Starting phenix.real_space_refine on Fri Aug 9 04:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzi_37953/08_2024/8wzi_37953.cif" } resolution = 3.0 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= 0.005 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 108 5.16 5 C 15891 2.51 5 N 4065 2.21 5 O 4907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 770": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C GLU 1108": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24971 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8008 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 47, 'TRANS': 978} Chain breaks: 7 Chain: "G" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "a" 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: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.31, per 1000 atoms: 0.53 Number of scatterers: 24971 At special positions: 0 Unit cell: (140.17, 170.13, 148.73, 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 108 16.00 O 4907 8.00 N 4065 7.00 C 15891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.01 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.02 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.02 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 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 ALPHA1-4 " NAG S 2 " - " MAN S 3 " " NAG T 2 " - " MAN T 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG G 1 " - " NAG G 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 O 1 " - " NAG O 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 706 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1071 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG O 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 714 " " NAG T 1 " - " ASN B 798 " " NAG U 1 " - " ASN B1071 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 616 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 4.2 seconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 36 sheets defined 26.2% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.061A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.529A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.729A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.884A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.807A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.847A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 removed outlier: 3.552A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 753 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.846A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.522A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.519A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.121A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (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: 3.545A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.578A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.213A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.620A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 753 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 846 through 853 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.843A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.531A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.512A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.652A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.813A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.248A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.749A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.675A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.840A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 753 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 846 through 853 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.840A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.524A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.519A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.616A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.266A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.196A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.742A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 172 removed outlier: 5.105A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.572A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.644A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.552A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.512A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.706A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1044 through 1047 removed outlier: 7.074A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.345A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.524A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.690A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 172 removed outlier: 5.427A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.530A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.623A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 453 removed outlier: 4.015A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.514A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.708A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1044 through 1047 removed outlier: 7.066A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.344A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.521A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.714A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 163 through 172 removed outlier: 5.886A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.662A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 355 through 356 Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.491A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.689A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1044 through 1047 removed outlier: 7.074A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.338A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1119 980 hydrogen bonds defined for protein. 2754 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: 10.87 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4015 1.31 - 1.45: 7237 1.45 - 1.58: 14127 1.58 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 25514 Sorted by residual: bond pdb=" C VAL B 988 " pdb=" O VAL B 988 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.29e-02 6.01e+03 2.00e+01 bond pdb=" C SER B 116 " pdb=" O SER B 116 " ideal model delta sigma weight residual 1.234 1.288 -0.054 1.22e-02 6.72e+03 1.96e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.453 1.492 -0.039 9.20e-03 1.18e+04 1.76e+01 bond pdb=" C PRO B 984 " pdb=" O PRO B 984 " ideal model delta sigma weight residual 1.237 1.184 0.054 1.32e-02 5.74e+03 1.65e+01 bond pdb=" N ILE C 468 " pdb=" CA ILE C 468 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.56e+01 ... (remaining 25509 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.17: 476 105.17 - 112.59: 12329 112.59 - 120.01: 11899 120.01 - 127.43: 9904 127.43 - 134.85: 107 Bond angle restraints: 34715 Sorted by residual: angle pdb=" CA ASP C 976 " pdb=" CB ASP C 976 " pdb=" CG ASP C 976 " ideal model delta sigma weight residual 112.60 118.88 -6.28 1.00e+00 1.00e+00 3.94e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 117.72 -7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N PRO C 983 " pdb=" CA PRO C 983 " pdb=" C PRO C 983 " ideal model delta sigma weight residual 110.70 117.23 -6.53 1.22e+00 6.72e-01 2.87e+01 angle pdb=" C VAL C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 121.61 125.67 -4.06 7.70e-01 1.69e+00 2.78e+01 angle pdb=" C PHE C 565 " pdb=" N GLY C 566 " pdb=" CA GLY C 566 " ideal model delta sigma weight residual 122.33 126.04 -3.71 7.30e-01 1.88e+00 2.58e+01 ... (remaining 34710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 15025 25.00 - 50.01: 861 50.01 - 75.01: 116 75.01 - 100.02: 36 100.02 - 125.02: 7 Dihedral angle restraints: 16045 sinusoidal: 7090 harmonic: 8955 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -1.73 -84.27 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 9.78 83.22 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A1079 " pdb=" SG CYS A1079 " pdb=" SG CYS A1123 " pdb=" CB CYS A1123 " ideal model delta sinusoidal sigma weight residual -86.00 -16.47 -69.53 1 1.00e+01 1.00e-02 6.24e+01 ... (remaining 16042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2632 0.076 - 0.152: 1294 0.152 - 0.229: 216 0.229 - 0.305: 15 0.305 - 0.381: 3 Chirality restraints: 4160 Sorted by residual: chirality pdb=" C1 MAN T 3 " pdb=" O4 NAG T 2 " pdb=" C2 MAN T 3 " pdb=" O5 MAN T 3 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.73e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.23e+01 chirality pdb=" C1 MAN c 3 " pdb=" O4 NAG c 2 " pdb=" C2 MAN c 3 " pdb=" O5 MAN c 3 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.69e+01 ... (remaining 4157 not shown) Planarity restraints: 4424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 738 " -0.059 2.00e-02 2.50e+03 3.01e-02 1.81e+01 pdb=" CG TYR A 738 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 738 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 738 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 738 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 738 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 738 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 738 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 532 " 0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" CG ASN B 532 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 532 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 532 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1104 " 0.019 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C ARG B1104 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG B1104 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B1105 " 0.024 2.00e-02 2.50e+03 ... (remaining 4421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1535 2.74 - 3.28: 25242 3.28 - 3.82: 38915 3.82 - 4.36: 50335 4.36 - 4.90: 81817 Nonbonded interactions: 197844 Sorted by model distance: nonbonded pdb=" O GLN C 962 " pdb=" OG SER C 965 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B1113 " pdb=" OD1 ASP B1115 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 800 " pdb=" OE1 GLN B 801 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.250 3.040 nonbonded pdb=" O GLY C 601 " pdb=" OG1 THR C 604 " model vdw 2.263 3.040 ... (remaining 197839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'g' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 66.090 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.210 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.013 0.058 25514 Z= 0.847 Angle : 1.558 7.474 34715 Z= 1.125 Chirality : 0.081 0.381 4160 Planarity : 0.007 0.042 4383 Dihedral : 15.506 125.024 10162 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 3.25 % Allowed : 13.94 % Favored : 82.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3030 helix: 1.11 (0.19), residues: 680 sheet: -0.13 (0.19), residues: 633 loop : -1.41 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP A 104 HIS 0.038 0.005 HIS A 49 PHE 0.057 0.006 PHE A 194 TYR 0.059 0.007 TYR A 738 ARG 0.034 0.003 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 209 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7684 (mp) cc_final: 0.7292 (pp) REVERT: A 309 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7294 (tm-30) REVERT: A 532 ASN cc_start: 0.8921 (t0) cc_final: 0.8454 (t0) REVERT: B 52 GLN cc_start: 0.6985 (tm130) cc_final: 0.6782 (tm130) REVERT: B 177 MET cc_start: 0.7321 (pmm) cc_final: 0.4728 (mmm) REVERT: B 195 LYS cc_start: 0.7294 (mttt) cc_final: 0.7064 (mttt) REVERT: B 275 PHE cc_start: 0.8075 (m-80) cc_final: 0.7871 (m-10) REVERT: B 309 GLU cc_start: 0.8020 (tp30) cc_final: 0.7778 (mm-30) REVERT: B 464 PHE cc_start: 0.8491 (m-10) cc_final: 0.8189 (m-80) REVERT: B 515 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6186 (p90) REVERT: B 975 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7947 (t0) REVERT: C 168 PHE cc_start: 0.7031 (m-80) cc_final: 0.6830 (m-80) outliers start: 87 outliers final: 46 residues processed: 285 average time/residue: 0.8467 time to fit residues: 303.0021 Evaluate side-chains 214 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 166 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 822 LYS Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1124 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN C 66 HIS C 207 HIS C 506 GLN C 898 GLN C 999 GLN C1007 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25514 Z= 0.173 Angle : 0.597 10.270 34715 Z= 0.307 Chirality : 0.044 0.266 4160 Planarity : 0.003 0.049 4383 Dihedral : 10.223 112.576 4798 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 3.25 % Allowed : 15.21 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.15), residues: 3030 helix: 1.58 (0.20), residues: 684 sheet: 0.07 (0.18), residues: 693 loop : -1.25 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS B1045 PHE 0.025 0.001 PHE C 55 TYR 0.020 0.001 TYR C 369 ARG 0.003 0.000 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 192 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7561 (mp) cc_final: 0.7211 (pp) REVERT: A 309 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7381 (tm-30) REVERT: A 356 LYS cc_start: 0.8611 (pptt) cc_final: 0.8371 (pptt) REVERT: A 532 ASN cc_start: 0.8984 (t0) cc_final: 0.8520 (t0) REVERT: A 975 ASN cc_start: 0.9107 (t0) cc_final: 0.8821 (t0) REVERT: A 1108 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 52 GLN cc_start: 0.7033 (tm130) cc_final: 0.6823 (tm130) REVERT: B 177 MET cc_start: 0.7543 (pmm) cc_final: 0.5088 (mmm) REVERT: B 309 GLU cc_start: 0.7987 (tp30) cc_final: 0.7766 (mm-30) REVERT: B 515 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.6114 (p90) REVERT: B 975 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.8102 (t0) REVERT: C 317 ASN cc_start: 0.7563 (m-40) cc_final: 0.6977 (m-40) REVERT: C 985 GLU cc_start: 0.7947 (pm20) cc_final: 0.7739 (pm20) outliers start: 87 outliers final: 42 residues processed: 270 average time/residue: 0.8524 time to fit residues: 288.9268 Evaluate side-chains 202 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 50.0000 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 278 optimal weight: 0.0570 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN A 759 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 898 GLN C 999 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25514 Z= 0.180 Angle : 0.572 11.356 34715 Z= 0.292 Chirality : 0.044 0.236 4160 Planarity : 0.004 0.056 4383 Dihedral : 9.484 110.940 4770 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 2.88 % Allowed : 16.22 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.15), residues: 3030 helix: 1.41 (0.20), residues: 687 sheet: 0.14 (0.19), residues: 682 loop : -1.24 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 436 HIS 0.002 0.000 HIS B1098 PHE 0.018 0.001 PHE C 55 TYR 0.017 0.001 TYR A1064 ARG 0.006 0.000 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 189 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7657 (mp) cc_final: 0.7308 (pp) REVERT: A 309 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7372 (tm-30) REVERT: A 532 ASN cc_start: 0.9066 (t0) cc_final: 0.8600 (t0) REVERT: A 975 ASN cc_start: 0.9112 (t0) cc_final: 0.8823 (t0) REVERT: A 1108 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 52 GLN cc_start: 0.7053 (tm130) cc_final: 0.6779 (tm130) REVERT: B 120 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (m) REVERT: B 177 MET cc_start: 0.7536 (pmm) cc_final: 0.5037 (mmm) REVERT: B 309 GLU cc_start: 0.8004 (tp30) cc_final: 0.7798 (mm-30) REVERT: B 453 TYR cc_start: 0.5882 (p90) cc_final: 0.5619 (p90) REVERT: B 515 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.6456 (p90) REVERT: B 748 ASN cc_start: 0.8487 (m110) cc_final: 0.8275 (m-40) REVERT: C 229 LEU cc_start: 0.8685 (mm) cc_final: 0.8302 (tm) REVERT: C 985 GLU cc_start: 0.7862 (pm20) cc_final: 0.7636 (pm20) outliers start: 77 outliers final: 43 residues processed: 255 average time/residue: 0.8203 time to fit residues: 262.7199 Evaluate side-chains 206 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 161 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1020 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN B 975 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25514 Z= 0.373 Angle : 0.645 9.411 34715 Z= 0.329 Chirality : 0.046 0.213 4160 Planarity : 0.004 0.059 4383 Dihedral : 9.227 113.664 4761 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 3.96 % Allowed : 16.52 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3030 helix: 0.97 (0.20), residues: 686 sheet: -0.04 (0.19), residues: 693 loop : -1.29 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 436 HIS 0.004 0.001 HIS C1080 PHE 0.022 0.002 PHE B 201 TYR 0.024 0.002 TYR A1064 ARG 0.007 0.001 ARG C 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 171 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8108 (m-10) cc_final: 0.7761 (m-80) REVERT: A 452 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7185 (mm) REVERT: A 532 ASN cc_start: 0.9165 (t0) cc_final: 0.8697 (t0) REVERT: A 975 ASN cc_start: 0.9123 (t0) cc_final: 0.8863 (t0) REVERT: A 1108 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 52 GLN cc_start: 0.7101 (tm130) cc_final: 0.6784 (tm130) REVERT: B 233 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.5012 (pt) REVERT: B 309 GLU cc_start: 0.8075 (tp30) cc_final: 0.7826 (mm-30) REVERT: B 453 TYR cc_start: 0.6195 (p90) cc_final: 0.5581 (p90) REVERT: B 515 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6897 (p90) REVERT: B 748 ASN cc_start: 0.8652 (m110) cc_final: 0.8451 (m-40) REVERT: C 229 LEU cc_start: 0.8732 (mm) cc_final: 0.8289 (tm) REVERT: C 985 GLU cc_start: 0.7987 (pm20) cc_final: 0.7756 (pm20) outliers start: 106 outliers final: 53 residues processed: 258 average time/residue: 0.7661 time to fit residues: 252.8718 Evaluate side-chains 211 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 252 optimal weight: 0.0670 chunk 204 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 910 GLN B1020 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25514 Z= 0.418 Angle : 0.668 8.935 34715 Z= 0.343 Chirality : 0.047 0.205 4160 Planarity : 0.004 0.055 4383 Dihedral : 9.174 115.679 4759 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 4.00 % Allowed : 17.75 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3030 helix: 0.70 (0.19), residues: 684 sheet: -0.18 (0.19), residues: 710 loop : -1.37 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 436 HIS 0.004 0.001 HIS B1080 PHE 0.018 0.002 PHE A1118 TYR 0.024 0.002 TYR A1064 ARG 0.007 0.001 ARG C 997 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 172 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.9163 (t0) cc_final: 0.8724 (t0) REVERT: A 571 ASP cc_start: 0.7497 (p0) cc_final: 0.7270 (p0) REVERT: A 852 PHE cc_start: 0.7017 (m-80) cc_final: 0.6647 (m-80) REVERT: A 975 ASN cc_start: 0.9122 (t0) cc_final: 0.8805 (t0) REVERT: A 1108 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7744 (tm-30) REVERT: B 52 GLN cc_start: 0.7181 (tm130) cc_final: 0.6848 (tm130) REVERT: B 233 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5088 (pt) REVERT: B 302 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8867 (t) REVERT: B 515 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6698 (p90) REVERT: C 229 LEU cc_start: 0.8827 (mm) cc_final: 0.8254 (tm) REVERT: C 985 GLU cc_start: 0.7951 (pm20) cc_final: 0.7519 (pm20) outliers start: 107 outliers final: 62 residues processed: 265 average time/residue: 0.7185 time to fit residues: 245.2537 Evaluate side-chains 218 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 153 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN B 748 ASN B 975 ASN C 207 HIS C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25514 Z= 0.254 Angle : 0.633 23.842 34715 Z= 0.320 Chirality : 0.046 0.301 4160 Planarity : 0.004 0.054 4383 Dihedral : 8.893 113.316 4759 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 3.70 % Allowed : 18.87 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3030 helix: 0.86 (0.20), residues: 680 sheet: -0.15 (0.19), residues: 711 loop : -1.34 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 436 HIS 0.002 0.001 HIS C1080 PHE 0.022 0.001 PHE B 201 TYR 0.020 0.001 TYR A1064 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 170 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.9258 (mm) cc_final: 0.9018 (pp) REVERT: A 532 ASN cc_start: 0.9168 (t0) cc_final: 0.8727 (t0) REVERT: A 975 ASN cc_start: 0.9073 (t0) cc_final: 0.8799 (t0) REVERT: A 1108 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 52 GLN cc_start: 0.7040 (tm130) cc_final: 0.6695 (tm130) REVERT: B 233 ILE cc_start: 0.5380 (OUTLIER) cc_final: 0.4877 (pt) REVERT: B 515 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6434 (p90) REVERT: C 985 GLU cc_start: 0.7962 (pm20) cc_final: 0.7742 (pm20) outliers start: 99 outliers final: 63 residues processed: 255 average time/residue: 0.7588 time to fit residues: 247.8921 Evaluate side-chains 223 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 158 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25514 Z= 0.268 Angle : 0.632 19.880 34715 Z= 0.320 Chirality : 0.045 0.308 4160 Planarity : 0.004 0.054 4383 Dihedral : 8.667 113.067 4757 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 3.51 % Allowed : 19.02 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3030 helix: 0.94 (0.20), residues: 679 sheet: -0.15 (0.19), residues: 717 loop : -1.33 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 104 HIS 0.002 0.001 HIS C1080 PHE 0.022 0.001 PHE A 852 TYR 0.021 0.001 TYR A1064 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 165 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.2490 (OUTLIER) cc_final: 0.0373 (t-90) REVERT: A 441 LEU cc_start: 0.9211 (mm) cc_final: 0.8953 (pp) REVERT: A 532 ASN cc_start: 0.9153 (t0) cc_final: 0.8703 (t0) REVERT: A 975 ASN cc_start: 0.9128 (t0) cc_final: 0.8776 (t0) REVERT: A 1108 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7695 (tm-30) REVERT: B 52 GLN cc_start: 0.7049 (tm130) cc_final: 0.6697 (tm130) REVERT: B 233 ILE cc_start: 0.5312 (OUTLIER) cc_final: 0.4503 (pt) REVERT: B 515 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6474 (p90) REVERT: B 1104 ARG cc_start: 0.7625 (mpt180) cc_final: 0.7420 (mpt-90) REVERT: C 177 MET cc_start: 0.7318 (mmp) cc_final: 0.6953 (mpp) REVERT: C 317 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: C 985 GLU cc_start: 0.7994 (pm20) cc_final: 0.7773 (pm20) outliers start: 94 outliers final: 63 residues processed: 243 average time/residue: 0.7631 time to fit residues: 236.3198 Evaluate side-chains 224 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 157 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 40.0000 chunk 268 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 207 HIS C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25514 Z= 0.190 Angle : 0.613 18.602 34715 Z= 0.309 Chirality : 0.045 0.294 4160 Planarity : 0.004 0.054 4383 Dihedral : 8.363 110.758 4757 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.77 % Allowed : 20.22 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3030 helix: 1.03 (0.20), residues: 686 sheet: -0.11 (0.19), residues: 716 loop : -1.33 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 436 HIS 0.002 0.001 HIS B1045 PHE 0.023 0.001 PHE B 201 TYR 0.019 0.001 TYR A1064 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 168 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7730 (mp) cc_final: 0.7322 (pp) REVERT: A 351 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (p90) REVERT: A 441 LEU cc_start: 0.9215 (mm) cc_final: 0.8983 (pp) REVERT: A 532 ASN cc_start: 0.9124 (t0) cc_final: 0.8674 (t0) REVERT: A 975 ASN cc_start: 0.9124 (t0) cc_final: 0.8769 (t0) REVERT: A 1108 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 52 GLN cc_start: 0.7044 (tm130) cc_final: 0.6729 (tm130) REVERT: B 515 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6405 (p90) REVERT: C 177 MET cc_start: 0.7403 (mmp) cc_final: 0.7121 (mmp) REVERT: C 197 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5702 (pt) REVERT: C 207 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6812 (m-70) REVERT: C 317 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: C 318 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8037 (p90) REVERT: C 985 GLU cc_start: 0.8031 (pm20) cc_final: 0.7802 (pm20) outliers start: 74 outliers final: 52 residues processed: 232 average time/residue: 0.8549 time to fit residues: 250.0089 Evaluate side-chains 210 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 993 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 215 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25514 Z= 0.269 Angle : 0.630 17.589 34715 Z= 0.318 Chirality : 0.045 0.281 4160 Planarity : 0.004 0.053 4383 Dihedral : 8.223 111.811 4753 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 2.95 % Allowed : 20.22 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3030 helix: 1.02 (0.20), residues: 687 sheet: -0.10 (0.19), residues: 713 loop : -1.33 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.007 0.001 HIS C 207 PHE 0.021 0.001 PHE A 852 TYR 0.032 0.002 TYR A 380 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 156 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ILE cc_start: 0.7788 (mp) cc_final: 0.7368 (pp) REVERT: A 441 LEU cc_start: 0.9190 (mm) cc_final: 0.8965 (pp) REVERT: A 532 ASN cc_start: 0.9151 (t0) cc_final: 0.8692 (t0) REVERT: A 975 ASN cc_start: 0.9125 (t0) cc_final: 0.8779 (t0) REVERT: A 1108 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 52 GLN cc_start: 0.7050 (tm130) cc_final: 0.6729 (tm130) REVERT: B 195 LYS cc_start: 0.7218 (mttt) cc_final: 0.6926 (mttt) REVERT: B 515 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6499 (p90) REVERT: B 1104 ARG cc_start: 0.7497 (mpt180) cc_final: 0.7225 (mtt90) REVERT: C 197 ILE cc_start: 0.6141 (OUTLIER) cc_final: 0.5673 (pt) REVERT: C 207 HIS cc_start: 0.7104 (OUTLIER) cc_final: 0.6859 (m-70) REVERT: C 317 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: C 318 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8117 (p90) REVERT: C 985 GLU cc_start: 0.8005 (pm20) cc_final: 0.7771 (pm20) outliers start: 79 outliers final: 63 residues processed: 226 average time/residue: 0.8176 time to fit residues: 237.5084 Evaluate side-chains 217 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 149 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 993 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.2980 chunk 177 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 207 HIS C 898 GLN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25514 Z= 0.176 Angle : 0.617 15.739 34715 Z= 0.309 Chirality : 0.045 0.261 4160 Planarity : 0.004 0.053 4383 Dihedral : 7.906 110.072 4753 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.43 % Allowed : 20.89 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3030 helix: 1.08 (0.20), residues: 687 sheet: -0.05 (0.19), residues: 701 loop : -1.30 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 436 HIS 0.016 0.001 HIS C 207 PHE 0.027 0.001 PHE B 201 TYR 0.025 0.001 TYR A 380 ARG 0.006 0.000 ARG A 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 157 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5942 (pp) REVERT: A 210 ILE cc_start: 0.7714 (mp) cc_final: 0.7323 (pp) REVERT: A 245 HIS cc_start: 0.2627 (OUTLIER) cc_final: 0.0511 (t-90) REVERT: A 441 LEU cc_start: 0.9191 (mm) cc_final: 0.8974 (pp) REVERT: A 532 ASN cc_start: 0.9116 (t0) cc_final: 0.8662 (t0) REVERT: A 975 ASN cc_start: 0.9128 (t0) cc_final: 0.8781 (t0) REVERT: A 1108 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 52 GLN cc_start: 0.7085 (tm130) cc_final: 0.6779 (tm130) REVERT: B 195 LYS cc_start: 0.7276 (mttt) cc_final: 0.7020 (mttt) REVERT: B 515 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.6332 (p90) REVERT: C 177 MET cc_start: 0.7054 (mmp) cc_final: 0.6690 (mpp) REVERT: C 197 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5780 (pt) REVERT: C 207 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6869 (m-70) REVERT: C 317 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7196 (m-40) REVERT: C 318 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8095 (p90) REVERT: C 985 GLU cc_start: 0.8037 (pm20) cc_final: 0.7807 (pm20) outliers start: 65 outliers final: 53 residues processed: 213 average time/residue: 0.8220 time to fit residues: 221.0532 Evaluate side-chains 208 residues out of total 2676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 148 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 993 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 0.0980 chunk 243 optimal weight: 50.0000 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 207 HIS ** C 999 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 = 0.4304 r_free = 0.4304 target = 0.145519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095085 restraints weight = 56370.986| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.45 r_work: 0.3274 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 25514 Z= 0.249 Angle : 0.626 16.097 34715 Z= 0.315 Chirality : 0.045 0.278 4160 Planarity : 0.004 0.100 4383 Dihedral : 7.767 110.796 4753 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.62 % Allowed : 20.63 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3030 helix: 1.05 (0.20), residues: 688 sheet: -0.01 (0.19), residues: 681 loop : -1.31 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 436 HIS 0.013 0.001 HIS C 207 PHE 0.023 0.001 PHE A 852 TYR 0.023 0.001 TYR A 380 ARG 0.019 0.000 ARG B1104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6389.43 seconds wall clock time: 114 minutes 31.06 seconds (6871.06 seconds total)