Starting phenix.real_space_refine on Mon Feb 19 12:38:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si6_40500/02_2024/8si6_40500_neut_trim_updated.pdb" } resolution = 2.44 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= 0.010 sd= 0.070 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 240 5.16 5 C 25600 2.51 5 N 6024 2.21 5 O 6736 1.98 5 H 36240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74889 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 18006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 18006 Classifications: {'peptide': 1107} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1062} Chain breaks: 3 Chain: "B" Number of atoms: 18006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 18006 Classifications: {'peptide': 1107} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1062} Chain breaks: 3 Chain: "C" Number of atoms: 18006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 18006 Classifications: {'peptide': 1107} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1062} Chain breaks: 3 Chain: "D" Number of atoms: 18006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 18006 Classifications: {'peptide': 1107} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1062} Chain breaks: 3 Chain: "A" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 768 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 14, 'ZY8': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 664 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 12, 'ZY8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 717 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 1, 'POV': 13, 'ZY8': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 716 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 13, 'ZY8': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 24.37, per 1000 atoms: 0.33 Number of scatterers: 74889 At special positions: 0 Unit cell: (180.11, 180.11, 159.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 240 16.00 P 48 15.00 O 6736 8.00 N 6024 7.00 C 25600 6.00 H 36240 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.05 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.05 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.04 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.04 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.05 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.04 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 48.27 Conformation dependent library (CDL) restraints added in 5.4 seconds 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 8 sheets defined 54.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.38 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.822A pdb=" N CYS A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.971A pdb=" N GLU A 76 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.708A pdb=" N LEU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.635A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.600A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 4.070A pdb=" N LEU A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.609A pdb=" N SER A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.944A pdb=" N THR A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.680A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.522A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.771A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 509 through 520 removed outlier: 3.545A pdb=" N LEU A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.515A pdb=" N LEU A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.618A pdb=" N ILE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.730A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 667 removed outlier: 3.578A pdb=" N LYS A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 700 removed outlier: 3.527A pdb=" N PHE A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.698A pdb=" N LEU A 772 " --> pdb=" O PRO A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.629A pdb=" N PHE A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 removed outlier: 4.038A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 874 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.901A pdb=" N SER A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.574A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.669A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 999 removed outlier: 3.810A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 995 " --> pdb=" O MET A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1031 through 1035 Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.962A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1085 removed outlier: 3.626A pdb=" N THR A1073 " --> pdb=" O THR A1070 " (cutoff:3.500A) Proline residue: A1074 - end of helix removed outlier: 3.535A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1119 removed outlier: 4.786A pdb=" N LEU A1101 " --> pdb=" O ASN A1097 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN A1102 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1146 removed outlier: 3.670A pdb=" N ILE A1138 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1139 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A1140 " --> pdb=" O HIS A1137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS A1143 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A1144 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A1145 " --> pdb=" O PHE A1142 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS A1146 " --> pdb=" O CYS A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1190 removed outlier: 3.610A pdb=" N LYS A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1229 removed outlier: 3.617A pdb=" N ARG A1198 " --> pdb=" O GLU A1194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A1226 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1227 " --> pdb=" O ARG A1223 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 removed outlier: 3.822A pdb=" N CYS B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.971A pdb=" N GLU B 76 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 removed outlier: 3.709A pdb=" N LEU B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.635A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.599A pdb=" N ARG B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 4.070A pdb=" N LEU B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.609A pdb=" N SER B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.944A pdb=" N THR B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.681A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.522A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.771A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'B' and resid 509 through 520 removed outlier: 3.545A pdb=" N LEU B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.515A pdb=" N LEU B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.618A pdb=" N ILE B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.729A pdb=" N GLN B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.577A pdb=" N LYS B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 700 removed outlier: 3.527A pdb=" N PHE B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 737 through 748 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.698A pdb=" N LEU B 772 " --> pdb=" O PRO B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 793 Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.628A pdb=" N PHE B 845 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 846 " --> pdb=" O THR B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 removed outlier: 4.038A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 874 " --> pdb=" O TYR B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 Processing helix chain 'B' and resid 912 through 921 removed outlier: 3.900A pdb=" N SER B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.573A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.670A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.811A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 995 " --> pdb=" O MET B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1022 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1031 through 1035 Processing helix chain 'B' and resid 1038 through 1045 removed outlier: 3.962A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1085 removed outlier: 3.626A pdb=" N THR B1073 " --> pdb=" O THR B1070 " (cutoff:3.500A) Proline residue: B1074 - end of helix removed outlier: 3.535A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B1082 " --> pdb=" O VAL B1079 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1119 removed outlier: 4.786A pdb=" N LEU B1101 " --> pdb=" O ASN B1097 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN B1102 " --> pdb=" O ASN B1098 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1146 removed outlier: 3.671A pdb=" N ILE B1138 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B1139 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1140 " --> pdb=" O HIS B1137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS B1143 " --> pdb=" O SER B1140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B1145 " --> pdb=" O PHE B1142 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS B1146 " --> pdb=" O CYS B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1190 removed outlier: 3.610A pdb=" N LYS B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1229 removed outlier: 3.616A pdb=" N ARG B1198 " --> pdb=" O GLU B1194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B1226 " --> pdb=" O LYS B1222 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B1227 " --> pdb=" O ARG B1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 removed outlier: 3.822A pdb=" N CYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN C 37 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.971A pdb=" N GLU C 76 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 removed outlier: 3.709A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.635A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.600A pdb=" N ARG C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.070A pdb=" N LEU C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.609A pdb=" N SER C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.944A pdb=" N THR C 367 " --> pdb=" O HIS C 363 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 392 through 401 removed outlier: 3.681A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 417 Processing helix chain 'C' and resid 420 through 426 Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.522A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 460 Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.771A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'C' and resid 509 through 520 removed outlier: 3.545A pdb=" N LEU C 514 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.514A pdb=" N LEU C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 631 removed outlier: 3.617A pdb=" N ILE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 removed outlier: 3.730A pdb=" N GLN C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 667 removed outlier: 3.577A pdb=" N LYS C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 700 removed outlier: 3.527A pdb=" N PHE C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 removed outlier: 3.698A pdb=" N LEU C 772 " --> pdb=" O PRO C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 793 Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.629A pdb=" N PHE C 845 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 846 " --> pdb=" O THR C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 removed outlier: 4.037A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL C 874 " --> pdb=" O TYR C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 Processing helix chain 'C' and resid 912 through 921 removed outlier: 3.900A pdb=" N SER C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 943 removed outlier: 3.574A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.670A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 999 removed outlier: 3.811A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 995 " --> pdb=" O MET C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1022 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1031 through 1035 Processing helix chain 'C' and resid 1038 through 1045 removed outlier: 3.962A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1085 removed outlier: 3.626A pdb=" N THR C1073 " --> pdb=" O THR C1070 " (cutoff:3.500A) Proline residue: C1074 - end of helix removed outlier: 3.534A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C1082 " --> pdb=" O VAL C1079 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1119 removed outlier: 4.785A pdb=" N LEU C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN C1102 " --> pdb=" O ASN C1098 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1146 removed outlier: 3.670A pdb=" N ILE C1138 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1139 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C1140 " --> pdb=" O HIS C1137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS C1143 " --> pdb=" O SER C1140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C1144 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C1145 " --> pdb=" O PHE C1142 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS C1146 " --> pdb=" O CYS C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1190 removed outlier: 3.611A pdb=" N LYS C1169 " --> pdb=" O GLU C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1229 removed outlier: 3.616A pdb=" N ARG C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C1226 " --> pdb=" O LYS C1222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C1227 " --> pdb=" O ARG C1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 removed outlier: 3.822A pdb=" N CYS D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN D 37 " --> pdb=" O CYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.971A pdb=" N GLU D 76 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.708A pdb=" N LEU D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.636A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 260 through 271 removed outlier: 3.600A pdb=" N ARG D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 4.070A pdb=" N LEU D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.609A pdb=" N SER D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.944A pdb=" N THR D 367 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 392 through 401 removed outlier: 3.681A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 420 through 426 Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.522A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 460 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 471 through 478 removed outlier: 3.772A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 494 Processing helix chain 'D' and resid 509 through 520 removed outlier: 3.545A pdb=" N LEU D 514 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.515A pdb=" N LEU D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 631 removed outlier: 3.618A pdb=" N ILE D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.729A pdb=" N GLN D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 667 removed outlier: 3.578A pdb=" N LYS D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 700 removed outlier: 3.528A pdb=" N PHE D 686 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D 700 " --> pdb=" O GLN D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 737 through 748 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 removed outlier: 3.698A pdb=" N LEU D 772 " --> pdb=" O PRO D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 793 Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.628A pdb=" N PHE D 845 " --> pdb=" O ILE D 841 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D 846 " --> pdb=" O THR D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 removed outlier: 4.037A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 874 " --> pdb=" O TYR D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 Processing helix chain 'D' and resid 912 through 921 removed outlier: 3.901A pdb=" N SER D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 943 removed outlier: 3.574A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.670A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 999 removed outlier: 3.810A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1022 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1031 through 1035 Processing helix chain 'D' and resid 1038 through 1045 removed outlier: 3.963A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1085 removed outlier: 3.625A pdb=" N THR D1073 " --> pdb=" O THR D1070 " (cutoff:3.500A) Proline residue: D1074 - end of helix removed outlier: 3.535A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D1082 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1119 removed outlier: 4.785A pdb=" N LEU D1101 " --> pdb=" O ASN D1097 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN D1102 " --> pdb=" O ASN D1098 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1146 removed outlier: 3.669A pdb=" N ILE D1138 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D1139 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D1140 " --> pdb=" O HIS D1137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N CYS D1143 " --> pdb=" O SER D1140 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS D1144 " --> pdb=" O LEU D1141 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D1145 " --> pdb=" O PHE D1142 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS D1146 " --> pdb=" O CYS D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1190 removed outlier: 3.611A pdb=" N LYS D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) Processing helix chain 'D' and resid 1193 through 1229 removed outlier: 3.617A pdb=" N ARG D1198 " --> pdb=" O GLU D1194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D1226 " --> pdb=" O LYS D1222 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D1227 " --> pdb=" O ARG D1223 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 13 through 15 Processing sheet with id= B, first strand: chain 'A' and resid 378 through 381 removed outlier: 7.310A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP A 170 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 139 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 172 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS A 200 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR A 173 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 202 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS A 244 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA A 205 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE A 246 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 13 through 15 Processing sheet with id= D, first strand: chain 'B' and resid 378 through 381 removed outlier: 7.310A pdb=" N VAL B 312 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N PHE B 381 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL B 314 " --> pdb=" O PHE B 381 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP B 170 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL B 139 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 172 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS B 200 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR B 173 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 202 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS B 244 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA B 205 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE B 246 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 13 through 15 Processing sheet with id= F, first strand: chain 'C' and resid 378 through 381 removed outlier: 7.311A pdb=" N VAL C 312 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE C 381 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 314 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP C 170 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL C 139 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 172 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS C 200 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR C 173 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 202 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS C 244 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA C 205 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE C 246 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 13 through 15 Processing sheet with id= H, first strand: chain 'D' and resid 378 through 381 removed outlier: 7.311A pdb=" N VAL D 312 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N PHE D 381 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL D 314 " --> pdb=" O PHE D 381 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP D 170 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 139 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 172 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS D 200 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR D 173 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 202 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS D 244 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ALA D 205 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE D 246 " --> pdb=" O ALA D 205 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3972 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: 24.40 Time building geometry restraints manager: 50.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 36172 1.03 - 1.24: 4514 1.24 - 1.44: 11560 1.44 - 1.64: 23122 1.64 - 1.85: 392 Bond restraints: 75760 Sorted by residual: bond pdb=" C6 ZY8 A1314 " pdb=" C7 ZY8 A1314 " ideal model delta sigma weight residual 1.797 1.514 0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C6 ZY8 C1314 " pdb=" C7 ZY8 C1314 " ideal model delta sigma weight residual 1.797 1.514 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C6 ZY8 B1313 " pdb=" C7 ZY8 B1313 " ideal model delta sigma weight residual 1.797 1.514 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C6 ZY8 D1316 " pdb=" C7 ZY8 D1316 " ideal model delta sigma weight residual 1.797 1.514 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C6 ZY8 B1313 " pdb=" N5 ZY8 B1313 " ideal model delta sigma weight residual 1.759 1.504 0.255 2.00e-02 2.50e+03 1.63e+02 ... (remaining 75755 not shown) Histogram of bond angle deviations from ideal: 59.32 - 74.59: 12 74.59 - 89.85: 0 89.85 - 105.11: 984 105.11 - 120.38: 113203 120.38 - 135.64: 21329 Bond angle restraints: 135528 Sorted by residual: angle pdb=" C19 ZY8 C1314 " pdb=" C18 ZY8 C1314 " pdb=" O23 ZY8 C1314 " ideal model delta sigma weight residual 108.05 127.28 -19.23 3.00e+00 1.11e-01 4.11e+01 angle pdb=" C19 ZY8 D1316 " pdb=" C18 ZY8 D1316 " pdb=" O23 ZY8 D1316 " ideal model delta sigma weight residual 108.05 127.23 -19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C19 ZY8 B1313 " pdb=" C18 ZY8 B1313 " pdb=" O23 ZY8 B1313 " ideal model delta sigma weight residual 108.05 127.22 -19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" C19 ZY8 A1314 " pdb=" C18 ZY8 A1314 " pdb=" O23 ZY8 A1314 " ideal model delta sigma weight residual 108.05 127.22 -19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" N PRO B1130 " pdb=" CA PRO B1130 " pdb=" C PRO B1130 " ideal model delta sigma weight residual 110.70 116.67 -5.97 1.22e+00 6.72e-01 2.39e+01 ... (remaining 135523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 35777 35.76 - 71.51: 1065 71.51 - 107.27: 154 107.27 - 143.03: 20 143.03 - 178.78: 48 Dihedral angle restraints: 37064 sinusoidal: 21332 harmonic: 15732 Sorted by residual: dihedral pdb=" CA LYS A 145 " pdb=" C LYS A 145 " pdb=" N PHE A 146 " pdb=" CA PHE A 146 " ideal model delta harmonic sigma weight residual 180.00 134.70 45.30 0 5.00e+00 4.00e-02 8.21e+01 dihedral pdb=" CA LYS D 145 " pdb=" C LYS D 145 " pdb=" N PHE D 146 " pdb=" CA PHE D 146 " ideal model delta harmonic sigma weight residual 180.00 134.74 45.26 0 5.00e+00 4.00e-02 8.19e+01 dihedral pdb=" CA LYS B 145 " pdb=" C LYS B 145 " pdb=" N PHE B 146 " pdb=" CA PHE B 146 " ideal model delta harmonic sigma weight residual 180.00 134.74 45.26 0 5.00e+00 4.00e-02 8.19e+01 ... (remaining 37061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4346 0.062 - 0.124: 1188 0.124 - 0.187: 126 0.187 - 0.249: 16 0.249 - 0.311: 8 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C2 POV D1306 " pdb=" C1 POV D1306 " pdb=" C3 POV D1306 " pdb=" O21 POV D1306 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C2 POV A1303 " pdb=" C1 POV A1303 " pdb=" C3 POV A1303 " pdb=" O21 POV A1303 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C2 POV B1303 " pdb=" C1 POV B1303 " pdb=" C3 POV B1303 " pdb=" O21 POV B1303 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 5681 not shown) Planarity restraints: 10592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 500 " -0.168 2.00e-02 2.50e+03 1.90e-01 5.41e+02 pdb=" CG ASN D 500 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 500 " 0.160 2.00e-02 2.50e+03 pdb=" ND2 ASN D 500 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 500 " 0.275 2.00e-02 2.50e+03 pdb="HD22 ASN D 500 " -0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 500 " -0.168 2.00e-02 2.50e+03 1.90e-01 5.39e+02 pdb=" CG ASN B 500 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 500 " 0.160 2.00e-02 2.50e+03 pdb=" ND2 ASN B 500 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 500 " 0.274 2.00e-02 2.50e+03 pdb="HD22 ASN B 500 " -0.293 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 500 " -0.168 2.00e-02 2.50e+03 1.90e-01 5.39e+02 pdb=" CG ASN C 500 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 500 " 0.160 2.00e-02 2.50e+03 pdb=" ND2 ASN C 500 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 500 " 0.274 2.00e-02 2.50e+03 pdb="HD22 ASN C 500 " -0.293 2.00e-02 2.50e+03 ... (remaining 10589 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 7095 2.26 - 2.84: 166388 2.84 - 3.43: 186426 3.43 - 4.01: 262493 4.01 - 4.60: 405429 Nonbonded interactions: 1027831 Sorted by model distance: nonbonded pdb=" O TYR A 113 " pdb="HH22 ARG A 261 " model vdw 1.673 1.850 nonbonded pdb=" O TYR B 113 " pdb="HH22 ARG B 261 " model vdw 1.673 1.850 nonbonded pdb=" O TYR D 113 " pdb="HH22 ARG D 261 " model vdw 1.673 1.850 nonbonded pdb=" O TYR C 113 " pdb="HH22 ARG C 261 " model vdw 1.674 1.850 nonbonded pdb=" HH TYR B 863 " pdb=" O TRP B 972 " model vdw 1.676 1.850 ... (remaining 1027826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1306 or resid 1308 through 1309 or (resi \ d 1310 through 1311 and (name N or name C1 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name P or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or na \ me C217 or name C218)))) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1306 or resid 1308 through 1310 or (resi \ d 1311 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or \ name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name O11 or name O12 or name \ O13 or name O14 or name O21 or name O22 or name P or name C210 or name C211 or \ name C212 or name C213 or name C214 or name C215 or name C216 or name C217 or na \ me C218)))) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 or (resid 1302 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name \ C29 or name C210 or name C211 or name C212 or name C213 or name C214 or name C21 \ 5 or name C216)) or resid 1303 or resid 1306 or resid 1308 through 1309 or (resi \ d 1310 through 1311 and (name N or name C1 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name P or name C210 or \ name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or na \ me C217 or name C218)))) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 through 1303 or resid 1306 or \ resid 1308 through 1309 or (resid 1310 through 1311 and (name N or name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name O11 or name O12 or name O13 or name O14 or name O21 or na \ me O22 or name P or name C210 or name C211 or name C212 or name C213 or name C21 \ 4 or name C215 or name C216 or name C217 or name C218)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.820 Extract box with map and model: 8.990 Check model and map are aligned: 0.840 Set scattering table: 0.530 Process input model: 181.650 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.310 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:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 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 : 0.012 0.283 39520 Z= 0.709 Angle : 1.105 19.230 53144 Z= 0.526 Chirality : 0.055 0.311 5684 Planarity : 0.009 0.204 6356 Dihedral : 19.282 178.784 16392 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.51 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -5.09 (0.09), residues: 4396 helix: -3.38 (0.06), residues: 2460 sheet: -3.02 (0.29), residues: 244 loop : -3.18 (0.12), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B1042 HIS 0.008 0.002 HIS D 850 PHE 0.060 0.003 PHE C 858 TYR 0.046 0.003 TYR A 870 ARG 0.016 0.002 ARG D 962 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.6321 (tt) cc_final: 0.5790 (tp) REVERT: A 156 LEU cc_start: 0.7474 (mt) cc_final: 0.7223 (mt) REVERT: A 320 ARG cc_start: 0.5900 (ttt90) cc_final: 0.5615 (ttm-80) REVERT: A 928 ASP cc_start: 0.5759 (m-30) cc_final: 0.5554 (m-30) REVERT: A 1176 GLN cc_start: 0.6695 (tt0) cc_final: 0.6481 (mp10) REVERT: A 1206 GLN cc_start: 0.6991 (mm110) cc_final: 0.6686 (pp30) REVERT: A 1214 VAL cc_start: 0.6917 (t) cc_final: 0.6585 (t) REVERT: B 186 ASP cc_start: 0.6522 (t0) cc_final: 0.6267 (t70) REVERT: B 320 ARG cc_start: 0.5869 (ttt90) cc_final: 0.5465 (ttm-80) REVERT: B 928 ASP cc_start: 0.5900 (m-30) cc_final: 0.5644 (m-30) REVERT: B 1176 GLN cc_start: 0.6739 (tt0) cc_final: 0.6421 (mp10) REVERT: B 1206 GLN cc_start: 0.6880 (mm110) cc_final: 0.6498 (pp30) REVERT: C 152 ILE cc_start: 0.6351 (tt) cc_final: 0.5778 (tp) REVERT: C 320 ARG cc_start: 0.5949 (ttt90) cc_final: 0.5675 (ttm-80) REVERT: C 1206 GLN cc_start: 0.6974 (mm110) cc_final: 0.6581 (pp30) REVERT: C 1214 VAL cc_start: 0.6762 (t) cc_final: 0.6374 (t) REVERT: D 320 ARG cc_start: 0.6045 (ttt90) cc_final: 0.5718 (ttm-80) REVERT: D 928 ASP cc_start: 0.5777 (m-30) cc_final: 0.5539 (m-30) REVERT: D 1176 GLN cc_start: 0.6790 (tt0) cc_final: 0.6423 (mp10) REVERT: D 1194 GLU cc_start: 0.8016 (tt0) cc_final: 0.7797 (mm-30) REVERT: D 1206 GLN cc_start: 0.6941 (mm110) cc_final: 0.6692 (pp30) REVERT: D 1214 VAL cc_start: 0.6719 (t) cc_final: 0.6426 (t) outliers start: 0 outliers final: 2 residues processed: 624 average time/residue: 2.3715 time to fit residues: 1841.2179 Evaluate side-chains 384 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1059 ASP Chi-restraints excluded: chain D residue 845 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 0.9980 chunk 333 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 113 optimal weight: 30.0000 chunk 224 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 209 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 399 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 276 HIS A 388 HIS A 461 ASN A 500 ASN A 700 GLN A 792 HIS A 859 ASN A 880 GLN A 955 ASN A1058 ASN A1084 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 388 HIS B 461 ASN B 500 ASN B 700 GLN B 792 HIS B 859 ASN B 880 GLN B 955 ASN B1058 ASN B1084 GLN C 50 GLN C 276 HIS C 388 HIS C 432 GLN C 461 ASN C 500 ASN C 792 HIS C 880 GLN C 955 ASN C1058 ASN ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1219 ASN D 50 GLN D 276 HIS D 388 HIS D 461 ASN D 500 ASN D 700 GLN D 792 HIS D 859 ASN D 880 GLN D 955 ASN D1084 GLN D1219 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39520 Z= 0.277 Angle : 0.789 20.465 53144 Z= 0.396 Chirality : 0.042 0.205 5684 Planarity : 0.006 0.111 6356 Dihedral : 21.873 177.451 7688 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.78 % Favored : 91.86 % Rotamer: Outliers : 2.19 % Allowed : 9.66 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 4396 helix: -1.30 (0.09), residues: 2560 sheet: -2.90 (0.31), residues: 212 loop : -2.83 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 758 HIS 0.006 0.001 HIS C 191 PHE 0.032 0.003 PHE A 468 TYR 0.024 0.002 TYR C 870 ARG 0.018 0.001 ARG C1217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 477 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 640 PHE cc_start: 0.6033 (t80) cc_final: 0.5542 (t80) REVERT: A 874 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.6834 (t) REVERT: A 1176 GLN cc_start: 0.6988 (tt0) cc_final: 0.6731 (mp10) REVERT: A 1206 GLN cc_start: 0.7168 (mm110) cc_final: 0.6772 (tm-30) REVERT: A 1212 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7357 (tmtp) REVERT: B 274 ARG cc_start: 0.4661 (ptp-170) cc_final: 0.4426 (mtp85) REVERT: B 450 ASP cc_start: 0.7004 (t70) cc_final: 0.6737 (t0) REVERT: B 640 PHE cc_start: 0.6084 (t80) cc_final: 0.5443 (t80) REVERT: B 874 VAL cc_start: 0.7430 (OUTLIER) cc_final: 0.6949 (t) REVERT: B 1176 GLN cc_start: 0.7085 (tt0) cc_final: 0.6698 (mp10) REVERT: B 1206 GLN cc_start: 0.6963 (mm110) cc_final: 0.6535 (tm-30) REVERT: B 1217 ARG cc_start: 0.6184 (ttm110) cc_final: 0.5861 (ttm-80) REVERT: C 1206 GLN cc_start: 0.7091 (mm110) cc_final: 0.6716 (tm-30) REVERT: C 1217 ARG cc_start: 0.6286 (ttm110) cc_final: 0.5874 (ttm-80) REVERT: D 640 PHE cc_start: 0.6167 (t80) cc_final: 0.5538 (t80) REVERT: D 874 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6724 (t) REVERT: D 1009 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7509 (tm) REVERT: D 1176 GLN cc_start: 0.7109 (tt0) cc_final: 0.6737 (mp10) REVERT: D 1180 MET cc_start: 0.6963 (mtt) cc_final: 0.6759 (mtt) REVERT: D 1206 GLN cc_start: 0.7033 (mm110) cc_final: 0.6626 (tm-30) outliers start: 86 outliers final: 27 residues processed: 528 average time/residue: 2.1451 time to fit residues: 1442.1362 Evaluate side-chains 372 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 340 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 662 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 667 LYS Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1009 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 20.0000 chunk 124 optimal weight: 0.1980 chunk 332 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 400 optimal weight: 0.9980 chunk 432 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 396 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 635 GLN A1098 ASN B 177 ASN B 635 GLN B1098 ASN C 177 ASN C 635 GLN C 859 ASN C1098 ASN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 635 GLN D1098 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.224 39520 Z= 0.395 Angle : 0.862 19.894 53144 Z= 0.420 Chirality : 0.045 0.233 5684 Planarity : 0.006 0.108 6356 Dihedral : 21.686 175.616 7684 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.58 % Favored : 90.97 % Rotamer: Outliers : 2.19 % Allowed : 10.63 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 4396 helix: -0.64 (0.09), residues: 2612 sheet: -2.98 (0.30), residues: 228 loop : -2.70 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 758 HIS 0.011 0.002 HIS C 956 PHE 0.040 0.003 PHE C 858 TYR 0.039 0.003 TYR B 870 ARG 0.023 0.001 ARG C 962 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 516 time to evaluate : 4.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5433 (tp30) cc_final: 0.5123 (tm-30) REVERT: A 274 ARG cc_start: 0.5235 (ptp-170) cc_final: 0.4929 (ptp-170) REVERT: A 440 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6480 (tt0) REVERT: A 661 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8500 (t) REVERT: A 917 LYS cc_start: 0.6286 (tppt) cc_final: 0.5832 (tttp) REVERT: A 928 ASP cc_start: 0.7172 (m-30) cc_final: 0.6818 (m-30) REVERT: A 1171 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.6075 (t-170) REVERT: A 1176 GLN cc_start: 0.7463 (tt0) cc_final: 0.7020 (mt0) REVERT: A 1180 MET cc_start: 0.7582 (mtt) cc_final: 0.7328 (mtp) REVERT: A 1206 GLN cc_start: 0.7201 (mm110) cc_final: 0.6938 (tm-30) REVERT: A 1212 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7564 (tmtm) REVERT: B 661 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8431 (t) REVERT: B 917 LYS cc_start: 0.6329 (tppt) cc_final: 0.5797 (tttp) REVERT: B 928 ASP cc_start: 0.7107 (m-30) cc_final: 0.6728 (m-30) REVERT: B 1171 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.5971 (t-170) REVERT: B 1176 GLN cc_start: 0.7408 (tt0) cc_final: 0.6906 (mt0) REVERT: B 1206 GLN cc_start: 0.7087 (mm110) cc_final: 0.6711 (tm-30) REVERT: C 8 GLU cc_start: 0.5365 (tp30) cc_final: 0.5101 (tm-30) REVERT: C 661 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8465 (t) REVERT: C 928 ASP cc_start: 0.7344 (m-30) cc_final: 0.6889 (m-30) REVERT: C 1171 HIS cc_start: 0.6254 (OUTLIER) cc_final: 0.5974 (t-170) REVERT: C 1206 GLN cc_start: 0.7203 (mm110) cc_final: 0.6817 (tm-30) REVERT: D 8 GLU cc_start: 0.5382 (tp30) cc_final: 0.5093 (tm-30) REVERT: D 212 ASN cc_start: 0.3187 (m-40) cc_final: 0.2885 (m-40) REVERT: D 661 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8430 (t) REVERT: D 928 ASP cc_start: 0.7169 (m-30) cc_final: 0.6729 (m-30) REVERT: D 1176 GLN cc_start: 0.7262 (tt0) cc_final: 0.6949 (mt0) REVERT: D 1206 GLN cc_start: 0.7126 (mm110) cc_final: 0.6820 (tm-30) outliers start: 86 outliers final: 27 residues processed: 560 average time/residue: 2.3701 time to fit residues: 1666.1214 Evaluate side-chains 408 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 373 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 661 SER Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 1171 HIS Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 1171 HIS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 667 LYS Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 883 SER Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1171 HIS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 773 MET Chi-restraints excluded: chain D residue 874 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 4.9990 chunk 425 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS A 715 ASN A 756 ASN A 787 GLN B 426 HIS B 715 ASN B 756 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 715 ASN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 715 ASN D 756 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.7990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 39520 Z= 0.267 Angle : 0.709 20.164 53144 Z= 0.351 Chirality : 0.041 0.187 5684 Planarity : 0.005 0.075 6356 Dihedral : 20.113 174.541 7684 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.08 % Favored : 91.54 % Rotamer: Outliers : 2.98 % Allowed : 12.69 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -1.53 (0.12), residues: 4396 helix: -0.00 (0.10), residues: 2564 sheet: -2.80 (0.30), residues: 220 loop : -2.39 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 972 HIS 0.022 0.002 HIS A 276 PHE 0.023 0.002 PHE C 858 TYR 0.026 0.002 TYR C 870 ARG 0.007 0.001 ARG D1217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 435 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 917 LYS cc_start: 0.6286 (tppt) cc_final: 0.5900 (tttp) REVERT: A 928 ASP cc_start: 0.7232 (m-30) cc_final: 0.6828 (m-30) REVERT: A 1009 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 1169 LYS cc_start: 0.8106 (mttt) cc_final: 0.7606 (mtpp) REVERT: A 1176 GLN cc_start: 0.7306 (tt0) cc_final: 0.6854 (mt0) REVERT: A 1212 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7581 (tmtm) REVERT: B 424 LYS cc_start: 0.7599 (ttpt) cc_final: 0.7361 (ptpt) REVERT: B 899 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7325 (tp30) REVERT: B 917 LYS cc_start: 0.6204 (tppt) cc_final: 0.5748 (tttp) REVERT: B 928 ASP cc_start: 0.7217 (m-30) cc_final: 0.6772 (m-30) REVERT: B 1171 HIS cc_start: 0.6552 (OUTLIER) cc_final: 0.6256 (t-170) REVERT: B 1176 GLN cc_start: 0.7262 (tt0) cc_final: 0.6761 (mt0) REVERT: B 1188 LYS cc_start: 0.8085 (tmmt) cc_final: 0.7734 (ttpp) REVERT: B 1206 GLN cc_start: 0.7046 (mm110) cc_final: 0.6720 (tm-30) REVERT: C 928 ASP cc_start: 0.7311 (m-30) cc_final: 0.6925 (m-30) REVERT: C 946 LYS cc_start: 0.6607 (pttp) cc_final: 0.6294 (pptt) REVERT: C 953 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: C 1009 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 1169 LYS cc_start: 0.8108 (mttt) cc_final: 0.7604 (mtpp) REVERT: C 1171 HIS cc_start: 0.6500 (t70) cc_final: 0.6240 (t-170) REVERT: C 1206 GLN cc_start: 0.7209 (mm110) cc_final: 0.6894 (tm-30) REVERT: D 424 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7446 (ptpt) REVERT: D 763 LEU cc_start: 0.7366 (mm) cc_final: 0.7144 (mt) REVERT: D 928 ASP cc_start: 0.7204 (m-30) cc_final: 0.6725 (m-30) REVERT: D 1009 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8000 (mp) REVERT: D 1169 LYS cc_start: 0.8016 (mttt) cc_final: 0.7506 (mtpp) REVERT: D 1188 LYS cc_start: 0.8042 (tmmt) cc_final: 0.7697 (ttpp) REVERT: D 1206 GLN cc_start: 0.7099 (mm110) cc_final: 0.6856 (tm-30) outliers start: 117 outliers final: 38 residues processed: 509 average time/residue: 2.3004 time to fit residues: 1492.6824 Evaluate side-chains 418 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 374 time to evaluate : 4.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 1171 HIS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 449 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 449 MET Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 782 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1009 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 9.9990 chunk 241 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 316 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 293 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 948 ASN A1123 HIS B 98 GLN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 948 ASN B1123 HIS C 98 GLN C 718 ASN D 98 GLN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 718 ASN D 948 ASN D1123 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 39520 Z= 0.368 Angle : 0.782 20.754 53144 Z= 0.384 Chirality : 0.043 0.176 5684 Planarity : 0.006 0.075 6356 Dihedral : 20.492 171.696 7684 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.33 % Favored : 90.22 % Rotamer: Outliers : 2.22 % Allowed : 14.93 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4396 helix: 0.01 (0.10), residues: 2592 sheet: -3.03 (0.28), residues: 232 loop : -2.48 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 78 HIS 0.008 0.002 HIS C 956 PHE 0.022 0.002 PHE D1096 TYR 0.024 0.002 TYR A 759 ARG 0.013 0.001 ARG C 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 435 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.5877 (mm) cc_final: 0.5642 (mt) REVERT: A 278 ARG cc_start: 0.6672 (ttm-80) cc_final: 0.5279 (ttm-80) REVERT: A 480 THR cc_start: 0.7215 (OUTLIER) cc_final: 0.6824 (t) REVERT: A 758 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.6978 (t60) REVERT: A 917 LYS cc_start: 0.6449 (tppt) cc_final: 0.6162 (ttmp) REVERT: A 928 ASP cc_start: 0.7211 (m-30) cc_final: 0.6883 (m-30) REVERT: A 1009 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8107 (mp) REVERT: A 1188 LYS cc_start: 0.8104 (tmmt) cc_final: 0.7772 (ttpp) REVERT: A 1212 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7537 (tmtm) REVERT: B 162 LYS cc_start: 0.6488 (tttm) cc_final: 0.6259 (tttm) REVERT: B 278 ARG cc_start: 0.6305 (ttm-80) cc_final: 0.4788 (ttm-80) REVERT: B 412 ILE cc_start: 0.7138 (mt) cc_final: 0.6868 (mp) REVERT: B 480 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6509 (t) REVERT: B 729 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7524 (mtt-85) REVERT: B 753 MET cc_start: 0.8523 (mmt) cc_final: 0.8315 (mmt) REVERT: B 758 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.7311 (t60) REVERT: B 775 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: B 904 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7210 (t) REVERT: B 917 LYS cc_start: 0.6350 (tppt) cc_final: 0.6011 (ttmp) REVERT: B 928 ASP cc_start: 0.7159 (m-30) cc_final: 0.6759 (m-30) REVERT: B 1206 GLN cc_start: 0.7064 (mm110) cc_final: 0.6863 (tm-30) REVERT: C 274 ARG cc_start: 0.5667 (mtp85) cc_final: 0.5459 (ptm160) REVERT: C 278 ARG cc_start: 0.6575 (ttm-80) cc_final: 0.5005 (ttm-80) REVERT: C 480 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.6775 (t) REVERT: C 918 VAL cc_start: 0.7845 (t) cc_final: 0.7640 (p) REVERT: C 928 ASP cc_start: 0.7325 (m-30) cc_final: 0.6946 (m-30) REVERT: C 946 LYS cc_start: 0.7004 (pttp) cc_final: 0.6513 (pptt) REVERT: C 1009 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8016 (tp) REVERT: D 278 ARG cc_start: 0.6423 (ttm-80) cc_final: 0.4791 (ttm-80) REVERT: D 412 ILE cc_start: 0.7261 (mt) cc_final: 0.6984 (mp) REVERT: D 480 THR cc_start: 0.7130 (OUTLIER) cc_final: 0.6678 (t) REVERT: D 729 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7503 (mtt-85) REVERT: D 754 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7338 (ttp-110) REVERT: D 758 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.7061 (t60) REVERT: D 763 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7317 (mt) REVERT: D 775 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5536 (mp0) REVERT: D 928 ASP cc_start: 0.7209 (m-30) cc_final: 0.6764 (m-30) REVERT: D 1009 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7980 (mp) REVERT: D 1188 LYS cc_start: 0.8114 (tmmt) cc_final: 0.7760 (ttpp) outliers start: 87 outliers final: 40 residues processed: 483 average time/residue: 2.2524 time to fit residues: 1370.6278 Evaluate side-chains 433 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 378 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 782 MET Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 374 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain D residue 782 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.0980 chunk 383 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 425 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 HIS A1206 GLN B 212 ASN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 HIS ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 425 ASN ** D 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.9640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39520 Z= 0.233 Angle : 0.651 20.311 53144 Z= 0.319 Chirality : 0.040 0.535 5684 Planarity : 0.004 0.045 6356 Dihedral : 19.333 170.598 7684 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 2.12 % Allowed : 16.08 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.05 (0.12), residues: 4396 helix: 0.45 (0.10), residues: 2568 sheet: -2.73 (0.30), residues: 220 loop : -2.27 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 747 HIS 0.012 0.001 HIS C 491 PHE 0.014 0.002 PHE B 408 TYR 0.016 0.002 TYR B 776 ARG 0.004 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 412 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.6054 (mm) cc_final: 0.5837 (mt) REVERT: A 379 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7437 (p) REVERT: A 449 MET cc_start: 0.7475 (ttm) cc_final: 0.7181 (mtm) REVERT: A 480 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6967 (t) REVERT: A 523 THR cc_start: 0.8154 (p) cc_final: 0.7801 (m) REVERT: A 758 TRP cc_start: 0.7381 (OUTLIER) cc_final: 0.6446 (t60) REVERT: A 928 ASP cc_start: 0.7211 (m-30) cc_final: 0.6856 (m-30) REVERT: A 1009 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 1161 PHE cc_start: 0.7364 (t80) cc_final: 0.6275 (m-80) REVERT: A 1212 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7575 (tmtm) REVERT: B 278 ARG cc_start: 0.6515 (ttm-80) cc_final: 0.5441 (ttm-80) REVERT: B 379 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7436 (p) REVERT: B 412 ILE cc_start: 0.7136 (mt) cc_final: 0.6918 (mp) REVERT: B 523 THR cc_start: 0.8221 (p) cc_final: 0.7862 (m) REVERT: B 729 ARG cc_start: 0.7715 (mtm180) cc_final: 0.7511 (mtt-85) REVERT: B 758 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6577 (t60) REVERT: B 917 LYS cc_start: 0.6403 (tppt) cc_final: 0.6047 (ttmm) REVERT: B 928 ASP cc_start: 0.7180 (m-30) cc_final: 0.6781 (m-30) REVERT: B 1161 PHE cc_start: 0.7358 (t80) cc_final: 0.6191 (m-80) REVERT: B 1165 GLU cc_start: 0.6662 (pm20) cc_final: 0.6327 (pm20) REVERT: C 278 ARG cc_start: 0.6746 (ttm-80) cc_final: 0.5614 (ttm-80) REVERT: C 379 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7356 (p) REVERT: C 480 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6697 (t) REVERT: C 523 THR cc_start: 0.8144 (p) cc_final: 0.7833 (m) REVERT: C 918 VAL cc_start: 0.7904 (t) cc_final: 0.7671 (p) REVERT: C 928 ASP cc_start: 0.7286 (m-30) cc_final: 0.6850 (m-30) REVERT: C 946 LYS cc_start: 0.7113 (pttp) cc_final: 0.6619 (pptt) REVERT: C 1009 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8029 (tp) REVERT: C 1161 PHE cc_start: 0.7399 (t80) cc_final: 0.6283 (m-80) REVERT: D 278 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.5375 (ttm-80) REVERT: D 379 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7425 (p) REVERT: D 474 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7330 (tp) REVERT: D 480 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6835 (t) REVERT: D 494 ARG cc_start: 0.6777 (ptp-170) cc_final: 0.6476 (ptt-90) REVERT: D 511 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: D 523 THR cc_start: 0.8236 (p) cc_final: 0.7874 (m) REVERT: D 729 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7491 (mtt-85) REVERT: D 758 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.6331 (t60) REVERT: D 904 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7074 (t) REVERT: D 928 ASP cc_start: 0.7254 (m-30) cc_final: 0.6814 (m-30) REVERT: D 946 LYS cc_start: 0.6169 (pptt) cc_final: 0.5958 (tmtt) REVERT: D 1009 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7929 (tp) REVERT: D 1161 PHE cc_start: 0.7297 (t80) cc_final: 0.6150 (m-80) REVERT: D 1188 LYS cc_start: 0.8101 (tmmt) cc_final: 0.7764 (ttpp) outliers start: 83 outliers final: 42 residues processed: 466 average time/residue: 2.2369 time to fit residues: 1316.0143 Evaluate side-chains 437 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 378 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 1212 LYS Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1212 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 424 optimal weight: 0.7980 chunk 265 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 HIS ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 276 HIS ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 HIS ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1123 HIS C1206 GLN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.0121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 39520 Z= 0.301 Angle : 0.695 20.542 53144 Z= 0.341 Chirality : 0.042 0.807 5684 Planarity : 0.005 0.045 6356 Dihedral : 19.175 168.603 7684 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.53 % Favored : 90.20 % Rotamer: Outliers : 2.32 % Allowed : 16.18 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 (0.12), residues: 4396 helix: 0.48 (0.10), residues: 2552 sheet: -2.62 (0.31), residues: 220 loop : -2.25 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 78 HIS 0.013 0.001 HIS D 491 PHE 0.022 0.002 PHE B 408 TYR 0.031 0.002 TYR A1122 ARG 0.013 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 412 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6837 (tttm) cc_final: 0.6589 (tttm) REVERT: A 270 ILE cc_start: 0.6201 (mm) cc_final: 0.5973 (mt) REVERT: A 278 ARG cc_start: 0.6994 (ttm-80) cc_final: 0.6755 (ttm-80) REVERT: A 379 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7542 (p) REVERT: A 480 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7241 (t) REVERT: A 488 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7742 (ttm) REVERT: A 758 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.6538 (t60) REVERT: A 917 LYS cc_start: 0.6567 (tppt) cc_final: 0.6347 (ttmm) REVERT: A 928 ASP cc_start: 0.7292 (m-30) cc_final: 0.6913 (m-30) REVERT: A 1009 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 1161 PHE cc_start: 0.7441 (t80) cc_final: 0.6427 (m-80) REVERT: A 1212 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (tmtm) REVERT: B 379 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 412 ILE cc_start: 0.7441 (mt) cc_final: 0.7175 (mp) REVERT: B 480 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.7036 (t) REVERT: B 729 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7526 (mtt-85) REVERT: B 758 TRP cc_start: 0.7273 (OUTLIER) cc_final: 0.6949 (t60) REVERT: B 759 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.7025 (m-10) REVERT: B 917 LYS cc_start: 0.6390 (tppt) cc_final: 0.6059 (ttmm) REVERT: B 928 ASP cc_start: 0.7206 (m-30) cc_final: 0.6769 (m-30) REVERT: B 1161 PHE cc_start: 0.7419 (t80) cc_final: 0.6239 (m-80) REVERT: B 1168 LYS cc_start: 0.7252 (mtpt) cc_final: 0.6775 (mppt) REVERT: C 270 ILE cc_start: 0.6313 (mm) cc_final: 0.6093 (mt) REVERT: C 278 ARG cc_start: 0.6830 (ttm-80) cc_final: 0.5798 (ttm-80) REVERT: C 379 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 480 THR cc_start: 0.7396 (OUTLIER) cc_final: 0.6982 (t) REVERT: C 758 TRP cc_start: 0.7485 (OUTLIER) cc_final: 0.7102 (t60) REVERT: C 904 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7721 (t) REVERT: C 918 VAL cc_start: 0.8158 (t) cc_final: 0.7936 (p) REVERT: C 928 ASP cc_start: 0.7191 (m-30) cc_final: 0.6802 (m-30) REVERT: C 946 LYS cc_start: 0.7178 (pttp) cc_final: 0.6623 (pptt) REVERT: C 953 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: C 1009 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 1161 PHE cc_start: 0.7531 (t80) cc_final: 0.6439 (m-80) REVERT: C 1168 LYS cc_start: 0.7321 (mtpt) cc_final: 0.6875 (mppt) REVERT: D 379 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7582 (p) REVERT: D 424 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7472 (ptpt) REVERT: D 480 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7075 (t) REVERT: D 729 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7505 (mtt-85) REVERT: D 758 TRP cc_start: 0.7271 (OUTLIER) cc_final: 0.6494 (t60) REVERT: D 904 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7300 (t) REVERT: D 917 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6185 (ttmm) REVERT: D 918 VAL cc_start: 0.7809 (t) cc_final: 0.7593 (p) REVERT: D 928 ASP cc_start: 0.7246 (m-30) cc_final: 0.6811 (m-30) REVERT: D 1009 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7931 (tp) REVERT: D 1161 PHE cc_start: 0.7384 (t80) cc_final: 0.6221 (m-80) REVERT: D 1168 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6779 (mppt) REVERT: D 1188 LYS cc_start: 0.8083 (tmmt) cc_final: 0.7750 (ttpp) outliers start: 91 outliers final: 42 residues processed: 468 average time/residue: 2.2373 time to fit residues: 1322.9138 Evaluate side-chains 426 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 362 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1206 GLN Chi-restraints excluded: chain C residue 1216 ASP Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1206 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 GLN C 212 ASN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 1.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 39520 Z= 0.299 Angle : 0.685 20.572 53144 Z= 0.336 Chirality : 0.041 0.217 5684 Planarity : 0.005 0.045 6356 Dihedral : 18.935 167.978 7684 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.74 % Favored : 90.99 % Rotamer: Outliers : 2.29 % Allowed : 16.85 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.96 (0.12), residues: 4396 helix: 0.49 (0.10), residues: 2552 sheet: -2.41 (0.32), residues: 220 loop : -2.20 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 78 HIS 0.010 0.001 HIS D 491 PHE 0.023 0.002 PHE B 408 TYR 0.022 0.002 TYR B 776 ARG 0.008 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 393 time to evaluate : 4.261 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: -0.0683 (OUTLIER) cc_final: -0.0913 (ttm) REVERT: A 379 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7627 (p) REVERT: A 488 MET cc_start: 0.8067 (mtp) cc_final: 0.7690 (ttm) REVERT: A 758 TRP cc_start: 0.7282 (OUTLIER) cc_final: 0.6587 (t60) REVERT: A 917 LYS cc_start: 0.6608 (tppt) cc_final: 0.6404 (ttmm) REVERT: A 918 VAL cc_start: 0.8051 (t) cc_final: 0.7802 (p) REVERT: A 928 ASP cc_start: 0.7295 (m-30) cc_final: 0.6881 (m-30) REVERT: A 946 LYS cc_start: 0.6163 (pptt) cc_final: 0.5835 (tmmt) REVERT: A 1009 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 1161 PHE cc_start: 0.7564 (t80) cc_final: 0.6564 (m-80) REVERT: A 1168 LYS cc_start: 0.7406 (mtpt) cc_final: 0.6853 (mttt) REVERT: A 1212 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7622 (tmtm) REVERT: B 278 ARG cc_start: 0.6948 (ttm-80) cc_final: 0.6694 (ttm-80) REVERT: B 379 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7710 (p) REVERT: B 412 ILE cc_start: 0.7484 (mt) cc_final: 0.7227 (mp) REVERT: B 662 MET cc_start: 0.8620 (mtm) cc_final: 0.8053 (mtp) REVERT: B 729 ARG cc_start: 0.7745 (mtm180) cc_final: 0.7535 (mtt-85) REVERT: B 758 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.6677 (t60) REVERT: B 917 LYS cc_start: 0.6524 (tppt) cc_final: 0.6250 (ttmm) REVERT: B 918 VAL cc_start: 0.7922 (t) cc_final: 0.7665 (p) REVERT: B 928 ASP cc_start: 0.7229 (m-30) cc_final: 0.6784 (m-30) REVERT: B 1161 PHE cc_start: 0.7496 (t80) cc_final: 0.6410 (m-80) REVERT: B 1168 LYS cc_start: 0.7341 (mtpt) cc_final: 0.6795 (mttt) REVERT: C 270 ILE cc_start: 0.6541 (mm) cc_final: 0.6324 (mt) REVERT: C 379 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7535 (p) REVERT: C 480 THR cc_start: 0.7470 (OUTLIER) cc_final: 0.7173 (t) REVERT: C 758 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6677 (t60) REVERT: C 928 ASP cc_start: 0.7192 (m-30) cc_final: 0.6766 (m-30) REVERT: C 946 LYS cc_start: 0.7288 (pttp) cc_final: 0.6680 (pptt) REVERT: C 953 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: C 1009 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8040 (tp) REVERT: C 1161 PHE cc_start: 0.7534 (t80) cc_final: 0.6496 (m-80) REVERT: C 1168 LYS cc_start: 0.7428 (mtpt) cc_final: 0.6914 (mttt) REVERT: C 1205 GLU cc_start: 0.7364 (tt0) cc_final: 0.6799 (tp30) REVERT: D 278 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6659 (ttm-80) REVERT: D 379 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7668 (p) REVERT: D 480 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7289 (t) REVERT: D 729 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7510 (mtt-85) REVERT: D 758 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.6481 (t60) REVERT: D 917 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6309 (ttmm) REVERT: D 918 VAL cc_start: 0.7911 (t) cc_final: 0.7668 (p) REVERT: D 928 ASP cc_start: 0.7252 (m-30) cc_final: 0.6816 (m-30) REVERT: D 1009 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7915 (tp) REVERT: D 1161 PHE cc_start: 0.7458 (t80) cc_final: 0.6379 (m-80) REVERT: D 1168 LYS cc_start: 0.7376 (mtpt) cc_final: 0.6817 (mttt) REVERT: D 1188 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7712 (ttpp) outliers start: 90 outliers final: 42 residues processed: 450 average time/residue: 2.2305 time to fit residues: 1267.6803 Evaluate side-chains 421 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 361 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1206 GLN Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 144 GLN Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1216 ASP Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1188 LYS Chi-restraints excluded: chain D residue 1212 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 5.9990 chunk 406 optimal weight: 4.9990 chunk 370 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 chunk 310 optimal weight: 0.7980 chunk 121 optimal weight: 20.0000 chunk 357 optimal weight: 0.4980 chunk 373 optimal weight: 9.9990 chunk 393 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 491 HIS C 212 ASN C 491 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 1.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39520 Z= 0.204 Angle : 0.629 20.327 53144 Z= 0.307 Chirality : 0.039 0.201 5684 Planarity : 0.004 0.041 6356 Dihedral : 18.213 166.054 7684 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.58 % Favored : 91.15 % Rotamer: Outliers : 1.91 % Allowed : 17.43 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4396 helix: 0.86 (0.10), residues: 2544 sheet: -2.24 (0.33), residues: 220 loop : -2.13 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 207 HIS 0.014 0.001 HIS C 491 PHE 0.019 0.001 PHE A 408 TYR 0.019 0.001 TYR D 711 ARG 0.008 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 375 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: A 379 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7606 (p) REVERT: A 488 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: A 758 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.6578 (t60) REVERT: A 918 VAL cc_start: 0.8076 (t) cc_final: 0.7834 (p) REVERT: A 928 ASP cc_start: 0.7250 (m-30) cc_final: 0.6844 (m-30) REVERT: A 1009 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 1161 PHE cc_start: 0.7560 (t80) cc_final: 0.6589 (m-80) REVERT: A 1168 LYS cc_start: 0.7376 (mtpt) cc_final: 0.6834 (mttt) REVERT: A 1212 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7559 (tmtm) REVERT: B 278 ARG cc_start: 0.6954 (ttm-80) cc_final: 0.6668 (ttm-80) REVERT: B 379 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7672 (p) REVERT: B 412 ILE cc_start: 0.7431 (mt) cc_final: 0.7184 (mp) REVERT: B 488 MET cc_start: 0.7973 (mtp) cc_final: 0.7628 (ttm) REVERT: B 729 ARG cc_start: 0.7726 (mtm180) cc_final: 0.7520 (mtt-85) REVERT: B 758 TRP cc_start: 0.7180 (OUTLIER) cc_final: 0.6603 (t60) REVERT: B 917 LYS cc_start: 0.6517 (tppt) cc_final: 0.6282 (ttmm) REVERT: B 918 VAL cc_start: 0.7944 (t) cc_final: 0.7704 (p) REVERT: B 928 ASP cc_start: 0.7186 (m-30) cc_final: 0.6745 (m-30) REVERT: B 1161 PHE cc_start: 0.7509 (t80) cc_final: 0.6414 (m-80) REVERT: B 1168 LYS cc_start: 0.7282 (mtpt) cc_final: 0.6756 (mttt) REVERT: C 60 MET cc_start: -0.0560 (OUTLIER) cc_final: -0.0817 (ttm) REVERT: C 270 ILE cc_start: 0.6544 (mm) cc_final: 0.6337 (OUTLIER) REVERT: C 379 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7539 (p) REVERT: C 480 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7229 (t) REVERT: C 662 MET cc_start: 0.8733 (mtm) cc_final: 0.8173 (mtp) REVERT: C 758 TRP cc_start: 0.7171 (OUTLIER) cc_final: 0.6785 (t60) REVERT: C 772 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8017 (mt) REVERT: C 928 ASP cc_start: 0.7200 (m-30) cc_final: 0.6766 (m-30) REVERT: C 946 LYS cc_start: 0.7318 (pttp) cc_final: 0.6679 (pptt) REVERT: C 953 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: C 1009 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 1161 PHE cc_start: 0.7551 (t80) cc_final: 0.6516 (m-80) REVERT: C 1168 LYS cc_start: 0.7360 (mtpt) cc_final: 0.6844 (mttt) REVERT: D 278 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6629 (ttm-80) REVERT: D 379 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7618 (p) REVERT: D 488 MET cc_start: 0.7938 (mtp) cc_final: 0.7709 (ttm) REVERT: D 494 ARG cc_start: 0.7223 (ptp-170) cc_final: 0.6929 (ptt-90) REVERT: D 729 ARG cc_start: 0.7704 (mtm180) cc_final: 0.7498 (mtt-85) REVERT: D 758 TRP cc_start: 0.7200 (OUTLIER) cc_final: 0.6470 (t60) REVERT: D 917 LYS cc_start: 0.6781 (tppt) cc_final: 0.6269 (ttmm) REVERT: D 918 VAL cc_start: 0.7916 (t) cc_final: 0.7659 (p) REVERT: D 928 ASP cc_start: 0.7242 (m-30) cc_final: 0.6801 (m-30) REVERT: D 1009 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7932 (tp) REVERT: D 1161 PHE cc_start: 0.7473 (t80) cc_final: 0.6386 (m-80) REVERT: D 1168 LYS cc_start: 0.7319 (mtpt) cc_final: 0.6739 (mttt) REVERT: D 1188 LYS cc_start: 0.8003 (tmmt) cc_final: 0.7676 (ttpp) outliers start: 75 outliers final: 34 residues processed: 422 average time/residue: 2.3653 time to fit residues: 1263.7624 Evaluate side-chains 417 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 366 time to evaluate : 4.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 7.9990 chunk 417 optimal weight: 2.9990 chunk 255 optimal weight: 20.0000 chunk 198 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 438 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 1.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 39520 Z= 0.373 Angle : 0.742 20.679 53144 Z= 0.364 Chirality : 0.043 0.183 5684 Planarity : 0.005 0.053 6356 Dihedral : 19.354 161.334 7684 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.74 % Favored : 89.99 % Rotamer: Outliers : 1.66 % Allowed : 17.56 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.93 (0.12), residues: 4396 helix: 0.46 (0.10), residues: 2552 sheet: -1.90 (0.35), residues: 212 loop : -2.18 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 78 HIS 0.016 0.002 HIS D 491 PHE 0.025 0.002 PHE B 408 TYR 0.029 0.003 TYR B 953 ARG 0.009 0.001 ARG B 754 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8792 Ramachandran restraints generated. 4396 Oldfield, 0 Emsley, 4396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 396 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.4110 (ttt-90) cc_final: 0.3357 (ttt-90) REVERT: A 131 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: A 379 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7747 (p) REVERT: A 488 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7729 (ttm) REVERT: A 662 MET cc_start: 0.8709 (mtm) cc_final: 0.8210 (mtp) REVERT: A 758 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.6744 (t60) REVERT: A 928 ASP cc_start: 0.7332 (m-30) cc_final: 0.6945 (m-30) REVERT: A 946 LYS cc_start: 0.6118 (pptt) cc_final: 0.5822 (tmmt) REVERT: A 1009 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7996 (tp) REVERT: A 1161 PHE cc_start: 0.7563 (t80) cc_final: 0.6596 (m-80) REVERT: A 1168 LYS cc_start: 0.7446 (mtpt) cc_final: 0.6881 (mttt) REVERT: A 1212 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7682 (tmtm) REVERT: B 379 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7827 (p) REVERT: B 412 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7238 (mp) REVERT: B 488 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: B 662 MET cc_start: 0.8608 (mtm) cc_final: 0.8089 (mtp) REVERT: B 758 TRP cc_start: 0.7229 (OUTLIER) cc_final: 0.6681 (t60) REVERT: B 918 VAL cc_start: 0.8112 (t) cc_final: 0.7909 (p) REVERT: B 928 ASP cc_start: 0.7256 (m-30) cc_final: 0.6847 (m-30) REVERT: B 1161 PHE cc_start: 0.7500 (t80) cc_final: 0.6447 (m-80) REVERT: B 1168 LYS cc_start: 0.7388 (mtpt) cc_final: 0.6822 (mttt) REVERT: C 60 MET cc_start: -0.0621 (ttp) cc_final: -0.0842 (ttm) REVERT: C 379 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7740 (p) REVERT: C 488 MET cc_start: 0.7960 (mtp) cc_final: 0.7722 (ttm) REVERT: C 662 MET cc_start: 0.8720 (mtm) cc_final: 0.8189 (mtp) REVERT: C 758 TRP cc_start: 0.7368 (OUTLIER) cc_final: 0.6793 (t60) REVERT: C 772 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8144 (mt) REVERT: C 913 SER cc_start: 0.5838 (m) cc_final: 0.5632 (p) REVERT: C 928 ASP cc_start: 0.7248 (m-30) cc_final: 0.6862 (m-30) REVERT: C 946 LYS cc_start: 0.7408 (pttp) cc_final: 0.6690 (pptt) REVERT: C 1009 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 1161 PHE cc_start: 0.7519 (t80) cc_final: 0.6536 (m-80) REVERT: C 1168 LYS cc_start: 0.7456 (mtpt) cc_final: 0.6904 (mttt) REVERT: D 278 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6777 (ttm-80) REVERT: D 379 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7810 (p) REVERT: D 488 MET cc_start: 0.7951 (mtp) cc_final: 0.7687 (ttm) REVERT: D 662 MET cc_start: 0.8653 (mtm) cc_final: 0.8130 (mtp) REVERT: D 729 ARG cc_start: 0.7732 (mtm180) cc_final: 0.7530 (mtt-85) REVERT: D 758 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.6585 (t60) REVERT: D 917 LYS cc_start: 0.6797 (tppt) cc_final: 0.6289 (ttmm) REVERT: D 918 VAL cc_start: 0.8153 (t) cc_final: 0.7950 (p) REVERT: D 928 ASP cc_start: 0.7246 (m-30) cc_final: 0.6798 (m-30) REVERT: D 946 LYS cc_start: 0.6096 (pptt) cc_final: 0.5769 (tmmt) REVERT: D 1009 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7910 (tp) REVERT: D 1161 PHE cc_start: 0.7451 (t80) cc_final: 0.6420 (m-80) REVERT: D 1168 LYS cc_start: 0.7379 (mtpt) cc_final: 0.6780 (mttt) REVERT: D 1188 LYS cc_start: 0.8077 (tmmt) cc_final: 0.7735 (ttpp) outliers start: 65 outliers final: 36 residues processed: 434 average time/residue: 2.2968 time to fit residues: 1254.2363 Evaluate side-chains 420 residues out of total 3924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 367 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 758 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 874 VAL Chi-restraints excluded: chain B residue 1206 GLN Chi-restraints excluded: chain C residue 44 CYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 758 TRP Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 465 MET Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 758 TRP Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 0.9990 chunk 371 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 239 ASN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 239 ASN C 486 ASN C 491 HIS ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 ASN D 239 ASN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.209407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131808 restraints weight = 118613.691| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.67 r_work: 0.3356 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 1.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39520 Z= 0.198 Angle : 0.629 20.284 53144 Z= 0.307 Chirality : 0.039 0.347 5684 Planarity : 0.004 0.043 6356 Dihedral : 18.288 158.749 7684 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.23 % Favored : 91.49 % Rotamer: Outliers : 1.33 % Allowed : 18.22 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.48 (0.13), residues: 4396 helix: 0.86 (0.10), residues: 2548 sheet: -1.91 (0.37), residues: 196 loop : -2.03 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 78 HIS 0.013 0.001 HIS A 491 PHE 0.020 0.001 PHE A 408 TYR 0.017 0.001 TYR B 953 ARG 0.007 0.001 ARG C 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23472.55 seconds wall clock time: 404 minutes 32.49 seconds (24272.49 seconds total)