Starting phenix.real_space_refine on Fri Mar 22 00:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjj_23875/03_2024/7mjj_23875.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 20126 2.51 5 N 5191 2.21 5 O 6230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31680 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.95, per 1000 atoms: 0.54 Number of scatterers: 31680 At special positions: 0 Unit cell: (138, 147, 247, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 6230 8.00 N 5191 7.00 C 20126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG H 1 " - " ASN A 17 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 17 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 17 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 5.7 seconds 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7402 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 73 sheets defined 21.1% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.837A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.626A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.158A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.668A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.936A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.520A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.005A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.858A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.833A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.623A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.074A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.519A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.574A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.656A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.915A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.107A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.152A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.814A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.825A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.555A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.651A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.972A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.595A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.250A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.030A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.604A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.530A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 90' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.633A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.665A pdb=" N LYS E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.613A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.609A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.524A pdb=" N ASP F 89 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.645A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.618A pdb=" N LYS G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.988A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.659A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.042A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.150A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.997A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.760A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.776A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.335A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.130A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.759A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.169A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 13.117A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.348A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.914A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.590A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.709A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.204A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.267A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.580A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.249A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.196A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.915A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.440A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.703A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.393A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.920A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.920A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.205A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.518A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.368A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.545A pdb=" N THR D 77 " --> pdb=" O HIS D 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.401A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.940A pdb=" N TYR D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 124 through 128 removed outlier: 4.090A pdb=" N GLY D 143 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 124 through 128 removed outlier: 4.090A pdb=" N GLY D 143 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.812A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.693A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.357A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.357A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.529A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 144 through 150 Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.544A pdb=" N THR F 77 " --> pdb=" O HIS F 72 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.386A pdb=" N TYR F 33 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.926A pdb=" N TYR F 106 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 124 through 128 removed outlier: 4.119A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 124 through 128 removed outlier: 4.119A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 155 through 158 removed outlier: 4.134A pdb=" N TYR F 198 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.689A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.366A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.366A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.570A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 144 through 150 1389 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.56 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9231 1.34 - 1.46: 7285 1.46 - 1.58: 15720 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 32402 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.38e-02 5.25e+03 6.33e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 32397 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 728 105.44 - 112.60: 16762 112.60 - 119.75: 10602 119.75 - 126.90: 15673 126.90 - 134.06: 344 Bond angle restraints: 44109 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.41 -5.71 1.22e+00 6.72e-01 2.19e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.30 -5.60 1.22e+00 6.72e-01 2.10e+01 angle pdb=" C GLY D 100 " pdb=" N ASP D 101 " pdb=" CA ASP D 101 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C GLY F 100 " pdb=" N ASP F 101 " pdb=" CA ASP F 101 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.82e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.85 -5.15 1.22e+00 6.72e-01 1.78e+01 ... (remaining 44104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18616 17.98 - 35.96: 1148 35.96 - 53.94: 227 53.94 - 71.92: 68 71.92 - 89.91: 34 Dihedral angle restraints: 20093 sinusoidal: 8564 harmonic: 11529 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.73 -59.73 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.24 -59.24 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CA CYS B 590 " pdb=" C CYS B 590 " pdb=" N SER B 591 " pdb=" CA SER B 591 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 20090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4111 0.063 - 0.125: 924 0.125 - 0.188: 107 0.188 - 0.250: 18 0.250 - 0.313: 5 Chirality restraints: 5165 Sorted by residual: chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 5162 not shown) Planarity restraints: 5663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLN C 920 " 0.049 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 213 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C LYS D 213 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS D 213 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS D 214 " 0.016 2.00e-02 2.50e+03 ... (remaining 5660 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7849 2.80 - 3.33: 26184 3.33 - 3.85: 53540 3.85 - 4.38: 62353 4.38 - 4.90: 107387 Nonbonded interactions: 257313 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.278 2.440 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.319 2.440 ... (remaining 257308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.150 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: 0.050 Extract box with map and model: 14.860 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 87.910 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.004 0.059 32402 Z= 0.275 Angle : 0.757 10.726 44109 Z= 0.406 Chirality : 0.053 0.313 5165 Planarity : 0.007 0.066 5621 Dihedral : 12.845 89.905 12541 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.12), residues: 3908 helix: 0.15 (0.18), residues: 673 sheet: 0.05 (0.15), residues: 1105 loop : -0.91 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 148 HIS 0.003 0.001 HIS C 66 PHE 0.039 0.002 PHE B 135 TYR 0.037 0.002 TYR A 200 ARG 0.008 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 4.051 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: A 55 PHE cc_start: 0.7715 (m-80) cc_final: 0.6755 (m-80) REVERT: A 365 TYR cc_start: 0.8958 (m-80) cc_final: 0.8430 (m-80) REVERT: A 390 LEU cc_start: 0.8420 (mt) cc_final: 0.7966 (mt) REVERT: A 508 TYR cc_start: 0.8404 (m-80) cc_final: 0.8143 (m-10) REVERT: A 751 ASN cc_start: 0.9312 (m-40) cc_final: 0.9094 (m-40) REVERT: A 936 ASP cc_start: 0.8803 (m-30) cc_final: 0.8471 (m-30) REVERT: B 51 THR cc_start: 0.9257 (t) cc_final: 0.8372 (t) REVERT: B 271 GLN cc_start: 0.9069 (mt0) cc_final: 0.8680 (mp10) REVERT: B 458 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8216 (mptt) REVERT: B 571 ASP cc_start: 0.8647 (m-30) cc_final: 0.7759 (t0) REVERT: B 574 ASP cc_start: 0.9002 (p0) cc_final: 0.8723 (p0) REVERT: B 858 LEU cc_start: 0.8845 (mt) cc_final: 0.8364 (pt) REVERT: B 950 ASP cc_start: 0.8774 (m-30) cc_final: 0.8468 (m-30) REVERT: B 964 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8842 (mmtt) REVERT: C 191 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8028 (mp0) REVERT: C 217 PRO cc_start: 0.8272 (Cg_endo) cc_final: 0.8038 (Cg_exo) REVERT: C 398 ASP cc_start: 0.8693 (m-30) cc_final: 0.8128 (m-30) REVERT: C 858 LEU cc_start: 0.8759 (mp) cc_final: 0.8473 (pp) REVERT: D 34 MET cc_start: 0.3217 (mmm) cc_final: 0.2811 (mmm) REVERT: D 81 GLN cc_start: 0.8657 (tp40) cc_final: 0.8448 (tm-30) REVERT: E 18 LYS cc_start: 0.2029 (tmmt) cc_final: 0.1051 (mttp) REVERT: F 38 ARG cc_start: 0.8191 (ptt180) cc_final: 0.7671 (ptt180) REVERT: G 54 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7445 (ttm110) REVERT: G 192 TYR cc_start: 0.1966 (m-80) cc_final: 0.1039 (m-80) outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 0.4914 time to fit residues: 354.2917 Evaluate side-chains 219 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 102 optimal weight: 0.0470 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 310 optimal weight: 0.0470 chunk 120 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 359 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 907 ASN A1142 GLN B 137 ASN B 360 ASN C1010 GLN G 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32402 Z= 0.156 Angle : 0.547 8.890 44109 Z= 0.284 Chirality : 0.044 0.257 5165 Planarity : 0.005 0.055 5621 Dihedral : 5.990 55.217 5519 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.93 % Allowed : 6.59 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 3908 helix: 1.64 (0.20), residues: 667 sheet: 0.49 (0.15), residues: 1093 loop : -0.58 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 50 HIS 0.004 0.001 HIS A 519 PHE 0.016 0.001 PHE C 168 TYR 0.021 0.001 TYR D 59 ARG 0.008 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 3.999 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: A 55 PHE cc_start: 0.7609 (m-80) cc_final: 0.6914 (m-80) REVERT: A 153 MET cc_start: 0.4839 (pmm) cc_final: 0.4596 (pmm) REVERT: A 168 PHE cc_start: 0.8771 (t80) cc_final: 0.8299 (t80) REVERT: A 170 TYR cc_start: 0.7820 (t80) cc_final: 0.7589 (t80) REVERT: A 242 LEU cc_start: 0.6752 (mp) cc_final: 0.6511 (mp) REVERT: A 299 THR cc_start: 0.9447 (m) cc_final: 0.9245 (p) REVERT: A 762 GLN cc_start: 0.8589 (mt0) cc_final: 0.8218 (mt0) REVERT: A 936 ASP cc_start: 0.8791 (m-30) cc_final: 0.8452 (m-30) REVERT: B 195 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8356 (mtmm) REVERT: B 201 PHE cc_start: 0.8690 (t80) cc_final: 0.8361 (t80) REVERT: B 271 GLN cc_start: 0.9053 (mt0) cc_final: 0.8722 (mp10) REVERT: B 458 LYS cc_start: 0.8467 (mmtm) cc_final: 0.8219 (mptt) REVERT: B 574 ASP cc_start: 0.8905 (p0) cc_final: 0.8614 (p0) REVERT: B 858 LEU cc_start: 0.8803 (mt) cc_final: 0.8378 (pt) REVERT: B 964 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8780 (mmtt) REVERT: C 191 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7966 (mp0) REVERT: C 378 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8178 (mppt) REVERT: C 398 ASP cc_start: 0.8628 (m-30) cc_final: 0.8129 (m-30) REVERT: D 46 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3828 (pm20) REVERT: D 61 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6430 (t0) REVERT: F 72 HIS cc_start: 0.7756 (t-90) cc_final: 0.7497 (t70) REVERT: F 83 ASN cc_start: 0.7951 (m-40) cc_final: 0.7719 (p0) REVERT: G 24 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7879 (ptp90) REVERT: G 54 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7537 (ttp-110) outliers start: 32 outliers final: 22 residues processed: 267 average time/residue: 0.4626 time to fit residues: 197.9540 Evaluate side-chains 214 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 360 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 320 optimal weight: 20.0000 chunk 357 optimal weight: 40.0000 chunk 122 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN C 703 ASN C 856 ASN C 926 GLN C1011 GLN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32402 Z= 0.246 Angle : 0.546 7.260 44109 Z= 0.284 Chirality : 0.044 0.282 5165 Planarity : 0.004 0.058 5621 Dihedral : 5.317 54.236 5519 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.30 % Allowed : 8.30 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 3908 helix: 1.95 (0.20), residues: 696 sheet: 0.56 (0.15), residues: 1105 loop : -0.50 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 158 HIS 0.031 0.001 HIS A 519 PHE 0.021 0.001 PHE C 515 TYR 0.026 0.001 TYR A 369 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7604 (m-80) cc_final: 0.6855 (m-80) REVERT: A 170 TYR cc_start: 0.7862 (t80) cc_final: 0.7359 (t80) REVERT: A 299 THR cc_start: 0.9492 (m) cc_final: 0.9285 (p) REVERT: A 762 GLN cc_start: 0.8629 (mt0) cc_final: 0.8311 (mt0) REVERT: A 773 GLU cc_start: 0.8722 (tt0) cc_final: 0.8460 (tp30) REVERT: A 936 ASP cc_start: 0.8750 (m-30) cc_final: 0.8392 (m-30) REVERT: B 201 PHE cc_start: 0.8795 (t80) cc_final: 0.8478 (t80) REVERT: B 271 GLN cc_start: 0.9168 (mt0) cc_final: 0.8784 (mp10) REVERT: B 458 LYS cc_start: 0.8481 (mmtm) cc_final: 0.8198 (mptt) REVERT: B 574 ASP cc_start: 0.8957 (p0) cc_final: 0.8674 (p0) REVERT: B 858 LEU cc_start: 0.8920 (mt) cc_final: 0.8458 (pt) REVERT: B 964 LYS cc_start: 0.9125 (mmtp) cc_final: 0.8760 (mmtt) REVERT: C 191 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8106 (mp0) REVERT: C 398 ASP cc_start: 0.8688 (m-30) cc_final: 0.8116 (m-30) REVERT: C 462 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8928 (mppt) REVERT: C 923 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9512 (mp) REVERT: D 46 GLU cc_start: 0.4208 (OUTLIER) cc_final: 0.3863 (pt0) REVERT: D 61 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6311 (t0) REVERT: E 32 TYR cc_start: 0.8575 (m-80) cc_final: 0.8257 (m-80) REVERT: E 195 GLU cc_start: 0.4707 (tt0) cc_final: 0.4368 (pt0) outliers start: 45 outliers final: 25 residues processed: 226 average time/residue: 0.4930 time to fit residues: 181.3439 Evaluate side-chains 194 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 20.0000 chunk 270 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 382 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 342 optimal weight: 20.0000 chunk 103 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: C 314 GLN C 856 ASN C 907 ASN C 913 GLN C 955 ASN C1011 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 32402 Z= 0.198 Angle : 0.506 6.732 44109 Z= 0.264 Chirality : 0.043 0.282 5165 Planarity : 0.004 0.045 5621 Dihedral : 4.882 53.499 5519 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.50 % Allowed : 8.96 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3908 helix: 2.11 (0.20), residues: 686 sheet: 0.58 (0.15), residues: 1107 loop : -0.39 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 50 HIS 0.004 0.001 HIS A 519 PHE 0.022 0.001 PHE C 515 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7443 (m-80) cc_final: 0.6730 (m-80) REVERT: A 100 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 168 PHE cc_start: 0.8690 (t80) cc_final: 0.7872 (t80) REVERT: A 386 LYS cc_start: 0.9651 (tppt) cc_final: 0.9451 (tppt) REVERT: A 762 GLN cc_start: 0.8557 (mt0) cc_final: 0.8299 (mt0) REVERT: A 780 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: A 936 ASP cc_start: 0.8766 (m-30) cc_final: 0.8448 (m-30) REVERT: B 201 PHE cc_start: 0.8856 (t80) cc_final: 0.8523 (t80) REVERT: B 226 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8911 (mm) REVERT: B 271 GLN cc_start: 0.9165 (mt0) cc_final: 0.8958 (mt0) REVERT: B 458 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8193 (mptt) REVERT: B 574 ASP cc_start: 0.8897 (p0) cc_final: 0.8634 (p0) REVERT: B 858 LEU cc_start: 0.9009 (mt) cc_final: 0.8550 (pt) REVERT: B 964 LYS cc_start: 0.9113 (mmtp) cc_final: 0.8744 (mmtt) REVERT: C 191 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8067 (mp0) REVERT: C 378 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: C 398 ASP cc_start: 0.8718 (m-30) cc_final: 0.8219 (m-30) REVERT: C 462 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8946 (mppt) REVERT: C 900 MET cc_start: 0.8705 (mtp) cc_final: 0.8475 (mtt) REVERT: C 923 ILE cc_start: 0.9719 (OUTLIER) cc_final: 0.9518 (mp) REVERT: D 34 MET cc_start: 0.2927 (mpp) cc_final: 0.2604 (mmt) REVERT: D 46 GLU cc_start: 0.4107 (OUTLIER) cc_final: 0.3783 (pt0) REVERT: D 61 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6244 (t70) REVERT: D 78 LEU cc_start: 0.1607 (OUTLIER) cc_final: 0.0887 (mm) REVERT: E 32 TYR cc_start: 0.8682 (m-80) cc_final: 0.8353 (m-80) REVERT: E 195 GLU cc_start: 0.4725 (tt0) cc_final: 0.4365 (pt0) REVERT: G 24 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7857 (mtm-85) REVERT: G 32 TYR cc_start: 0.8380 (m-80) cc_final: 0.8145 (m-80) REVERT: G 117 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.5999 (mm) outliers start: 52 outliers final: 27 residues processed: 226 average time/residue: 0.4527 time to fit residues: 166.9367 Evaluate side-chains 202 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 856 ASN C 907 ASN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32402 Z= 0.249 Angle : 0.528 8.174 44109 Z= 0.273 Chirality : 0.043 0.293 5165 Planarity : 0.004 0.088 5621 Dihedral : 4.829 53.782 5519 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.50 % Allowed : 10.03 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 3908 helix: 2.10 (0.20), residues: 694 sheet: 0.63 (0.16), residues: 1071 loop : -0.36 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS A1088 PHE 0.014 0.001 PHE C 515 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7610 (m-80) cc_final: 0.7302 (m-80) REVERT: A 762 GLN cc_start: 0.8595 (mt0) cc_final: 0.8338 (mt0) REVERT: A 776 LYS cc_start: 0.8881 (tttm) cc_final: 0.8677 (tmtt) REVERT: A 780 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: A 936 ASP cc_start: 0.8847 (m-30) cc_final: 0.8527 (m-30) REVERT: B 195 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8369 (mtmm) REVERT: B 201 PHE cc_start: 0.8885 (t80) cc_final: 0.8669 (t80) REVERT: B 271 GLN cc_start: 0.9178 (mt0) cc_final: 0.8906 (mt0) REVERT: B 458 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8225 (tppt) REVERT: B 574 ASP cc_start: 0.8924 (p0) cc_final: 0.8666 (p0) REVERT: B 858 LEU cc_start: 0.9113 (mt) cc_final: 0.8584 (pt) REVERT: B 964 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8781 (mmtt) REVERT: C 170 TYR cc_start: 0.8529 (t80) cc_final: 0.8140 (t80) REVERT: C 378 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: C 398 ASP cc_start: 0.8730 (m-30) cc_final: 0.8252 (m-30) REVERT: C 462 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8919 (mppt) REVERT: C 923 ILE cc_start: 0.9734 (OUTLIER) cc_final: 0.9518 (mp) REVERT: D 34 MET cc_start: 0.3049 (mpp) cc_final: 0.2701 (mmt) REVERT: D 46 GLU cc_start: 0.3986 (OUTLIER) cc_final: 0.3633 (pt0) REVERT: D 61 ASP cc_start: 0.6443 (p0) cc_final: 0.6163 (t70) REVERT: D 78 LEU cc_start: 0.1589 (OUTLIER) cc_final: 0.0889 (mm) REVERT: E 32 TYR cc_start: 0.8738 (m-80) cc_final: 0.8385 (m-80) REVERT: E 195 GLU cc_start: 0.4719 (tt0) cc_final: 0.4349 (pt0) REVERT: F 158 TRP cc_start: 0.2056 (m100) cc_final: 0.1622 (m100) REVERT: G 117 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.5966 (mm) outliers start: 52 outliers final: 35 residues processed: 214 average time/residue: 0.4375 time to fit residues: 152.8653 Evaluate side-chains 194 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 75 optimal weight: 0.0000 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 383 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B1002 GLN C 493 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32402 Z= 0.296 Angle : 0.550 7.284 44109 Z= 0.285 Chirality : 0.044 0.295 5165 Planarity : 0.004 0.076 5621 Dihedral : 4.935 53.823 5519 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.68 % Allowed : 10.67 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3908 helix: 2.03 (0.20), residues: 701 sheet: 0.54 (0.16), residues: 1079 loop : -0.34 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 158 HIS 0.004 0.001 HIS A 66 PHE 0.035 0.001 PHE C 338 TYR 0.020 0.001 TYR A 904 ARG 0.008 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 168 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7865 (m-80) cc_final: 0.7381 (m-80) REVERT: A 365 TYR cc_start: 0.9019 (m-80) cc_final: 0.8719 (m-10) REVERT: A 762 GLN cc_start: 0.8599 (mt0) cc_final: 0.8357 (mt0) REVERT: A 780 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 904 TYR cc_start: 0.8422 (m-10) cc_final: 0.8222 (m-80) REVERT: A 936 ASP cc_start: 0.8852 (m-30) cc_final: 0.8537 (m-30) REVERT: B 195 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8283 (mtmm) REVERT: B 200 TYR cc_start: 0.9502 (m-80) cc_final: 0.9216 (m-80) REVERT: B 226 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 458 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8238 (tppt) REVERT: B 574 ASP cc_start: 0.9010 (p0) cc_final: 0.8808 (p0) REVERT: B 858 LEU cc_start: 0.9170 (mt) cc_final: 0.8628 (pt) REVERT: B 954 GLN cc_start: 0.8539 (mt0) cc_final: 0.8323 (mt0) REVERT: B 964 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8795 (mmtt) REVERT: C 378 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8332 (mtmm) REVERT: C 398 ASP cc_start: 0.8773 (m-30) cc_final: 0.8211 (m-30) REVERT: C 462 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8932 (mppt) REVERT: D 34 MET cc_start: 0.3215 (mpp) cc_final: 0.2600 (mmm) REVERT: D 46 GLU cc_start: 0.3921 (OUTLIER) cc_final: 0.3624 (pt0) REVERT: D 61 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.6032 (t70) REVERT: E 32 TYR cc_start: 0.8756 (m-80) cc_final: 0.8359 (m-80) REVERT: E 195 GLU cc_start: 0.4737 (tt0) cc_final: 0.4360 (pt0) REVERT: F 158 TRP cc_start: 0.2029 (m100) cc_final: 0.1773 (m100) REVERT: G 117 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.5974 (mm) outliers start: 58 outliers final: 43 residues processed: 215 average time/residue: 0.4148 time to fit residues: 149.4116 Evaluate side-chains 195 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 146 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 chunk 279 optimal weight: 0.3980 chunk 216 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 381 optimal weight: 20.0000 chunk 238 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 175 GLN ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32402 Z= 0.256 Angle : 0.534 9.561 44109 Z= 0.277 Chirality : 0.044 0.298 5165 Planarity : 0.004 0.073 5621 Dihedral : 4.920 53.615 5519 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 11.13 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3908 helix: 2.13 (0.20), residues: 690 sheet: 0.47 (0.15), residues: 1101 loop : -0.31 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS A 66 PHE 0.028 0.001 PHE C 759 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 162 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7904 (m-80) cc_final: 0.7402 (m-80) REVERT: A 133 PHE cc_start: 0.7612 (m-80) cc_final: 0.6737 (t80) REVERT: A 135 PHE cc_start: 0.6372 (m-80) cc_final: 0.6113 (m-10) REVERT: A 936 ASP cc_start: 0.8848 (m-30) cc_final: 0.8536 (m-30) REVERT: B 195 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8270 (mtmm) REVERT: B 200 TYR cc_start: 0.9505 (m-80) cc_final: 0.9239 (m-80) REVERT: B 226 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8834 (mm) REVERT: B 271 GLN cc_start: 0.9215 (mt0) cc_final: 0.8894 (mt0) REVERT: B 458 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8286 (tppt) REVERT: B 574 ASP cc_start: 0.9002 (p0) cc_final: 0.8799 (p0) REVERT: B 858 LEU cc_start: 0.9196 (mt) cc_final: 0.8639 (pt) REVERT: B 954 GLN cc_start: 0.8536 (mt0) cc_final: 0.8299 (mt0) REVERT: B 964 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8769 (mmtt) REVERT: C 378 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8353 (mtmm) REVERT: C 398 ASP cc_start: 0.8787 (m-30) cc_final: 0.8241 (m-30) REVERT: C 462 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8935 (mppt) REVERT: D 11 LEU cc_start: 0.6386 (tp) cc_final: 0.6130 (tp) REVERT: D 34 MET cc_start: 0.3250 (mpp) cc_final: 0.2634 (mmm) REVERT: D 46 GLU cc_start: 0.4001 (OUTLIER) cc_final: 0.3745 (pt0) REVERT: D 61 ASP cc_start: 0.6231 (OUTLIER) cc_final: 0.5972 (t70) REVERT: E 32 TYR cc_start: 0.8801 (m-80) cc_final: 0.8425 (m-80) REVERT: E 195 GLU cc_start: 0.4739 (tt0) cc_final: 0.4361 (pt0) REVERT: F 158 TRP cc_start: 0.2101 (m100) cc_final: 0.1868 (m100) REVERT: G 117 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6003 (mm) outliers start: 62 outliers final: 44 residues processed: 212 average time/residue: 0.4230 time to fit residues: 148.0484 Evaluate side-chains 203 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 142 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 0.0570 chunk 114 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 300 optimal weight: 0.4980 overall best weight: 1.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN C 121 ASN C 703 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS F 81 GLN G 137 ASN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32402 Z= 0.232 Angle : 0.526 9.902 44109 Z= 0.274 Chirality : 0.044 0.297 5165 Planarity : 0.004 0.072 5621 Dihedral : 4.853 53.507 5519 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.56 % Allowed : 11.77 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 3908 helix: 2.15 (0.20), residues: 694 sheet: 0.44 (0.16), residues: 1092 loop : -0.30 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.016 0.001 HIS D 72 PHE 0.028 0.001 PHE A 201 TYR 0.032 0.001 TYR A 904 ARG 0.004 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 3.597 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: A 55 PHE cc_start: 0.7803 (m-80) cc_final: 0.7324 (m-80) REVERT: A 168 PHE cc_start: 0.8732 (t80) cc_final: 0.8409 (t80) REVERT: A 936 ASP cc_start: 0.8855 (m-30) cc_final: 0.8546 (m-30) REVERT: B 200 TYR cc_start: 0.9489 (m-80) cc_final: 0.9147 (m-80) REVERT: B 226 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8850 (mm) REVERT: B 773 GLU cc_start: 0.8383 (tp30) cc_final: 0.8154 (tt0) REVERT: B 858 LEU cc_start: 0.9198 (mt) cc_final: 0.8618 (pt) REVERT: B 954 GLN cc_start: 0.8515 (mt0) cc_final: 0.8275 (mt0) REVERT: B 964 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8768 (mmtt) REVERT: C 378 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: C 398 ASP cc_start: 0.8764 (m-30) cc_final: 0.8229 (m-30) REVERT: C 462 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8919 (mppt) REVERT: D 11 LEU cc_start: 0.6249 (tp) cc_final: 0.5983 (tp) REVERT: D 34 MET cc_start: 0.3259 (mpp) cc_final: 0.2687 (mmm) REVERT: D 46 GLU cc_start: 0.3996 (OUTLIER) cc_final: 0.3747 (pt0) REVERT: D 61 ASP cc_start: 0.6205 (p0) cc_final: 0.5969 (t70) REVERT: E 32 TYR cc_start: 0.8829 (m-80) cc_final: 0.8420 (m-80) REVERT: E 195 GLU cc_start: 0.4742 (tt0) cc_final: 0.4395 (pt0) REVERT: G 117 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6253 (mm) outliers start: 54 outliers final: 44 residues processed: 207 average time/residue: 0.4129 time to fit residues: 143.0828 Evaluate side-chains 196 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 279 optimal weight: 0.0000 chunk 109 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 498 GLN A 655 HIS A 755 GLN A 762 GLN B 245 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 121 ASN C 703 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS G 147 GLN ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 32402 Z= 0.552 Angle : 0.752 11.290 44109 Z= 0.385 Chirality : 0.048 0.305 5165 Planarity : 0.005 0.080 5621 Dihedral : 5.939 56.140 5519 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.71 % Allowed : 12.06 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 3908 helix: 1.67 (0.20), residues: 697 sheet: 0.26 (0.15), residues: 1082 loop : -0.63 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP F 158 HIS 0.008 0.002 HIS A 66 PHE 0.019 0.002 PHE C 392 TYR 0.046 0.002 TYR A 904 ARG 0.007 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 150 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7887 (m-80) cc_final: 0.7335 (m-80) REVERT: A 168 PHE cc_start: 0.8817 (t80) cc_final: 0.8501 (t80) REVERT: A 309 GLU cc_start: 0.8858 (mp0) cc_final: 0.8653 (mp0) REVERT: A 936 ASP cc_start: 0.8908 (m-30) cc_final: 0.8633 (m-30) REVERT: B 200 TYR cc_start: 0.9479 (m-80) cc_final: 0.9201 (m-80) REVERT: B 226 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8879 (mm) REVERT: B 271 GLN cc_start: 0.9326 (mt0) cc_final: 0.8981 (mt0) REVERT: B 340 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8718 (tm-30) REVERT: B 458 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8313 (tppt) REVERT: B 858 LEU cc_start: 0.9292 (mt) cc_final: 0.8660 (pt) REVERT: B 954 GLN cc_start: 0.8599 (mt0) cc_final: 0.8326 (mt0) REVERT: B 964 LYS cc_start: 0.9122 (mmtp) cc_final: 0.8843 (mmtt) REVERT: C 378 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: C 398 ASP cc_start: 0.8863 (m-30) cc_final: 0.8313 (m-30) REVERT: C 462 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8888 (mppt) REVERT: D 11 LEU cc_start: 0.5928 (tp) cc_final: 0.5662 (tp) REVERT: D 34 MET cc_start: 0.3674 (mpp) cc_final: 0.3181 (mmm) REVERT: D 61 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6116 (t70) REVERT: E 32 TYR cc_start: 0.8885 (m-80) cc_final: 0.8467 (m-80) REVERT: E 195 GLU cc_start: 0.4509 (tt0) cc_final: 0.4137 (pt0) REVERT: G 117 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.5333 (mm) outliers start: 59 outliers final: 46 residues processed: 197 average time/residue: 0.4227 time to fit residues: 137.6341 Evaluate side-chains 191 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 0.9990 chunk 376 optimal weight: 8.9990 chunk 229 optimal weight: 30.0000 chunk 178 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 363 optimal weight: 30.0000 chunk 314 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 762 GLN A1036 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 703 ASN C1005 GLN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32402 Z= 0.214 Angle : 0.548 9.790 44109 Z= 0.286 Chirality : 0.044 0.305 5165 Planarity : 0.004 0.100 5621 Dihedral : 5.353 52.722 5519 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.30 % Allowed : 12.72 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 3908 helix: 2.07 (0.20), residues: 697 sheet: 0.26 (0.16), residues: 1059 loop : -0.44 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 158 HIS 0.003 0.001 HIS A 66 PHE 0.025 0.001 PHE A 201 TYR 0.030 0.001 TYR G 192 ARG 0.005 0.000 ARG D 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7816 Ramachandran restraints generated. 3908 Oldfield, 0 Emsley, 3908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7908 (m-80) cc_final: 0.7405 (m-80) REVERT: A 133 PHE cc_start: 0.7540 (m-80) cc_final: 0.7286 (t80) REVERT: A 168 PHE cc_start: 0.8772 (t80) cc_final: 0.8458 (t80) REVERT: A 309 GLU cc_start: 0.8832 (mp0) cc_final: 0.8630 (mp0) REVERT: A 936 ASP cc_start: 0.8853 (m-30) cc_final: 0.8550 (m-30) REVERT: B 200 TYR cc_start: 0.9487 (m-80) cc_final: 0.9172 (m-80) REVERT: B 226 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8800 (mm) REVERT: B 271 GLN cc_start: 0.9300 (mt0) cc_final: 0.9013 (mt0) REVERT: B 340 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8686 (tm-30) REVERT: B 858 LEU cc_start: 0.9266 (mt) cc_final: 0.8703 (pt) REVERT: B 954 GLN cc_start: 0.8496 (mt0) cc_final: 0.8225 (mt0) REVERT: B 964 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8814 (mmtt) REVERT: C 378 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: C 398 ASP cc_start: 0.8800 (m-30) cc_final: 0.8262 (m-30) REVERT: C 462 LYS cc_start: 0.9296 (mmmt) cc_final: 0.8945 (mppt) REVERT: D 11 LEU cc_start: 0.5909 (tp) cc_final: 0.5679 (tp) REVERT: D 34 MET cc_start: 0.3630 (mpp) cc_final: 0.3070 (mmm) REVERT: E 32 TYR cc_start: 0.8864 (m-80) cc_final: 0.8451 (m-80) REVERT: E 195 GLU cc_start: 0.4749 (tt0) cc_final: 0.4369 (pt0) REVERT: G 54 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7391 (ttp-110) REVERT: G 117 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5375 (mm) outliers start: 45 outliers final: 37 residues processed: 197 average time/residue: 0.4286 time to fit residues: 139.0480 Evaluate side-chains 186 residues out of total 3458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 142 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 6.9990 chunk 334 optimal weight: 0.0000 chunk 96 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 314 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.093526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057368 restraints weight = 123625.351| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.49 r_work: 0.2982 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32402 Z= 0.157 Angle : 0.524 9.993 44109 Z= 0.272 Chirality : 0.044 0.289 5165 Planarity : 0.004 0.088 5621 Dihedral : 4.863 53.274 5519 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.24 % Allowed : 12.98 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3908 helix: 2.36 (0.20), residues: 680 sheet: 0.40 (0.15), residues: 1105 loop : -0.35 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 158 HIS 0.003 0.000 HIS G 189 PHE 0.044 0.001 PHE C 392 TYR 0.029 0.001 TYR B 904 ARG 0.008 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6491.46 seconds wall clock time: 118 minutes 38.56 seconds (7118.56 seconds total)