdb=" O SER Y 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS Y 23 " --> pdb=" O PHE Y 71 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU Y 70 " --> pdb=" O SER Y 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.307A pdb=" N LEU Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 40 removed outlier: 5.101A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.957A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.249A pdb=" N VAL C 56 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR B 659 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 634 " --> pdb=" O VAL B 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.581A pdb=" N TYR C 249 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.523A pdb=" N LYS C 114 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 174 through 175 removed outlier: 7.146A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 310 through 318 removed outlier: 3.636A pdb=" N PHE C 684 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 680 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 316 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY C 678 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG C 679 " --> pdb=" O ARG C 696 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG C 696 " --> pdb=" O ARG C 679 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 719 " --> pdb=" O VAL C 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.525A pdb=" N GLY C 634 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR C 659 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.871A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 398 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.567A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 588 " --> pdb=" O GLN C 585 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AB9, first strand: chain 'C' and resid 484 through 485 Processing sheet with id=AC1, first strand: chain 'C' and resid 563 through 564 Processing sheet with id=AC2, first strand: chain 'C' and resid 730 through 737 removed outlier: 6.857A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 770 " --> pdb=" O TYR C 730 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N SER C 732 " --> pdb=" O ASN C 770 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 777 through 779 Processing sheet with id=AC4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.493A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN C 802 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE C1151 " --> pdb=" O ASN C 802 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 804 " --> pdb=" O ILE C1149 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C1149 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE C 806 " --> pdb=" O TYR C1147 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C1147 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.493A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN C 802 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE C1151 " --> pdb=" O ASN C 802 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 804 " --> pdb=" O ILE C1149 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C1149 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE C 806 " --> pdb=" O TYR C1147 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C1147 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG C1162 " --> pdb=" O ASN C1184 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C1184 " --> pdb=" O ARG C1162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C1192 " --> pdb=" O TYR C1181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.089A pdb=" N LYS C 813 " --> pdb=" O LEU C 951 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 870 through 872 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.674A pdb=" N VAL C 883 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 886 " --> pdb=" O VAL C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1167 through 1168 removed outlier: 3.609A pdb=" N LEU C1167 " --> pdb=" O ILE C1175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1176 " --> pdb=" O VAL C1208 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.712A pdb=" N TRP H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR H 21 " --> pdb=" O TRP H 7 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU H 16 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 33 through 39 removed outlier: 4.077A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.573A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.324A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AD7, first strand: chain 'A' and resid 36 through 40 removed outlier: 5.098A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.934A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.674A pdb=" N TYR A 249 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 201 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.524A pdb=" N LYS A 114 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 187 through 189 removed outlier: 7.460A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 310 through 318 removed outlier: 3.649A pdb=" N PHE A 684 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 680 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 316 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY A 678 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 679 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG A 696 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 719 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.532A pdb=" N GLY A 634 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR A 659 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 355 through 357 removed outlier: 6.567A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.567A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AE8, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AE9, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AF1, first strand: chain 'A' and resid 730 through 737 removed outlier: 6.838A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 777 through 779 Processing sheet with id=AF3, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.510A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 802 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A1151 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 804 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A1149 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 806 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A1147 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.510A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 802 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A1151 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 804 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A1149 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 806 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A1147 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A1162 " --> pdb=" O ASN A1184 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A1184 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1192 " --> pdb=" O TYR A1181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 813 through 816 removed outlier: 4.082A pdb=" N LYS A 813 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.716A pdb=" N VAL A 883 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 886 " --> pdb=" O VAL A 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 3.609A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1176 " --> pdb=" O VAL A1208 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.715A pdb=" N TRP D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 21 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU D 16 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 33 through 39 removed outlier: 4.068A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.538A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.329A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AG5, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.104A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.510A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.588A pdb=" N TYR B 249 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 201 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 110 through 114 removed outlier: 3.531A pdb=" N LYS B 114 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 187 through 189 removed outlier: 7.440A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 310 through 318 removed outlier: 3.670A pdb=" N PHE B 684 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 680 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 316 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLY B 678 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG B 679 " --> pdb=" O ARG B 696 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 696 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 719 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.922A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 398 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 437 " --> pdb=" O CYS B 589 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.582A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 588 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AH5, first strand: chain 'B' and resid 484 through 485 Processing sheet with id=AH6, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AH7, first strand: chain 'B' and resid 730 through 737 removed outlier: 6.864A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.530A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 802 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B1151 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 804 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B1149 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE B 806 " --> pdb=" O TYR B1147 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B1147 " --> pdb=" O PHE B 806 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.530A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 802 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B1151 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 804 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B1149 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE B 806 " --> pdb=" O TYR B1147 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B1147 " --> pdb=" O PHE B 806 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG B1162 " --> pdb=" O ASN B1184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN B1184 " --> pdb=" O ARG B1162 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B1192 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 813 through 816 removed outlier: 4.110A pdb=" N LYS B 813 " --> pdb=" O LEU B 951 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.666A pdb=" N VAL B 883 " --> pdb=" O ILE B 886 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 886 " --> pdb=" O VAL B 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'B' and resid 1167 through 1168 removed outlier: 3.625A pdb=" N LEU B1167 " --> pdb=" O ILE B1175 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B1176 " --> pdb=" O VAL B1208 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3381 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: 17.38 Time building geometry restraints manager: 13.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10511 1.34 - 1.47: 8533 1.47 - 1.59: 14373 1.59 - 1.71: 0 1.71 - 1.83: 261 Bond restraints: 33678 Sorted by residual: bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 NAG B1405 " pdb=" O5 NAG B1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C1 NAG C1401 " pdb=" O5 NAG C1401 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.86e+00 ... (remaining 33673 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.47: 803 106.47 - 113.37: 17998 113.37 - 120.28: 11780 120.28 - 127.18: 15007 127.18 - 134.09: 261 Bond angle restraints: 45849 Sorted by residual: angle pdb=" C GLY C1130 " pdb=" N ASN C1131 " pdb=" CA ASN C1131 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C GLY A1130 " pdb=" N ASN A1131 " pdb=" CA ASN A1131 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C GLY B1130 " pdb=" N ASN B1131 " pdb=" CA ASN B1131 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C ASN B 379 " pdb=" N ASN B 380 " pdb=" CA ASN B 380 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C ASN A 379 " pdb=" N ASN A 380 " pdb=" CA ASN A 380 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 ... (remaining 45844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 18890 21.68 - 43.37: 1141 43.37 - 65.05: 120 65.05 - 86.73: 21 86.73 - 108.42: 9 Dihedral angle restraints: 20181 sinusoidal: 7911 harmonic: 12270 Sorted by residual: dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual 93.00 147.35 -54.35 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " pdb=" SG CYS C 169 " pdb=" CB CYS C 169 " ideal model delta sinusoidal sigma weight residual 93.00 146.89 -53.89 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 169 " pdb=" CB CYS B 169 " ideal model delta sinusoidal sigma weight residual 93.00 146.68 -53.68 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 20178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 5085 0.125 - 0.250: 105 0.250 - 0.374: 3 0.374 - 0.499: 0 0.499 - 0.624: 3 Chirality restraints: 5196 Sorted by residual: chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 ... (remaining 5193 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 889 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 890 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 889 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO C 890 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 890 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 890 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 889 " -0.047 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO B 890 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.039 5.00e-02 4.00e+02 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10146 2.83 - 3.34: 26483 3.34 - 3.86: 54527 3.86 - 4.38: 60124 4.38 - 4.90: 107610 Nonbonded interactions: 258890 Sorted by model distance: nonbonded pdb=" OH TYR A 836 " pdb=" OD1 ASP A1080 " model vdw 2.308 2.440 nonbonded pdb=" OG SER A 348 " pdb=" OD1 ASN A 351 " model vdw 2.322 2.440 nonbonded pdb=" OH TYR C 836 " pdb=" OD1 ASP C1080 " model vdw 2.323 2.440 nonbonded pdb=" OG SER B 348 " pdb=" OD1 ASN B 351 " model vdw 2.324 2.440 nonbonded pdb=" O CYS C 930 " pdb=" OH TYR C 945 " model vdw 2.326 2.440 ... (remaining 258885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 8.540 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 86.820 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.190 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 33678 Z= 0.216 Angle : 0.644 9.598 45849 Z= 0.350 Chirality : 0.050 0.624 5196 Planarity : 0.006 0.071 5883 Dihedral : 13.235 108.416 12150 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4170 helix: -1.30 (0.16), residues: 798 sheet: -0.28 (0.17), residues: 924 loop : -1.16 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 114 HIS 0.005 0.001 HIS B 215 PHE 0.017 0.001 PHE B 122 TYR 0.014 0.001 TYR A 625 ARG 0.003 0.000 ARG C1125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 804 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 33 TYR cc_start: 0.5912 (m-10) cc_final: 0.5549 (m-10) REVERT: C 57 TYR cc_start: 0.6261 (m-80) cc_final: 0.5553 (m-80) REVERT: C 61 THR cc_start: 0.6315 (p) cc_final: 0.5967 (p) REVERT: C 199 TYR cc_start: 0.6412 (t80) cc_final: 0.5200 (t80) REVERT: C 233 VAL cc_start: 0.5972 (m) cc_final: 0.5688 (m) REVERT: C 289 ASP cc_start: 0.5962 (t0) cc_final: 0.5298 (t0) REVERT: C 292 SER cc_start: 0.8653 (t) cc_final: 0.7984 (p) REVERT: C 293 ASP cc_start: 0.7146 (p0) cc_final: 0.6594 (p0) REVERT: C 301 LYS cc_start: 0.7295 (tptp) cc_final: 0.7017 (ttpt) REVERT: C 326 TYR cc_start: 0.7282 (t80) cc_final: 0.7027 (t80) REVERT: C 380 ASN cc_start: 0.7691 (m-40) cc_final: 0.7279 (m110) REVERT: C 382 ASP cc_start: 0.7137 (p0) cc_final: 0.6894 (p0) REVERT: C 411 LEU cc_start: 0.8709 (tp) cc_final: 0.8471 (tt) REVERT: C 723 LEU cc_start: 0.6839 (mt) cc_final: 0.6639 (mt) REVERT: C 848 THR cc_start: 0.6149 (t) cc_final: 0.5906 (p) REVERT: C 946 LYS cc_start: 0.7318 (mmtp) cc_final: 0.6972 (mtpp) REVERT: C 950 VAL cc_start: 0.6539 (t) cc_final: 0.6325 (m) REVERT: C 1051 GLN cc_start: 0.5901 (mm-40) cc_final: 0.5329 (mm-40) REVERT: C 1056 PHE cc_start: 0.7955 (m-80) cc_final: 0.7749 (m-80) REVERT: C 1059 ILE cc_start: 0.8444 (pt) cc_final: 0.8238 (mt) REVERT: H 94 TYR cc_start: 0.4982 (m-80) cc_final: 0.4752 (m-80) REVERT: A 230 THR cc_start: 0.7323 (m) cc_final: 0.6717 (p) REVERT: A 298 ILE cc_start: 0.7236 (mm) cc_final: 0.7012 (mt) REVERT: A 301 LYS cc_start: 0.7035 (tptp) cc_final: 0.6614 (ttmt) REVERT: A 326 TYR cc_start: 0.7556 (t80) cc_final: 0.7317 (t80) REVERT: A 379 ASN cc_start: 0.7518 (t0) cc_final: 0.7302 (t0) REVERT: A 380 ASN cc_start: 0.7616 (m-40) cc_final: 0.7392 (m110) REVERT: A 409 LEU cc_start: 0.8033 (mt) cc_final: 0.7791 (mp) REVERT: A 631 LEU cc_start: 0.8651 (mt) cc_final: 0.8442 (mt) REVERT: A 642 THR cc_start: 0.7811 (p) cc_final: 0.7519 (t) REVERT: A 720 ASP cc_start: 0.4861 (m-30) cc_final: 0.4549 (m-30) REVERT: A 723 LEU cc_start: 0.6758 (mt) cc_final: 0.6490 (mt) REVERT: A 835 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5768 (mt-10) REVERT: A 838 SER cc_start: 0.6185 (t) cc_final: 0.4976 (t) REVERT: A 848 THR cc_start: 0.5880 (t) cc_final: 0.5447 (p) REVERT: A 950 VAL cc_start: 0.6374 (t) cc_final: 0.5982 (t) REVERT: A 951 LEU cc_start: 0.6116 (mt) cc_final: 0.5620 (mp) REVERT: A 1059 ILE cc_start: 0.8048 (pt) cc_final: 0.7639 (mt) REVERT: B 289 ASP cc_start: 0.6859 (t0) cc_final: 0.6400 (t70) REVERT: B 293 ASP cc_start: 0.7268 (p0) cc_final: 0.6528 (p0) REVERT: B 301 LYS cc_start: 0.7086 (tptp) cc_final: 0.6714 (ttpt) REVERT: B 591 ILE cc_start: 0.7981 (mt) cc_final: 0.7685 (mm) REVERT: B 596 ILE cc_start: 0.7973 (mp) cc_final: 0.7736 (mt) REVERT: B 642 THR cc_start: 0.7769 (p) cc_final: 0.7501 (t) REVERT: B 666 THR cc_start: 0.7337 (p) cc_final: 0.6957 (p) REVERT: B 720 ASP cc_start: 0.5299 (m-30) cc_final: 0.4816 (m-30) REVERT: B 1046 ASN cc_start: 0.6964 (t0) cc_final: 0.6740 (t0) REVERT: B 1067 LEU cc_start: 0.7483 (mt) cc_final: 0.7266 (mp) outliers start: 1 outliers final: 0 residues processed: 805 average time/residue: 0.4480 time to fit residues: 574.3029 Evaluate side-chains 639 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 9.9990 chunk 316 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 326 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 378 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN C 552 HIS ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN ** C 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 GLN C 851 ASN C1050 GLN ** C1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN A 208 ASN A 303 GLN A 363 ASN A 475 HIS A 481 GLN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN A 655 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1054 ASN ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 215 HIS B 303 GLN B 331 ASN B 363 ASN B 552 HIS B 728 ASN ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN B 851 ASN B 858 GLN B1054 ASN B1096 GLN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33678 Z= 0.175 Angle : 0.577 8.875 45849 Z= 0.308 Chirality : 0.045 0.499 5196 Planarity : 0.005 0.083 5883 Dihedral : 6.770 100.406 4887 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.37 % Allowed : 8.88 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4170 helix: -0.12 (0.17), residues: 786 sheet: -0.20 (0.16), residues: 999 loop : -0.87 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 452 HIS 0.017 0.001 HIS B 177 PHE 0.021 0.002 PHE B 484 TYR 0.022 0.001 TYR A 435 ARG 0.012 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 670 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.6441 (m-80) cc_final: 0.5872 (m-80) REVERT: C 106 LYS cc_start: 0.8052 (tttt) cc_final: 0.7610 (tttm) REVERT: C 143 ARG cc_start: 0.4276 (ttt180) cc_final: 0.3746 (ttt180) REVERT: C 213 TYR cc_start: 0.6502 (m-80) cc_final: 0.5602 (m-80) REVERT: C 230 THR cc_start: 0.7317 (m) cc_final: 0.6948 (t) REVERT: C 289 ASP cc_start: 0.6197 (t0) cc_final: 0.5901 (t70) REVERT: C 292 SER cc_start: 0.8646 (t) cc_final: 0.8037 (p) REVERT: C 293 ASP cc_start: 0.7137 (p0) cc_final: 0.6521 (p0) REVERT: C 435 TYR cc_start: 0.7110 (p90) cc_final: 0.6708 (p90) REVERT: C 451 THR cc_start: 0.6069 (p) cc_final: 0.4788 (m) REVERT: C 611 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6914 (tm-30) REVERT: C 671 MET cc_start: 0.6268 (mmm) cc_final: 0.5613 (mmm) REVERT: C 720 ASP cc_start: 0.5087 (m-30) cc_final: 0.4794 (m-30) REVERT: C 1056 PHE cc_start: 0.7953 (m-80) cc_final: 0.7666 (m-80) REVERT: A 106 LYS cc_start: 0.7926 (tttt) cc_final: 0.7716 (tttm) REVERT: A 143 ARG cc_start: 0.3888 (ttp-170) cc_final: 0.3652 (ttt180) REVERT: A 230 THR cc_start: 0.7425 (m) cc_final: 0.6791 (p) REVERT: A 298 ILE cc_start: 0.7530 (mm) cc_final: 0.7191 (mt) REVERT: A 624 ASN cc_start: 0.6438 (p0) cc_final: 0.6120 (p0) REVERT: A 631 LEU cc_start: 0.8890 (mt) cc_final: 0.8400 (mp) REVERT: A 642 THR cc_start: 0.7929 (p) cc_final: 0.7501 (t) REVERT: A 671 MET cc_start: 0.6051 (mmm) cc_final: 0.5505 (mmm) REVERT: A 720 ASP cc_start: 0.5335 (m-30) cc_final: 0.5006 (m-30) REVERT: A 804 VAL cc_start: 0.1624 (m) cc_final: 0.0788 (t) REVERT: A 965 LEU cc_start: 0.7200 (tt) cc_final: 0.6973 (tt) REVERT: A 1049 LEU cc_start: 0.8312 (tp) cc_final: 0.8038 (tt) REVERT: A 1050 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7094 (mm-40) REVERT: A 1054 ASN cc_start: 0.7151 (m110) cc_final: 0.6772 (m110) REVERT: A 1059 ILE cc_start: 0.7989 (pt) cc_final: 0.7640 (mt) REVERT: A 1068 SER cc_start: 0.7345 (p) cc_final: 0.7125 (p) REVERT: F 46 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7436 (pp) REVERT: B 57 TYR cc_start: 0.6750 (m-80) cc_final: 0.6044 (m-80) REVERT: B 203 PHE cc_start: 0.6937 (m-80) cc_final: 0.6354 (m-80) REVERT: B 289 ASP cc_start: 0.6928 (t0) cc_final: 0.6614 (t70) REVERT: B 293 ASP cc_start: 0.6942 (p0) cc_final: 0.6440 (p0) REVERT: B 295 MET cc_start: 0.5210 (ppp) cc_final: 0.4905 (ptm) REVERT: B 340 TRP cc_start: 0.7573 (t-100) cc_final: 0.7196 (t-100) REVERT: B 591 ILE cc_start: 0.8086 (mt) cc_final: 0.7610 (mm) REVERT: B 624 ASN cc_start: 0.6297 (p0) cc_final: 0.5836 (p0) REVERT: B 631 LEU cc_start: 0.8798 (mt) cc_final: 0.8553 (mp) REVERT: B 642 THR cc_start: 0.7859 (p) cc_final: 0.7498 (t) REVERT: B 666 THR cc_start: 0.7243 (p) cc_final: 0.6672 (p) REVERT: B 694 LEU cc_start: 0.7178 (tp) cc_final: 0.6959 (tt) REVERT: B 711 ARG cc_start: 0.6204 (mtm180) cc_final: 0.5890 (mtm180) REVERT: B 720 ASP cc_start: 0.5605 (m-30) cc_final: 0.5117 (m-30) REVERT: B 951 LEU cc_start: 0.6567 (mt) cc_final: 0.5979 (mp) REVERT: B 1049 LEU cc_start: 0.8242 (tp) cc_final: 0.8036 (tt) REVERT: B 1064 GLN cc_start: 0.7326 (tt0) cc_final: 0.7123 (tt0) outliers start: 50 outliers final: 32 residues processed: 684 average time/residue: 0.4371 time to fit residues: 483.5270 Evaluate side-chains 660 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 627 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 856 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 0.0980 chunk 117 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 379 optimal weight: 0.5980 chunk 409 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 ASN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN C 707 ASN C1050 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN A 208 ASN A 363 ASN A 380 ASN A 714 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 GLN A1226 ASN F 92 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 363 ASN B 481 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN B 714 GLN B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 GLN ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33678 Z= 0.236 Angle : 0.613 9.742 45849 Z= 0.327 Chirality : 0.046 0.460 5196 Planarity : 0.004 0.056 5883 Dihedral : 6.342 97.306 4887 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.95 % Allowed : 11.38 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.74 (0.12), residues: 4170 helix: 0.04 (0.17), residues: 789 sheet: -0.06 (0.16), residues: 984 loop : -0.84 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 452 HIS 0.009 0.002 HIS B 177 PHE 0.026 0.002 PHE A1013 TYR 0.027 0.002 TYR A 274 ARG 0.006 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 695 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 33 TYR cc_start: 0.6196 (m-10) cc_final: 0.5969 (m-10) REVERT: C 57 TYR cc_start: 0.6888 (m-80) cc_final: 0.6072 (m-80) REVERT: C 106 LYS cc_start: 0.8240 (tttt) cc_final: 0.7843 (tttm) REVERT: C 230 THR cc_start: 0.7695 (m) cc_final: 0.7330 (t) REVERT: C 289 ASP cc_start: 0.6644 (t0) cc_final: 0.5907 (t70) REVERT: C 292 SER cc_start: 0.8455 (t) cc_final: 0.8076 (p) REVERT: C 357 PHE cc_start: 0.6890 (m-10) cc_final: 0.6433 (m-10) REVERT: C 401 ILE cc_start: 0.7921 (mm) cc_final: 0.7445 (mt) REVERT: C 451 THR cc_start: 0.6054 (p) cc_final: 0.4857 (m) REVERT: C 452 TRP cc_start: 0.7073 (p-90) cc_final: 0.6687 (p-90) REVERT: C 671 MET cc_start: 0.6228 (mmm) cc_final: 0.5728 (mmm) REVERT: C 673 ARG cc_start: 0.6691 (mtp85) cc_final: 0.6289 (mtp85) REVERT: C 720 ASP cc_start: 0.5428 (m-30) cc_final: 0.4987 (m-30) REVERT: C 799 THR cc_start: 0.2870 (t) cc_final: 0.1731 (m) REVERT: C 804 VAL cc_start: 0.3012 (m) cc_final: 0.2534 (t) REVERT: C 816 ILE cc_start: 0.7687 (mm) cc_final: 0.7396 (mt) REVERT: C 833 LEU cc_start: 0.7783 (tp) cc_final: 0.7503 (mt) REVERT: C 927 TYR cc_start: 0.6922 (m-80) cc_final: 0.6709 (m-80) REVERT: C 1056 PHE cc_start: 0.7941 (m-80) cc_final: 0.7731 (m-80) REVERT: C 1097 GLN cc_start: 0.6893 (tp40) cc_final: 0.6678 (mp10) REVERT: A 106 LYS cc_start: 0.8058 (tttt) cc_final: 0.7806 (ttpp) REVERT: A 143 ARG cc_start: 0.4115 (ttp-170) cc_final: 0.3086 (mtp180) REVERT: A 230 THR cc_start: 0.7612 (m) cc_final: 0.7104 (p) REVERT: A 298 ILE cc_start: 0.7713 (mm) cc_final: 0.7380 (mt) REVERT: A 357 PHE cc_start: 0.6833 (m-10) cc_final: 0.6574 (m-10) REVERT: A 363 ASN cc_start: 0.5087 (OUTLIER) cc_final: 0.4813 (p0) REVERT: A 368 MET cc_start: 0.7169 (mpp) cc_final: 0.6809 (mtt) REVERT: A 377 THR cc_start: 0.7586 (m) cc_final: 0.7330 (p) REVERT: A 601 ASN cc_start: 0.7700 (p0) cc_final: 0.7364 (p0) REVERT: A 602 SER cc_start: 0.8248 (t) cc_final: 0.7940 (m) REVERT: A 631 LEU cc_start: 0.8858 (mt) cc_final: 0.8399 (mp) REVERT: A 635 ILE cc_start: 0.8099 (pt) cc_final: 0.7829 (pt) REVERT: A 642 THR cc_start: 0.8031 (p) cc_final: 0.7664 (t) REVERT: A 720 ASP cc_start: 0.5508 (m-30) cc_final: 0.4621 (m-30) REVERT: A 728 ASN cc_start: 0.8430 (m-40) cc_final: 0.8202 (m-40) REVERT: A 799 THR cc_start: 0.3524 (t) cc_final: 0.2458 (m) REVERT: A 833 LEU cc_start: 0.7468 (mt) cc_final: 0.7184 (mt) REVERT: A 949 LYS cc_start: 0.7615 (mttt) cc_final: 0.7358 (mttt) REVERT: A 1050 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.6996 (mm-40) REVERT: A 1054 ASN cc_start: 0.7344 (m110) cc_final: 0.6987 (m110) REVERT: D 112 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: F 4 MET cc_start: 0.3054 (OUTLIER) cc_final: 0.2744 (tpt) REVERT: B 143 ARG cc_start: 0.4826 (ttt180) cc_final: 0.4389 (ttp-170) REVERT: B 230 THR cc_start: 0.7706 (m) cc_final: 0.7298 (t) REVERT: B 293 ASP cc_start: 0.6844 (p0) cc_final: 0.6512 (p0) REVERT: B 295 MET cc_start: 0.5501 (ppp) cc_final: 0.5195 (ptm) REVERT: B 322 ILE cc_start: 0.8161 (mm) cc_final: 0.7855 (mm) REVERT: B 591 ILE cc_start: 0.8298 (mt) cc_final: 0.7851 (mm) REVERT: B 631 LEU cc_start: 0.8734 (mt) cc_final: 0.8470 (mp) REVERT: B 671 MET cc_start: 0.6161 (mmm) cc_final: 0.5447 (mmm) REVERT: B 711 ARG cc_start: 0.6458 (mtm180) cc_final: 0.6109 (mtm180) REVERT: B 720 ASP cc_start: 0.5694 (m-30) cc_final: 0.5326 (m-30) REVERT: B 799 THR cc_start: 0.2784 (t) cc_final: 0.1794 (m) REVERT: B 804 VAL cc_start: 0.2759 (m) cc_final: 0.2522 (m) REVERT: B 852 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5760 (mt-10) REVERT: B 951 LEU cc_start: 0.7177 (mt) cc_final: 0.6940 (mt) REVERT: B 1049 LEU cc_start: 0.8468 (tp) cc_final: 0.8120 (tt) REVERT: B 1050 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6756 (mm-40) REVERT: B 1065 GLU cc_start: 0.5844 (mt-10) cc_final: 0.5519 (mm-30) REVERT: B 1069 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6709 (ptm160) outliers start: 71 outliers final: 42 residues processed: 721 average time/residue: 0.4305 time to fit residues: 505.5748 Evaluate side-chains 686 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 640 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1050 GLN Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 948 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 380 optimal weight: 0.9990 chunk 403 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN C 418 GLN C 453 ASN C 481 GLN ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN C 802 ASN ** C1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1226 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 481 GLN A 552 HIS A 573 GLN A 649 ASN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 ASN ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 336 ASN B 380 ASN B 481 GLN B 590 ASN B 649 ASN B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 33678 Z= 0.458 Angle : 0.802 10.908 45849 Z= 0.437 Chirality : 0.052 0.414 5196 Planarity : 0.006 0.108 5883 Dihedral : 6.546 86.062 4887 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 3.08 % Allowed : 13.69 % Favored : 83.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.12), residues: 4170 helix: -0.30 (0.18), residues: 759 sheet: -0.45 (0.16), residues: 942 loop : -1.08 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP Y 35 HIS 0.015 0.003 HIS C 215 PHE 0.036 0.004 PHE A 104 TYR 0.046 0.003 TYR B 68 ARG 0.015 0.001 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 752 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 112 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: C 57 TYR cc_start: 0.7463 (m-80) cc_final: 0.7215 (m-80) REVERT: C 143 ARG cc_start: 0.4756 (ttt180) cc_final: 0.3559 (mtp180) REVERT: C 230 THR cc_start: 0.7815 (m) cc_final: 0.7485 (p) REVERT: C 344 LYS cc_start: 0.7948 (ptpt) cc_final: 0.7570 (ptpt) REVERT: C 368 MET cc_start: 0.7603 (mtt) cc_final: 0.7396 (mtm) REVERT: C 377 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7654 (p) REVERT: C 425 ASP cc_start: 0.7328 (t70) cc_final: 0.7114 (t0) REVERT: C 549 ILE cc_start: 0.8150 (pt) cc_final: 0.7528 (mt) REVERT: C 605 THR cc_start: 0.7933 (m) cc_final: 0.7394 (t) REVERT: C 720 ASP cc_start: 0.5881 (m-30) cc_final: 0.5615 (m-30) REVERT: C 848 THR cc_start: 0.7600 (p) cc_final: 0.6253 (t) REVERT: C 852 GLU cc_start: 0.6473 (mt-10) cc_final: 0.6061 (mt-10) REVERT: C 1052 LEU cc_start: 0.8472 (tp) cc_final: 0.8191 (tp) REVERT: C 1064 GLN cc_start: 0.7669 (tt0) cc_final: 0.7445 (tt0) REVERT: C 1079 ILE cc_start: 0.8331 (mt) cc_final: 0.8038 (mm) REVERT: H 112 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 106 LYS cc_start: 0.8310 (tttt) cc_final: 0.8073 (ttpp) REVERT: A 143 ARG cc_start: 0.4482 (ttp-170) cc_final: 0.4206 (ttt180) REVERT: A 230 THR cc_start: 0.7643 (m) cc_final: 0.7345 (p) REVERT: A 293 ASP cc_start: 0.7588 (p0) cc_final: 0.7103 (p0) REVERT: A 298 ILE cc_start: 0.7992 (mm) cc_final: 0.7708 (mt) REVERT: A 311 VAL cc_start: 0.6726 (t) cc_final: 0.6461 (p) REVERT: A 319 VAL cc_start: 0.8167 (t) cc_final: 0.7883 (p) REVERT: A 368 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7644 (mtt) REVERT: A 377 THR cc_start: 0.7918 (m) cc_final: 0.7568 (p) REVERT: A 417 LEU cc_start: 0.8316 (mt) cc_final: 0.8057 (mp) REVERT: A 475 HIS cc_start: 0.7702 (m170) cc_final: 0.6945 (m170) REVERT: A 601 ASN cc_start: 0.7591 (p0) cc_final: 0.7369 (p0) REVERT: A 602 SER cc_start: 0.8208 (t) cc_final: 0.7725 (m) REVERT: A 631 LEU cc_start: 0.8963 (mt) cc_final: 0.8579 (mt) REVERT: A 635 ILE cc_start: 0.8250 (pt) cc_final: 0.7902 (pt) REVERT: A 671 MET cc_start: 0.5757 (mmt) cc_final: 0.5521 (mmm) REVERT: A 728 ASN cc_start: 0.8435 (m-40) cc_final: 0.8211 (m-40) REVERT: A 833 LEU cc_start: 0.7729 (mt) cc_final: 0.7250 (mt) REVERT: A 848 THR cc_start: 0.7790 (p) cc_final: 0.7588 (t) REVERT: A 863 ASN cc_start: 0.5720 (t0) cc_final: 0.5370 (t0) REVERT: A 949 LYS cc_start: 0.8046 (mttt) cc_final: 0.7833 (mttt) REVERT: A 1079 ILE cc_start: 0.8070 (mt) cc_final: 0.7811 (mm) REVERT: A 1141 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7623 (t0) REVERT: D 112 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: B 143 ARG cc_start: 0.5104 (ttt180) cc_final: 0.4353 (ttp-170) REVERT: B 159 LEU cc_start: 0.6975 (mt) cc_final: 0.6611 (mt) REVERT: B 230 THR cc_start: 0.7980 (m) cc_final: 0.7760 (t) REVERT: B 298 ILE cc_start: 0.7844 (mm) cc_final: 0.7632 (mm) REVERT: B 322 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 329 LYS cc_start: 0.7659 (tttp) cc_final: 0.7447 (tttp) REVERT: B 344 LYS cc_start: 0.7854 (ptpt) cc_final: 0.7570 (ptpt) REVERT: B 363 ASN cc_start: 0.5454 (OUTLIER) cc_final: 0.4807 (p0) REVERT: B 379 ASN cc_start: 0.8197 (t0) cc_final: 0.7957 (t0) REVERT: B 591 ILE cc_start: 0.8483 (mt) cc_final: 0.8009 (mm) REVERT: B 652 TYR cc_start: 0.7775 (m-80) cc_final: 0.7542 (m-80) REVERT: B 670 PHE cc_start: 0.6280 (m-80) cc_final: 0.6056 (m-80) REVERT: B 671 MET cc_start: 0.6000 (mmm) cc_final: 0.5625 (mmt) REVERT: B 711 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6586 (mtm180) REVERT: B 720 ASP cc_start: 0.5975 (m-30) cc_final: 0.5141 (m-30) REVERT: B 803 MET cc_start: 0.3720 (OUTLIER) cc_final: 0.3484 (mmm) REVERT: B 852 GLU cc_start: 0.6447 (mt-10) cc_final: 0.6168 (mt-10) REVERT: B 1049 LEU cc_start: 0.8590 (tp) cc_final: 0.8333 (tt) REVERT: B 1050 GLN cc_start: 0.7533 (mm-40) cc_final: 0.6736 (mm-40) REVERT: B 1065 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5674 (mm-30) REVERT: B 1067 LEU cc_start: 0.8303 (tp) cc_final: 0.7895 (tt) REVERT: B 1083 ILE cc_start: 0.7846 (pt) cc_final: 0.7561 (mt) outliers start: 112 outliers final: 68 residues processed: 804 average time/residue: 0.4245 time to fit residues: 559.5950 Evaluate side-chains 769 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 692 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 94 TYR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 829 CYS Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 1139 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 941 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 0.0870 chunk 343 optimal weight: 0.6980 chunk 278 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 205 optimal weight: 0.9980 chunk 361 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN C 239 ASN C 481 GLN C 601 ASN ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 ASN A 481 GLN A 573 GLN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN B 858 GLN ** B1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 GLN B1096 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 33678 Z= 0.199 Angle : 0.628 13.234 45849 Z= 0.331 Chirality : 0.047 0.442 5196 Planarity : 0.004 0.059 5883 Dihedral : 6.026 87.555 4887 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 2.56 % Allowed : 15.69 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.85 (0.13), residues: 4170 helix: 0.26 (0.18), residues: 765 sheet: -0.36 (0.16), residues: 1005 loop : -0.91 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 452 HIS 0.011 0.001 HIS A 475 PHE 0.020 0.002 PHE B 490 TYR 0.048 0.002 TYR C 963 ARG 0.006 0.001 ARG C 571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 702 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7573 (mt) REVERT: C 143 ARG cc_start: 0.4529 (ttt180) cc_final: 0.4303 (ttt180) REVERT: C 230 THR cc_start: 0.7689 (m) cc_final: 0.7424 (t) REVERT: C 311 VAL cc_start: 0.6637 (t) cc_final: 0.6350 (p) REVERT: C 326 TYR cc_start: 0.7233 (t80) cc_final: 0.6899 (t80) REVERT: C 327 ARG cc_start: 0.7060 (mmm-85) cc_final: 0.6791 (mmm-85) REVERT: C 328 ARG cc_start: 0.5668 (mpt180) cc_final: 0.5357 (mpt180) REVERT: C 344 LYS cc_start: 0.7740 (ptpt) cc_final: 0.7497 (ptpt) REVERT: C 380 ASN cc_start: 0.8069 (m-40) cc_final: 0.7688 (m-40) REVERT: C 425 ASP cc_start: 0.7115 (t70) cc_final: 0.6860 (t70) REVERT: C 671 MET cc_start: 0.5609 (mmm) cc_final: 0.5166 (mtp) REVERT: C 720 ASP cc_start: 0.5741 (m-30) cc_final: 0.5530 (m-30) REVERT: C 816 ILE cc_start: 0.7863 (mm) cc_final: 0.7614 (mt) REVERT: C 833 LEU cc_start: 0.7873 (tp) cc_final: 0.7624 (mt) REVERT: C 848 THR cc_start: 0.7457 (p) cc_final: 0.5997 (t) REVERT: C 852 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5786 (mt-10) REVERT: C 1052 LEU cc_start: 0.8293 (tp) cc_final: 0.7996 (tp) REVERT: C 1079 ILE cc_start: 0.8232 (mt) cc_final: 0.7996 (mm) REVERT: A 106 LYS cc_start: 0.8290 (tttt) cc_final: 0.7974 (ttpp) REVERT: A 118 MET cc_start: 0.5513 (tpp) cc_final: 0.5005 (tpt) REVERT: A 143 ARG cc_start: 0.4175 (ttp-170) cc_final: 0.3897 (ttt180) REVERT: A 230 THR cc_start: 0.7543 (m) cc_final: 0.7243 (p) REVERT: A 293 ASP cc_start: 0.7521 (p0) cc_final: 0.7067 (p0) REVERT: A 298 ILE cc_start: 0.7882 (mm) cc_final: 0.7446 (mt) REVERT: A 326 TYR cc_start: 0.7762 (t80) cc_final: 0.7238 (t80) REVERT: A 368 MET cc_start: 0.7778 (mpp) cc_final: 0.7468 (mtp) REVERT: A 377 THR cc_start: 0.7730 (m) cc_final: 0.7456 (p) REVERT: A 395 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7141 (p) REVERT: A 397 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: A 422 TYR cc_start: 0.8048 (t80) cc_final: 0.7680 (t80) REVERT: A 601 ASN cc_start: 0.7274 (p0) cc_final: 0.6815 (p0) REVERT: A 630 ILE cc_start: 0.8139 (mp) cc_final: 0.7682 (mm) REVERT: A 631 LEU cc_start: 0.8902 (mt) cc_final: 0.8600 (mt) REVERT: A 635 ILE cc_start: 0.8189 (pt) cc_final: 0.7923 (pt) REVERT: A 642 THR cc_start: 0.8097 (p) cc_final: 0.7737 (t) REVERT: A 668 ARG cc_start: 0.7402 (ttp-110) cc_final: 0.7122 (ttm110) REVERT: A 720 ASP cc_start: 0.5746 (m-30) cc_final: 0.4964 (m-30) REVERT: A 833 LEU cc_start: 0.7565 (mt) cc_final: 0.7075 (mt) REVERT: A 863 ASN cc_start: 0.5711 (t0) cc_final: 0.5345 (t0) REVERT: A 927 TYR cc_start: 0.7252 (m-80) cc_final: 0.7049 (m-80) REVERT: A 949 LYS cc_start: 0.7785 (mttt) cc_final: 0.7575 (mttt) REVERT: A 1050 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6956 (mm-40) REVERT: A 1079 ILE cc_start: 0.7916 (mt) cc_final: 0.7698 (mm) REVERT: D 112 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: F 4 MET cc_start: 0.3166 (OUTLIER) cc_final: 0.2858 (tpt) REVERT: B 106 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7967 (ttmm) REVERT: B 143 ARG cc_start: 0.4937 (ttt180) cc_final: 0.4423 (ttp-170) REVERT: B 230 THR cc_start: 0.7843 (m) cc_final: 0.7527 (p) REVERT: B 298 ILE cc_start: 0.7940 (mm) cc_final: 0.7523 (mm) REVERT: B 311 VAL cc_start: 0.6722 (t) cc_final: 0.6380 (p) REVERT: B 322 ILE cc_start: 0.8227 (mm) cc_final: 0.7924 (mm) REVERT: B 326 TYR cc_start: 0.7691 (t80) cc_final: 0.7078 (t80) REVERT: B 329 LYS cc_start: 0.7570 (tttp) cc_final: 0.7261 (tttp) REVERT: B 344 LYS cc_start: 0.7655 (ptpt) cc_final: 0.7447 (ptpt) REVERT: B 363 ASN cc_start: 0.5347 (OUTLIER) cc_final: 0.4889 (p0) REVERT: B 549 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 591 ILE cc_start: 0.8463 (mt) cc_final: 0.7965 (mm) REVERT: B 645 ASN cc_start: 0.7900 (t0) cc_final: 0.7696 (t0) REVERT: B 671 MET cc_start: 0.6050 (mmm) cc_final: 0.5633 (mmt) REVERT: B 699 LYS cc_start: 0.6119 (mmmm) cc_final: 0.5700 (mmmm) REVERT: B 711 ARG cc_start: 0.6771 (mtm180) cc_final: 0.6481 (mtm180) REVERT: B 720 ASP cc_start: 0.5953 (m-30) cc_final: 0.5007 (m-30) REVERT: B 852 GLU cc_start: 0.6322 (mt-10) cc_final: 0.6033 (mt-10) REVERT: B 999 MET cc_start: 0.2634 (tmm) cc_final: 0.2390 (tpp) REVERT: B 1049 LEU cc_start: 0.8486 (tp) cc_final: 0.8127 (tt) REVERT: B 1050 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6257 (mm-40) REVERT: B 1059 ILE cc_start: 0.8646 (mt) cc_final: 0.8387 (mm) REVERT: B 1065 GLU cc_start: 0.5774 (mt-10) cc_final: 0.5544 (mm-30) REVERT: B 1067 LEU cc_start: 0.8214 (tp) cc_final: 0.7901 (tt) REVERT: B 1083 ILE cc_start: 0.7845 (pt) cc_final: 0.7458 (mt) outliers start: 93 outliers final: 63 residues processed: 745 average time/residue: 0.4186 time to fit residues: 505.3015 Evaluate side-chains 741 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 671 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 94 TYR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 949 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 403 optimal weight: 0.8980 chunk 334 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 649 ASN ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1226 ASN L 90 GLN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 475 HIS A 481 GLN A 573 GLN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 33678 Z= 0.402 Angle : 0.749 13.799 45849 Z= 0.404 Chirality : 0.052 1.056 5196 Planarity : 0.005 0.077 5883 Dihedral : 6.380 88.583 4887 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.33 % Favored : 93.60 % Rotamer: Outliers : 3.24 % Allowed : 16.65 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4170 helix: 0.02 (0.18), residues: 744 sheet: -0.73 (0.16), residues: 1047 loop : -1.15 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 452 HIS 0.014 0.002 HIS C 215 PHE 0.028 0.003 PHE A 104 TYR 0.051 0.003 TYR C 963 ARG 0.010 0.001 ARG A1125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 731 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 112 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: C 57 TYR cc_start: 0.7420 (m-80) cc_final: 0.7164 (m-80) REVERT: C 64 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7580 (mt) REVERT: C 143 ARG cc_start: 0.4607 (ttt180) cc_final: 0.3955 (ttp-170) REVERT: C 230 THR cc_start: 0.7864 (m) cc_final: 0.7513 (p) REVERT: C 311 VAL cc_start: 0.6753 (t) cc_final: 0.6464 (p) REVERT: C 327 ARG cc_start: 0.7196 (mmm-85) cc_final: 0.6981 (mmm-85) REVERT: C 363 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5420 (p0) REVERT: C 380 ASN cc_start: 0.8196 (m-40) cc_final: 0.7822 (m-40) REVERT: C 425 ASP cc_start: 0.7048 (t70) cc_final: 0.6791 (t70) REVERT: C 549 ILE cc_start: 0.8233 (pt) cc_final: 0.7581 (mt) REVERT: C 599 ASP cc_start: 0.7426 (t70) cc_final: 0.7127 (t70) REVERT: C 605 THR cc_start: 0.8166 (m) cc_final: 0.7646 (t) REVERT: C 671 MET cc_start: 0.5795 (mmm) cc_final: 0.5478 (mtp) REVERT: C 720 ASP cc_start: 0.6312 (m-30) cc_final: 0.6098 (m-30) REVERT: C 816 ILE cc_start: 0.7908 (mm) cc_final: 0.7690 (mt) REVERT: C 848 THR cc_start: 0.7619 (p) cc_final: 0.6393 (t) REVERT: C 849 GLU cc_start: 0.6282 (pt0) cc_final: 0.5821 (pt0) REVERT: C 852 GLU cc_start: 0.6496 (mt-10) cc_final: 0.5979 (mt-10) REVERT: C 1052 LEU cc_start: 0.8477 (tp) cc_final: 0.8191 (tp) REVERT: C 1074 GLU cc_start: 0.7125 (tt0) cc_final: 0.6908 (tt0) REVERT: H 112 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: A 106 LYS cc_start: 0.8359 (tttt) cc_final: 0.8096 (ttpp) REVERT: A 143 ARG cc_start: 0.4433 (ttp-170) cc_final: 0.4110 (ttt180) REVERT: A 293 ASP cc_start: 0.7478 (p0) cc_final: 0.6973 (p0) REVERT: A 298 ILE cc_start: 0.7970 (mm) cc_final: 0.7561 (mt) REVERT: A 311 VAL cc_start: 0.6729 (t) cc_final: 0.6412 (p) REVERT: A 312 TYR cc_start: 0.7267 (m-10) cc_final: 0.7002 (m-10) REVERT: A 368 MET cc_start: 0.7846 (mpp) cc_final: 0.7516 (mtp) REVERT: A 377 THR cc_start: 0.7938 (m) cc_final: 0.7669 (p) REVERT: A 397 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: A 451 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6566 (p) REVERT: A 547 VAL cc_start: 0.8532 (p) cc_final: 0.8319 (m) REVERT: A 601 ASN cc_start: 0.7446 (p0) cc_final: 0.6913 (p0) REVERT: A 602 SER cc_start: 0.8059 (t) cc_final: 0.7619 (m) REVERT: A 631 LEU cc_start: 0.8953 (mt) cc_final: 0.8591 (mt) REVERT: A 635 ILE cc_start: 0.8257 (pt) cc_final: 0.7917 (pt) REVERT: A 652 TYR cc_start: 0.7512 (m-80) cc_final: 0.7164 (m-80) REVERT: A 668 ARG cc_start: 0.7544 (ttp-110) cc_final: 0.7191 (ttm110) REVERT: A 830 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7736 (mmtp) REVERT: A 1050 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6892 (mm-40) REVERT: A 1135 ILE cc_start: 0.4018 (mt) cc_final: 0.3775 (mt) REVERT: D 112 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 64 LEU cc_start: 0.8004 (tt) cc_final: 0.7789 (tt) REVERT: B 106 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7960 (ttmm) REVERT: B 118 MET cc_start: 0.5834 (mmt) cc_final: 0.5609 (tpp) REVERT: B 143 ARG cc_start: 0.5215 (ttt180) cc_final: 0.4531 (ttp-170) REVERT: B 298 ILE cc_start: 0.8192 (mm) cc_final: 0.7849 (mm) REVERT: B 322 ILE cc_start: 0.8312 (mm) cc_final: 0.8003 (mm) REVERT: B 326 TYR cc_start: 0.7873 (t80) cc_final: 0.7414 (t80) REVERT: B 363 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.4683 (p0) REVERT: B 477 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7468 (m) REVERT: B 545 SER cc_start: 0.8224 (p) cc_final: 0.7955 (t) REVERT: B 591 ILE cc_start: 0.8583 (mt) cc_final: 0.8111 (mm) REVERT: B 631 LEU cc_start: 0.8740 (mt) cc_final: 0.8342 (mp) REVERT: B 671 MET cc_start: 0.6037 (mmm) cc_final: 0.5726 (mmt) REVERT: B 699 LYS cc_start: 0.6423 (mmmm) cc_final: 0.6221 (mmmm) REVERT: B 711 ARG cc_start: 0.6971 (mtm180) cc_final: 0.6702 (mtm180) REVERT: B 720 ASP cc_start: 0.6602 (m-30) cc_final: 0.5743 (m-30) REVERT: B 999 MET cc_start: 0.2856 (tmm) cc_final: 0.2606 (tpp) REVERT: B 1049 LEU cc_start: 0.8644 (tp) cc_final: 0.8266 (tt) REVERT: B 1050 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6465 (mm-40) REVERT: B 1065 GLU cc_start: 0.6024 (mt-10) cc_final: 0.5672 (mm-30) REVERT: B 1067 LEU cc_start: 0.8373 (tp) cc_final: 0.7962 (tt) REVERT: B 1083 ILE cc_start: 0.7901 (pt) cc_final: 0.7471 (mt) outliers start: 118 outliers final: 80 residues processed: 783 average time/residue: 0.4259 time to fit residues: 544.2714 Evaluate side-chains 791 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 702 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 94 TYR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 601 ASN Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 818 CYS Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 1068 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 229 optimal weight: 0.4980 chunk 294 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 339 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1050 GLN C1096 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 858 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 33678 Z= 0.208 Angle : 0.664 14.770 45849 Z= 0.349 Chirality : 0.047 0.428 5196 Planarity : 0.004 0.048 5883 Dihedral : 5.821 83.990 4887 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 2.67 % Allowed : 18.36 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4170 helix: 0.34 (0.18), residues: 756 sheet: -0.62 (0.16), residues: 972 loop : -1.00 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 340 HIS 0.008 0.001 HIS A 215 PHE 0.024 0.002 PHE A1013 TYR 0.045 0.002 TYR C 963 ARG 0.005 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 713 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.6902 (mt) cc_final: 0.6632 (mt) REVERT: C 64 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (mt) REVERT: C 143 ARG cc_start: 0.4498 (ttt180) cc_final: 0.3283 (mtp180) REVERT: C 230 THR cc_start: 0.7719 (m) cc_final: 0.7511 (t) REVERT: C 311 VAL cc_start: 0.6664 (t) cc_final: 0.6379 (p) REVERT: C 343 ASP cc_start: 0.6887 (t0) cc_final: 0.6589 (t0) REVERT: C 344 LYS cc_start: 0.7919 (tppt) cc_final: 0.6977 (tppt) REVERT: C 425 ASP cc_start: 0.7023 (t70) cc_final: 0.6702 (t70) REVERT: C 599 ASP cc_start: 0.7298 (t70) cc_final: 0.7020 (t70) REVERT: C 671 MET cc_start: 0.5706 (mmm) cc_final: 0.5367 (mtp) REVERT: C 720 ASP cc_start: 0.6174 (m-30) cc_final: 0.5966 (m-30) REVERT: C 816 ILE cc_start: 0.7784 (mm) cc_final: 0.7576 (mt) REVERT: C 833 LEU cc_start: 0.7811 (tp) cc_final: 0.7564 (mt) REVERT: C 848 THR cc_start: 0.7325 (p) cc_final: 0.6451 (t) REVERT: C 852 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5887 (mt-10) REVERT: C 1052 LEU cc_start: 0.8309 (tp) cc_final: 0.8004 (tp) REVERT: A 143 ARG cc_start: 0.4115 (ttp-170) cc_final: 0.3865 (ttt180) REVERT: A 293 ASP cc_start: 0.7378 (p0) cc_final: 0.6944 (p0) REVERT: A 298 ILE cc_start: 0.7857 (mm) cc_final: 0.7497 (mt) REVERT: A 311 VAL cc_start: 0.6691 (t) cc_final: 0.6394 (p) REVERT: A 344 LYS cc_start: 0.7934 (tptp) cc_final: 0.7409 (tppt) REVERT: A 368 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7461 (mtt) REVERT: A 377 THR cc_start: 0.7864 (m) cc_final: 0.7589 (p) REVERT: A 435 TYR cc_start: 0.7329 (p90) cc_final: 0.6937 (p90) REVERT: A 596 ILE cc_start: 0.8421 (mp) cc_final: 0.8083 (mt) REVERT: A 601 ASN cc_start: 0.7159 (p0) cc_final: 0.6722 (p0) REVERT: A 602 SER cc_start: 0.7642 (t) cc_final: 0.7324 (m) REVERT: A 630 ILE cc_start: 0.8146 (mp) cc_final: 0.7476 (tp) REVERT: A 631 LEU cc_start: 0.8936 (mt) cc_final: 0.8605 (mt) REVERT: A 635 ILE cc_start: 0.8165 (pt) cc_final: 0.7880 (pt) REVERT: A 652 TYR cc_start: 0.7306 (m-80) cc_final: 0.7084 (m-80) REVERT: A 668 ARG cc_start: 0.7424 (ttp-110) cc_final: 0.7079 (ttm110) REVERT: A 830 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7741 (mmtp) REVERT: A 863 ASN cc_start: 0.5823 (t0) cc_final: 0.5479 (t0) REVERT: A 928 ASN cc_start: 0.6779 (m-40) cc_final: 0.6557 (m-40) REVERT: A 1050 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6652 (mm-40) REVERT: D 112 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: B 143 ARG cc_start: 0.5132 (ttt180) cc_final: 0.4507 (ttp-170) REVERT: B 298 ILE cc_start: 0.8096 (mm) cc_final: 0.7628 (mm) REVERT: B 311 VAL cc_start: 0.6603 (t) cc_final: 0.6295 (p) REVERT: B 322 ILE cc_start: 0.8223 (mm) cc_final: 0.7901 (mm) REVERT: B 326 TYR cc_start: 0.7670 (t80) cc_final: 0.7243 (t80) REVERT: B 363 ASN cc_start: 0.5439 (OUTLIER) cc_final: 0.4701 (p0) REVERT: B 477 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.7246 (m) REVERT: B 545 SER cc_start: 0.8282 (p) cc_final: 0.7935 (t) REVERT: B 591 ILE cc_start: 0.8515 (mt) cc_final: 0.8102 (mm) REVERT: B 631 LEU cc_start: 0.8724 (mt) cc_final: 0.8323 (mp) REVERT: B 671 MET cc_start: 0.6048 (mmm) cc_final: 0.5738 (mmt) REVERT: B 711 ARG cc_start: 0.6735 (mtm180) cc_final: 0.6482 (mtm180) REVERT: B 720 ASP cc_start: 0.6573 (m-30) cc_final: 0.5720 (m-30) REVERT: B 852 GLU cc_start: 0.6312 (mt-10) cc_final: 0.6067 (mt-10) REVERT: B 1050 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6317 (mm-40) REVERT: B 1059 ILE cc_start: 0.8594 (mt) cc_final: 0.8359 (mm) REVERT: B 1067 LEU cc_start: 0.8172 (tp) cc_final: 0.7807 (tt) REVERT: B 1083 ILE cc_start: 0.7873 (pt) cc_final: 0.7469 (mt) REVERT: B 1112 MET cc_start: 0.6056 (mpp) cc_final: 0.5769 (mtm) REVERT: B 1210 MET cc_start: 0.2925 (ppp) cc_final: 0.0973 (pmm) outliers start: 97 outliers final: 70 residues processed: 754 average time/residue: 0.4361 time to fit residues: 532.2279 Evaluate side-chains 756 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 681 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 818 CYS Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain C residue 1096 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 949 LYS Chi-restraints excluded: chain B residue 1068 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 255 optimal weight: 0.5980 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1050 GLN C1096 GLN A 280 GLN A 714 GLN ** A 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33678 Z= 0.255 Angle : 0.681 13.707 45849 Z= 0.359 Chirality : 0.047 0.418 5196 Planarity : 0.004 0.047 5883 Dihedral : 5.528 74.086 4887 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 3.16 % Allowed : 18.66 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4170 helix: 0.29 (0.18), residues: 744 sheet: -0.48 (0.16), residues: 972 loop : -1.04 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 340 HIS 0.009 0.002 HIS A 215 PHE 0.030 0.002 PHE A 458 TYR 0.042 0.002 TYR C 963 ARG 0.006 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 710 time to evaluate : 3.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.6964 (mt) cc_final: 0.6701 (mt) REVERT: X 112 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: C 64 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7608 (mt) REVERT: C 143 ARG cc_start: 0.4382 (ttt180) cc_final: 0.3717 (ttp-170) REVERT: C 230 THR cc_start: 0.7759 (m) cc_final: 0.7405 (p) REVERT: C 261 THR cc_start: 0.7246 (m) cc_final: 0.6857 (p) REVERT: C 311 VAL cc_start: 0.6688 (t) cc_final: 0.6440 (p) REVERT: C 380 ASN cc_start: 0.8292 (m-40) cc_final: 0.7774 (m-40) REVERT: C 599 ASP cc_start: 0.7239 (t70) cc_final: 0.6951 (t70) REVERT: C 605 THR cc_start: 0.8170 (m) cc_final: 0.7641 (t) REVERT: C 671 MET cc_start: 0.5617 (mmm) cc_final: 0.5213 (mtp) REVERT: C 720 ASP cc_start: 0.6349 (m-30) cc_final: 0.6088 (m-30) REVERT: C 833 LEU cc_start: 0.7791 (tp) cc_final: 0.7553 (mt) REVERT: C 848 THR cc_start: 0.7365 (p) cc_final: 0.6483 (t) REVERT: C 849 GLU cc_start: 0.6151 (pt0) cc_final: 0.5758 (pt0) REVERT: C 852 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5892 (mt-10) REVERT: C 1052 LEU cc_start: 0.8335 (tp) cc_final: 0.8079 (tp) REVERT: C 1074 GLU cc_start: 0.7015 (tt0) cc_final: 0.6750 (tt0) REVERT: A 143 ARG cc_start: 0.4253 (ttp-170) cc_final: 0.3737 (ttp-170) REVERT: A 187 LEU cc_start: 0.6893 (tp) cc_final: 0.6613 (tp) REVERT: A 200 LYS cc_start: 0.7314 (mppt) cc_final: 0.6512 (mmmt) REVERT: A 293 ASP cc_start: 0.7356 (p0) cc_final: 0.6914 (p0) REVERT: A 298 ILE cc_start: 0.7899 (mm) cc_final: 0.7579 (mt) REVERT: A 311 VAL cc_start: 0.6658 (t) cc_final: 0.6396 (p) REVERT: A 344 LYS cc_start: 0.8226 (tptp) cc_final: 0.7840 (tppt) REVERT: A 377 THR cc_start: 0.7885 (m) cc_final: 0.7624 (p) REVERT: A 435 TYR cc_start: 0.7415 (p90) cc_final: 0.7014 (p90) REVERT: A 437 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7042 (mm) REVERT: A 451 THR cc_start: 0.6790 (OUTLIER) cc_final: 0.6588 (p) REVERT: A 602 SER cc_start: 0.7744 (t) cc_final: 0.7389 (m) REVERT: A 630 ILE cc_start: 0.8131 (mp) cc_final: 0.7460 (tp) REVERT: A 631 LEU cc_start: 0.8958 (mt) cc_final: 0.8546 (mt) REVERT: A 635 ILE cc_start: 0.8146 (pt) cc_final: 0.7809 (pt) REVERT: A 652 TYR cc_start: 0.7322 (m-80) cc_final: 0.7104 (m-80) REVERT: A 668 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.7098 (ttm110) REVERT: A 863 ASN cc_start: 0.5803 (t0) cc_final: 0.5514 (t0) REVERT: A 928 ASN cc_start: 0.6992 (m-40) cc_final: 0.6764 (m-40) REVERT: A 1050 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6680 (mm-40) REVERT: A 1156 THR cc_start: 0.2735 (OUTLIER) cc_final: 0.1250 (m) REVERT: D 112 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: B 143 ARG cc_start: 0.5125 (ttt180) cc_final: 0.4505 (ttp-170) REVERT: B 298 ILE cc_start: 0.8133 (mm) cc_final: 0.7696 (mm) REVERT: B 311 VAL cc_start: 0.6690 (t) cc_final: 0.6372 (p) REVERT: B 322 ILE cc_start: 0.8321 (mm) cc_final: 0.8007 (mm) REVERT: B 326 TYR cc_start: 0.7675 (t80) cc_final: 0.7230 (t80) REVERT: B 329 LYS cc_start: 0.7678 (tttp) cc_final: 0.7326 (tttp) REVERT: B 331 ASN cc_start: 0.6776 (p0) cc_final: 0.6558 (p0) REVERT: B 477 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 545 SER cc_start: 0.8249 (p) cc_final: 0.7911 (t) REVERT: B 591 ILE cc_start: 0.8575 (mt) cc_final: 0.8149 (mm) REVERT: B 631 LEU cc_start: 0.8717 (mt) cc_final: 0.8285 (mp) REVERT: B 671 MET cc_start: 0.6052 (mmm) cc_final: 0.5730 (mmt) REVERT: B 711 ARG cc_start: 0.6762 (mtm180) cc_final: 0.6499 (mtm180) REVERT: B 720 ASP cc_start: 0.6575 (m-30) cc_final: 0.6360 (m-30) REVERT: B 852 GLU cc_start: 0.6305 (mt-10) cc_final: 0.6062 (mt-10) REVERT: B 1050 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6229 (mm-40) REVERT: B 1059 ILE cc_start: 0.8603 (mt) cc_final: 0.8349 (mm) REVERT: B 1067 LEU cc_start: 0.8151 (tp) cc_final: 0.7810 (tt) REVERT: B 1083 ILE cc_start: 0.7901 (pt) cc_final: 0.7497 (mt) outliers start: 115 outliers final: 82 residues processed: 762 average time/residue: 0.4275 time to fit residues: 529.1489 Evaluate side-chains 784 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 695 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1043 GLU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 340 TRP Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 CYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 365 optimal weight: 3.9990 chunk 385 optimal weight: 8.9990 chunk 351 optimal weight: 0.9980 chunk 374 optimal weight: 0.8980 chunk 384 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 294 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 338 optimal weight: 0.8980 chunk 354 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN C 418 GLN ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1050 GLN C1096 GLN A 770 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN B 410 GLN ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN B1096 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33678 Z= 0.212 Angle : 0.676 14.921 45849 Z= 0.351 Chirality : 0.046 0.413 5196 Planarity : 0.004 0.044 5883 Dihedral : 5.286 62.444 4887 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 2.61 % Allowed : 19.43 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.94 (0.13), residues: 4170 helix: 0.38 (0.18), residues: 747 sheet: -0.46 (0.17), residues: 942 loop : -1.00 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 452 HIS 0.008 0.001 HIS A 215 PHE 0.032 0.002 PHE A 458 TYR 0.040 0.002 TYR C 963 ARG 0.009 0.001 ARG C1086 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 698 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.6983 (mt) cc_final: 0.6722 (mt) REVERT: X 112 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: C 64 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7590 (mt) REVERT: C 143 ARG cc_start: 0.4378 (ttt180) cc_final: 0.3821 (ttp-170) REVERT: C 230 THR cc_start: 0.7803 (m) cc_final: 0.7480 (p) REVERT: C 311 VAL cc_start: 0.6692 (t) cc_final: 0.6417 (p) REVERT: C 380 ASN cc_start: 0.8196 (m-40) cc_final: 0.7843 (m-40) REVERT: C 671 MET cc_start: 0.5482 (mmm) cc_final: 0.5059 (mtp) REVERT: C 720 ASP cc_start: 0.6387 (m-30) cc_final: 0.6159 (m-30) REVERT: C 816 ILE cc_start: 0.7882 (mp) cc_final: 0.7511 (mt) REVERT: C 833 LEU cc_start: 0.7717 (tp) cc_final: 0.7402 (tt) REVERT: C 848 THR cc_start: 0.7413 (p) cc_final: 0.6496 (t) REVERT: C 849 GLU cc_start: 0.6130 (pt0) cc_final: 0.5791 (pt0) REVERT: C 852 GLU cc_start: 0.6279 (mt-10) cc_final: 0.5976 (mt-10) REVERT: C 1052 LEU cc_start: 0.8295 (tp) cc_final: 0.8063 (tp) REVERT: C 1074 GLU cc_start: 0.7002 (tt0) cc_final: 0.6737 (tt0) REVERT: A 143 ARG cc_start: 0.4180 (ttp-170) cc_final: 0.3736 (ttp-170) REVERT: A 187 LEU cc_start: 0.6743 (tp) cc_final: 0.6488 (tp) REVERT: A 200 LYS cc_start: 0.7342 (mppt) cc_final: 0.6568 (mmmt) REVERT: A 293 ASP cc_start: 0.7365 (p0) cc_final: 0.6935 (p0) REVERT: A 298 ILE cc_start: 0.7829 (mm) cc_final: 0.7467 (mt) REVERT: A 311 VAL cc_start: 0.6623 (t) cc_final: 0.6337 (p) REVERT: A 377 THR cc_start: 0.7863 (m) cc_final: 0.7624 (p) REVERT: A 397 ASP cc_start: 0.7050 (p0) cc_final: 0.6769 (p0) REVERT: A 409 LEU cc_start: 0.8496 (mt) cc_final: 0.8223 (mp) REVERT: A 435 TYR cc_start: 0.7396 (p90) cc_final: 0.7109 (p90) REVERT: A 602 SER cc_start: 0.7689 (t) cc_final: 0.7354 (m) REVERT: A 630 ILE cc_start: 0.8076 (mp) cc_final: 0.7495 (tp) REVERT: A 631 LEU cc_start: 0.8870 (mt) cc_final: 0.8632 (mt) REVERT: A 635 ILE cc_start: 0.8143 (pt) cc_final: 0.7789 (pt) REVERT: A 644 TYR cc_start: 0.7334 (m-80) cc_final: 0.6846 (m-80) REVERT: A 652 TYR cc_start: 0.7246 (m-80) cc_final: 0.7026 (m-80) REVERT: A 668 ARG cc_start: 0.7433 (ttp-110) cc_final: 0.7066 (ttm110) REVERT: A 728 ASN cc_start: 0.8314 (m110) cc_final: 0.8109 (m110) REVERT: A 830 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7777 (mmtm) REVERT: A 863 ASN cc_start: 0.5758 (t0) cc_final: 0.5510 (t0) REVERT: A 1050 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6601 (mm-40) REVERT: A 1136 ILE cc_start: 0.4945 (mp) cc_final: 0.4743 (tp) REVERT: A 1156 THR cc_start: 0.2544 (OUTLIER) cc_final: 0.0992 (m) REVERT: D 112 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: B 106 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8021 (tttp) REVERT: B 143 ARG cc_start: 0.4942 (ttt180) cc_final: 0.4351 (ttp-170) REVERT: B 235 LYS cc_start: 0.7494 (pttm) cc_final: 0.7236 (pttm) REVERT: B 298 ILE cc_start: 0.8107 (mm) cc_final: 0.7718 (mm) REVERT: B 311 VAL cc_start: 0.6640 (t) cc_final: 0.6355 (p) REVERT: B 322 ILE cc_start: 0.8261 (mm) cc_final: 0.7921 (mm) REVERT: B 326 TYR cc_start: 0.7583 (t80) cc_final: 0.7199 (t80) REVERT: B 331 ASN cc_start: 0.6766 (p0) cc_final: 0.6564 (p0) REVERT: B 477 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7399 (m) REVERT: B 545 SER cc_start: 0.8262 (p) cc_final: 0.7990 (t) REVERT: B 591 ILE cc_start: 0.8573 (mt) cc_final: 0.8137 (mm) REVERT: B 671 MET cc_start: 0.6024 (mmm) cc_final: 0.5709 (mmt) REVERT: B 711 ARG cc_start: 0.6757 (mtm180) cc_final: 0.6473 (mtm180) REVERT: B 830 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7917 (mmtp) REVERT: B 852 GLU cc_start: 0.6309 (mt-10) cc_final: 0.6017 (mt-10) REVERT: B 1050 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6108 (mm-40) REVERT: B 1059 ILE cc_start: 0.8581 (mt) cc_final: 0.8322 (mm) REVERT: B 1083 ILE cc_start: 0.7887 (pt) cc_final: 0.7459 (mt) REVERT: B 1210 MET cc_start: 0.2911 (ppp) cc_final: 0.0973 (pmm) outliers start: 95 outliers final: 78 residues processed: 745 average time/residue: 0.4403 time to fit residues: 530.5717 Evaluate side-chains 762 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 679 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1043 GLU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 606 CYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 373 optimal weight: 0.0870 chunk 245 optimal weight: 2.9990 chunk 396 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 415 optimal weight: 0.4980 chunk 382 optimal weight: 8.9990 chunk 330 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 GLN ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33678 Z= 0.216 Angle : 0.684 15.189 45849 Z= 0.355 Chirality : 0.046 0.405 5196 Planarity : 0.004 0.044 5883 Dihedral : 5.140 48.471 4887 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 19.92 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4170 helix: 0.34 (0.18), residues: 759 sheet: -0.33 (0.16), residues: 981 loop : -0.99 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 452 HIS 0.008 0.001 HIS A 215 PHE 0.040 0.002 PHE A 458 TYR 0.040 0.002 TYR C 963 ARG 0.008 0.001 ARG A 571 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 701 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.6991 (mt) cc_final: 0.6738 (mt) REVERT: X 112 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: C 64 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7587 (mt) REVERT: C 143 ARG cc_start: 0.4376 (ttt180) cc_final: 0.3975 (ttp-170) REVERT: C 230 THR cc_start: 0.7763 (m) cc_final: 0.7448 (p) REVERT: C 311 VAL cc_start: 0.6681 (t) cc_final: 0.6421 (p) REVERT: C 380 ASN cc_start: 0.8285 (m-40) cc_final: 0.7917 (m-40) REVERT: C 671 MET cc_start: 0.5465 (mmm) cc_final: 0.4977 (mtp) REVERT: C 720 ASP cc_start: 0.6554 (m-30) cc_final: 0.6245 (m-30) REVERT: C 816 ILE cc_start: 0.7882 (mp) cc_final: 0.7520 (mt) REVERT: C 833 LEU cc_start: 0.7689 (tp) cc_final: 0.7429 (tt) REVERT: C 852 GLU cc_start: 0.6324 (mt-10) cc_final: 0.5902 (mt-10) REVERT: C 1052 LEU cc_start: 0.8309 (tp) cc_final: 0.8100 (tp) REVERT: A 143 ARG cc_start: 0.4169 (ttp-170) cc_final: 0.3787 (ttp-170) REVERT: A 187 LEU cc_start: 0.6678 (tp) cc_final: 0.6431 (tp) REVERT: A 200 LYS cc_start: 0.7342 (mppt) cc_final: 0.6948 (mppt) REVERT: A 293 ASP cc_start: 0.7294 (p0) cc_final: 0.6846 (p0) REVERT: A 298 ILE cc_start: 0.7895 (mm) cc_final: 0.7536 (mt) REVERT: A 311 VAL cc_start: 0.6706 (t) cc_final: 0.6434 (p) REVERT: A 397 ASP cc_start: 0.7046 (p0) cc_final: 0.6678 (p0) REVERT: A 409 LEU cc_start: 0.8445 (mt) cc_final: 0.8205 (mp) REVERT: A 435 TYR cc_start: 0.7408 (p90) cc_final: 0.7130 (p90) REVERT: A 596 ILE cc_start: 0.8302 (mp) cc_final: 0.7871 (mt) REVERT: A 602 SER cc_start: 0.7677 (t) cc_final: 0.7359 (m) REVERT: A 630 ILE cc_start: 0.8100 (mp) cc_final: 0.7487 (tp) REVERT: A 631 LEU cc_start: 0.8863 (mt) cc_final: 0.8601 (mt) REVERT: A 635 ILE cc_start: 0.8109 (pt) cc_final: 0.7817 (pt) REVERT: A 644 TYR cc_start: 0.7354 (m-80) cc_final: 0.6890 (m-80) REVERT: A 668 ARG cc_start: 0.7414 (ttp-110) cc_final: 0.7068 (ttm110) REVERT: A 679 ARG cc_start: 0.6506 (mtp85) cc_final: 0.6017 (mtp85) REVERT: A 728 ASN cc_start: 0.8303 (m110) cc_final: 0.8041 (m110) REVERT: A 830 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7771 (mmtm) REVERT: A 863 ASN cc_start: 0.5681 (t0) cc_final: 0.5424 (t0) REVERT: A 866 MET cc_start: 0.5392 (ptp) cc_final: 0.4815 (ptp) REVERT: A 1050 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6614 (mm-40) REVERT: A 1136 ILE cc_start: 0.4985 (mp) cc_final: 0.4778 (tp) REVERT: A 1147 TYR cc_start: 0.6064 (t80) cc_final: 0.5825 (t80) REVERT: A 1156 THR cc_start: 0.2087 (OUTLIER) cc_final: 0.0519 (m) REVERT: D 112 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: B 106 LYS cc_start: 0.8350 (ttmm) cc_final: 0.8034 (tttp) REVERT: B 143 ARG cc_start: 0.4938 (ttt180) cc_final: 0.4337 (ttp-170) REVERT: B 235 LYS cc_start: 0.7417 (pttm) cc_final: 0.7148 (pttm) REVERT: B 311 VAL cc_start: 0.6673 (t) cc_final: 0.6442 (p) REVERT: B 322 ILE cc_start: 0.8254 (mm) cc_final: 0.7930 (mm) REVERT: B 326 TYR cc_start: 0.7601 (t80) cc_final: 0.7222 (t80) REVERT: B 329 LYS cc_start: 0.7687 (tttp) cc_final: 0.7286 (tttp) REVERT: B 331 ASN cc_start: 0.6782 (p0) cc_final: 0.6572 (p0) REVERT: B 406 LYS cc_start: 0.8037 (tptt) cc_final: 0.7816 (tptt) REVERT: B 477 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 545 SER cc_start: 0.8243 (p) cc_final: 0.7956 (t) REVERT: B 559 LYS cc_start: 0.7627 (pttt) cc_final: 0.7294 (pttt) REVERT: B 591 ILE cc_start: 0.8559 (mt) cc_final: 0.8165 (mm) REVERT: B 599 ASP cc_start: 0.7153 (t0) cc_final: 0.6932 (t70) REVERT: B 671 MET cc_start: 0.6007 (mmm) cc_final: 0.5716 (mmt) REVERT: B 711 ARG cc_start: 0.6777 (mtm180) cc_final: 0.6542 (mtm180) REVERT: B 830 LYS cc_start: 0.8304 (mmmm) cc_final: 0.7907 (mmtp) REVERT: B 852 GLU cc_start: 0.6305 (mt-10) cc_final: 0.6035 (mt-10) REVERT: B 1050 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6060 (mm-40) REVERT: B 1059 ILE cc_start: 0.8518 (mt) cc_final: 0.8311 (mm) REVERT: B 1083 ILE cc_start: 0.7916 (pt) cc_final: 0.7511 (mt) REVERT: B 1210 MET cc_start: 0.2970 (ppp) cc_final: 0.1024 (pmm) outliers start: 86 outliers final: 73 residues processed: 745 average time/residue: 0.4406 time to fit residues: 528.4873 Evaluate side-chains 765 residues out of total 3639 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 687 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 312 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 571 ARG Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1043 GLU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 370 PHE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 202 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 305 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 331 optimal weight: 0.2980 chunk 138 optimal weight: 0.0870 chunk 340 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C1050 GLN B 573 GLN ** B1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.192033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.160247 restraints weight = 57766.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165165 restraints weight = 30510.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168434 restraints weight = 18829.908| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33678 Z= 0.192 Angle : 0.670 15.377 45849 Z= 0.347 Chirality : 0.046 0.403 5196 Planarity : 0.004 0.044 5883 Dihedral : 5.012 50.576 4887 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 2.23 % Allowed : 20.36 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.79 (0.13), residues: 4170 helix: 0.40 (0.18), residues: 762 sheet: -0.28 (0.17), residues: 951 loop : -0.91 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 452 HIS 0.006 0.001 HIS A 215 PHE 0.027 0.002 PHE A 458 TYR 0.055 0.001 TYR C 963 ARG 0.008 0.001 ARG A 571 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8607.88 seconds wall clock time: 155 minutes 6.37 seconds (9306.37 seconds total)