Starting phenix.real_space_refine on Fri Mar 6 23:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v85_31790/03_2026/7v85_31790.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.040 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 169 5.16 5 C 22353 2.51 5 N 5738 2.21 5 O 6841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35101 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" 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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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: 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: "d" 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: "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: 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: "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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 8.44, per 1000 atoms: 0.24 Number of scatterers: 35101 At special positions: 0 Unit cell: (177.1, 158.4, 240.9, 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 169 16.00 O 6841 8.00 N 5738 7.00 C 22353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.02 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 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 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 234 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 331 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 52 sheets defined 34.8% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.750A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.520A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.983A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.550A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.808A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.611A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.952A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.244A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.590A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.158A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.092A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.205A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.662A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.137A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.617A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.197A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.671A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.023A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.929A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.706A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.870A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.656A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.646A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 157 through 171 removed outlier: 3.573A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 221 through 231 removed outlier: 3.749A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.931A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.199A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.641A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.207A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.588A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.477A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.736A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.549A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.596A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.948A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 4.018A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.740A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.556A pdb=" N VAL H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 101 removed outlier: 4.004A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.999A pdb=" N ARG H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.517A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 231 removed outlier: 3.939A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 279 through 283 removed outlier: 3.742A pdb=" N VAL H 283 " --> pdb=" O SER H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.629A pdb=" N SER H 331 " --> pdb=" O PHE H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.558A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.573A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 412 removed outlier: 4.514A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.628A pdb=" N LEU H 418 " --> pdb=" O THR H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.510A pdb=" N GLU H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 512 through 532 removed outlier: 3.809A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 547 through 559 Processing helix chain 'H' and resid 560 through 564 removed outlier: 4.224A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.591A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 588 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.501A pdb=" N PHE H 592 " --> pdb=" O PHE H 588 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.205A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.917A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.523A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.552A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.685A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.539A 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 326 removed outlier: 5.450A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.805A 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: 7.428A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.927A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.994A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.407A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.662A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.912A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.896A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.885A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.149A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.409A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.022A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.592A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.680A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.008A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.535A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.397A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.556A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.899A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.783A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.282A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.922A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.648A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.123A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.549A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.557A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 349 1466 hydrogen bonds defined for protein. 4098 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: 8.01 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10922 1.34 - 1.46: 7345 1.46 - 1.58: 17427 1.58 - 1.70: 1 1.70 - 1.82: 238 Bond restraints: 35933 Sorted by residual: bond pdb=" CB PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.361 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C CYS B 617 " pdb=" N THR B 618 " ideal model delta sigma weight residual 1.332 1.304 0.029 1.40e-02 5.10e+03 4.24e+00 bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.494 0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 35928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 48378 2.61 - 5.22: 459 5.22 - 7.83: 39 7.83 - 10.44: 5 10.44 - 13.05: 1 Bond angle restraints: 48882 Sorted by residual: angle pdb=" CA PRO B 26 " pdb=" N PRO B 26 " pdb=" CD PRO B 26 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" C GLN F 89 " pdb=" N ASN F 90 " pdb=" CA ASN F 90 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PRO B 26 " pdb=" CD PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 103.20 97.29 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N GLN B1002 " pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " ideal model delta sigma weight residual 110.12 115.62 -5.50 1.47e+00 4.63e-01 1.40e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 129.35 -13.05 3.50e+00 8.16e-02 1.39e+01 ... (remaining 48877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 19998 17.80 - 35.60: 1836 35.60 - 53.40: 339 53.40 - 71.19: 103 71.19 - 88.99: 42 Dihedral angle restraints: 22318 sinusoidal: 9753 harmonic: 12565 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 179.77 -86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.44 -84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.16 82.16 1 1.00e+01 1.00e-02 8.29e+01 ... (remaining 22315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 5634 0.214 - 0.427: 7 0.427 - 0.641: 1 0.641 - 0.854: 1 0.854 - 1.068: 2 Chirality restraints: 5645 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 5642 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.06e+00 pdb=" CG ASN C 165 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG C2002 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLN F 89 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 986 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 816 2.67 - 3.23: 34785 3.23 - 3.78: 54627 3.78 - 4.34: 70860 4.34 - 4.90: 116349 Nonbonded interactions: 277437 Sorted by model distance: nonbonded pdb=" OE2 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.111 3.120 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.136 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.139 3.040 nonbonded pdb=" O TYR H 215 " pdb=" OG1 THR H 567 " model vdw 2.144 3.040 ... (remaining 277432 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' and resid 14 through 2004) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 34.900 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.005 0.118 36052 Z= 0.233 Angle : 0.700 16.500 49195 Z= 0.349 Chirality : 0.052 1.068 5645 Planarity : 0.004 0.051 6228 Dihedral : 14.309 88.993 14098 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4254 helix: 1.12 (0.14), residues: 1334 sheet: -0.34 (0.19), residues: 728 loop : -1.82 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.016 0.001 TYR C1067 PHE 0.032 0.001 PHE B 906 TRP 0.033 0.001 TRP F 271 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00508 (35933) covalent geometry : angle 0.66454 (48882) SS BOND : bond 0.00337 ( 44) SS BOND : angle 1.41137 ( 88) hydrogen bonds : bond 0.12954 ( 1450) hydrogen bonds : angle 6.11755 ( 4098) link_BETA1-4 : bond 0.00394 ( 31) link_BETA1-4 : angle 2.20657 ( 93) link_NAG-ASN : bond 0.00475 ( 44) link_NAG-ASN : angle 3.80830 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.2961 (ptm) cc_final: 0.2534 (ptt) REVERT: F 376 MET cc_start: -0.2848 (tpp) cc_final: -0.3384 (mmt) REVERT: H 190 MET cc_start: 0.0384 (mmp) cc_final: -0.0583 (tmm) REVERT: H 213 ASP cc_start: 0.6226 (m-30) cc_final: 0.5846 (t70) REVERT: H 360 MET cc_start: 0.0268 (tpp) cc_final: -0.0325 (mtp) REVERT: H 455 MET cc_start: 0.0396 (ppp) cc_final: 0.0103 (ttp) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1926 time to fit residues: 45.3333 Evaluate side-chains 93 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 0.2980 chunk 155 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 804 GLN B 901 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 487 ASN C 914 ASN C 919 ASN F 63 ASN F 98 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.115628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.073816 restraints weight = 164022.761| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 7.51 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36052 Z= 0.117 Angle : 0.601 14.609 49195 Z= 0.299 Chirality : 0.046 0.607 5645 Planarity : 0.004 0.052 6228 Dihedral : 7.138 59.892 6196 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 0.27 % Allowed : 5.72 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4254 helix: 1.30 (0.14), residues: 1369 sheet: -0.05 (0.19), residues: 719 loop : -1.71 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.029 0.001 TYR C 421 PHE 0.015 0.001 PHE B 906 TRP 0.018 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00251 (35933) covalent geometry : angle 0.57413 (48882) SS BOND : bond 0.00287 ( 44) SS BOND : angle 1.28038 ( 88) hydrogen bonds : bond 0.04352 ( 1450) hydrogen bonds : angle 4.98754 ( 4098) link_BETA1-4 : bond 0.00394 ( 31) link_BETA1-4 : angle 1.71912 ( 93) link_NAG-ASN : bond 0.00406 ( 44) link_NAG-ASN : angle 3.06828 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.7940 (mmm) cc_final: 0.7730 (mmm) REVERT: A 775 ASP cc_start: 0.8627 (t0) cc_final: 0.8225 (m-30) REVERT: B 200 TYR cc_start: 0.9702 (m-80) cc_final: 0.9439 (t80) REVERT: B 754 LEU cc_start: 0.9274 (mt) cc_final: 0.9065 (mt) REVERT: B 869 MET cc_start: 0.9027 (mtt) cc_final: 0.8686 (mtt) REVERT: B 1010 GLN cc_start: 0.9255 (mm-40) cc_final: 0.8953 (mm-40) REVERT: C 298 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 1050 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7889 (ptt) REVERT: F 323 MET cc_start: 0.3079 (ptm) cc_final: 0.2454 (ptt) REVERT: F 376 MET cc_start: -0.3283 (tpp) cc_final: -0.4073 (tpt) REVERT: H 152 MET cc_start: -0.5495 (ptm) cc_final: -0.5840 (ppp) REVERT: H 190 MET cc_start: 0.0888 (mmp) cc_final: 0.0016 (tmm) REVERT: H 213 ASP cc_start: 0.6161 (m-30) cc_final: 0.5658 (t70) REVERT: H 270 MET cc_start: -0.2496 (mmm) cc_final: -0.2724 (mmm) REVERT: H 366 MET cc_start: 0.2771 (mmt) cc_final: 0.2568 (mmt) REVERT: H 455 MET cc_start: 0.0122 (ppp) cc_final: -0.0518 (ttp) outliers start: 10 outliers final: 4 residues processed: 125 average time/residue: 0.2035 time to fit residues: 44.7589 Evaluate side-chains 102 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 159 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 129 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 345 optimal weight: 50.0000 chunk 287 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A1005 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.114652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.075546 restraints weight = 166100.950| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 7.27 r_work: 0.3019 rms_B_bonded: 5.99 restraints_weight: 2.0000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36052 Z= 0.139 Angle : 0.579 13.838 49195 Z= 0.287 Chirality : 0.045 0.541 5645 Planarity : 0.004 0.056 6228 Dihedral : 6.612 59.639 6196 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 0.69 % Allowed : 8.56 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4254 helix: 1.40 (0.14), residues: 1365 sheet: -0.02 (0.19), residues: 730 loop : -1.69 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.017 0.001 TYR C1067 PHE 0.019 0.001 PHE C1121 TRP 0.016 0.001 TRP H 610 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00312 (35933) covalent geometry : angle 0.55247 (48882) SS BOND : bond 0.00271 ( 44) SS BOND : angle 1.19488 ( 88) hydrogen bonds : bond 0.04227 ( 1450) hydrogen bonds : angle 4.85504 ( 4098) link_BETA1-4 : bond 0.00338 ( 31) link_BETA1-4 : angle 1.66100 ( 93) link_NAG-ASN : bond 0.00334 ( 44) link_NAG-ASN : angle 3.00208 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.9197 (pm20) REVERT: B 117 LEU cc_start: 0.9411 (tp) cc_final: 0.9202 (mp) REVERT: B 869 MET cc_start: 0.9220 (mtt) cc_final: 0.8896 (mtt) REVERT: B 1010 GLN cc_start: 0.9380 (mm-40) cc_final: 0.9167 (mm-40) REVERT: B 1111 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 725 GLU cc_start: 0.8572 (tt0) cc_final: 0.8303 (tt0) REVERT: H 190 MET cc_start: 0.0259 (mmp) cc_final: -0.0655 (tmm) REVERT: H 213 ASP cc_start: 0.6222 (m-30) cc_final: 0.5822 (t70) REVERT: H 360 MET cc_start: -0.0700 (mtp) cc_final: -0.1032 (mtt) REVERT: H 366 MET cc_start: 0.3147 (mmt) cc_final: 0.2900 (mmt) REVERT: H 408 MET cc_start: 0.6717 (pmm) cc_final: 0.6516 (pmm) REVERT: H 455 MET cc_start: 0.0615 (ppp) cc_final: 0.0385 (ttp) outliers start: 26 outliers final: 14 residues processed: 117 average time/residue: 0.1838 time to fit residues: 38.6248 Evaluate side-chains 109 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 227 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 412 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 408 optimal weight: 8.9990 chunk 405 optimal weight: 40.0000 chunk 218 optimal weight: 0.0050 chunk 103 optimal weight: 40.0000 chunk 346 optimal weight: 30.0000 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A1036 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1048 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.114177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071671 restraints weight = 165324.891| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 7.94 r_work: 0.2963 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36052 Z= 0.161 Angle : 0.585 13.957 49195 Z= 0.289 Chirality : 0.045 0.523 5645 Planarity : 0.004 0.058 6228 Dihedral : 6.328 58.602 6196 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 1.11 % Allowed : 10.65 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4254 helix: 1.44 (0.14), residues: 1364 sheet: -0.00 (0.19), residues: 722 loop : -1.72 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE C1121 TRP 0.024 0.001 TRP H 610 HIS 0.010 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00366 (35933) covalent geometry : angle 0.55989 (48882) SS BOND : bond 0.00280 ( 44) SS BOND : angle 1.24808 ( 88) hydrogen bonds : bond 0.04102 ( 1450) hydrogen bonds : angle 4.81389 ( 4098) link_BETA1-4 : bond 0.00301 ( 31) link_BETA1-4 : angle 1.55756 ( 93) link_NAG-ASN : bond 0.00314 ( 44) link_NAG-ASN : angle 2.97895 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 775 ASP cc_start: 0.9191 (t0) cc_final: 0.8702 (m-30) REVERT: B 120 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.9081 (p) REVERT: B 200 TYR cc_start: 0.9594 (m-80) cc_final: 0.9305 (t80) REVERT: B 229 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9170 (mm) REVERT: B 731 MET cc_start: 0.9209 (ptp) cc_final: 0.8984 (ptm) REVERT: B 869 MET cc_start: 0.9256 (mtt) cc_final: 0.8883 (mtt) REVERT: B 1010 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9218 (mm-40) REVERT: B 1111 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8532 (tm-30) REVERT: C 298 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: C 1029 MET cc_start: 0.9055 (tpp) cc_final: 0.8782 (tpp) REVERT: C 1050 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8244 (ptt) REVERT: F 408 MET cc_start: 0.0608 (mtp) cc_final: 0.0268 (ppp) REVERT: H 190 MET cc_start: 0.0238 (mmp) cc_final: -0.0760 (tmm) REVERT: H 213 ASP cc_start: 0.6132 (m-30) cc_final: 0.5717 (t70) REVERT: H 360 MET cc_start: -0.0668 (mtp) cc_final: -0.1151 (mtt) REVERT: H 366 MET cc_start: 0.3539 (mmt) cc_final: 0.3287 (mmt) REVERT: H 408 MET cc_start: 0.6778 (pmm) cc_final: 0.6547 (pmm) REVERT: H 455 MET cc_start: 0.0733 (ppp) cc_final: 0.0365 (ttp) REVERT: H 480 MET cc_start: 0.3530 (ptt) cc_final: 0.3027 (ptt) outliers start: 42 outliers final: 20 residues processed: 133 average time/residue: 0.1829 time to fit residues: 44.2500 Evaluate side-chains 117 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 233 optimal weight: 8.9990 chunk 373 optimal weight: 20.0000 chunk 381 optimal weight: 50.0000 chunk 425 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 250 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A1048 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 901 GLN C 957 GLN F 524 GLN H 96 GLN H 340 GLN H 417 HIS H 572 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.112502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073422 restraints weight = 166558.254| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 7.68 r_work: 0.2972 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 36052 Z= 0.280 Angle : 0.688 14.999 49195 Z= 0.342 Chirality : 0.048 0.536 5645 Planarity : 0.004 0.056 6228 Dihedral : 6.580 59.610 6196 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.07 % Rotamer: Outliers : 1.96 % Allowed : 12.32 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 4254 helix: 1.25 (0.14), residues: 1362 sheet: -0.40 (0.20), residues: 661 loop : -1.83 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.024 0.002 TYR C1067 PHE 0.032 0.002 PHE C1121 TRP 0.028 0.001 TRP H 610 HIS 0.013 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00639 (35933) covalent geometry : angle 0.66329 (48882) SS BOND : bond 0.00430 ( 44) SS BOND : angle 1.51586 ( 88) hydrogen bonds : bond 0.04756 ( 1450) hydrogen bonds : angle 5.10832 ( 4098) link_BETA1-4 : bond 0.00239 ( 31) link_BETA1-4 : angle 1.61854 ( 93) link_NAG-ASN : bond 0.00450 ( 44) link_NAG-ASN : angle 3.21153 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 96 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9546 (OUTLIER) cc_final: 0.9131 (pm20) REVERT: A 858 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9138 (pp) REVERT: A 873 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: A 1029 MET cc_start: 0.9233 (tpp) cc_final: 0.8954 (tpp) REVERT: B 120 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 200 TYR cc_start: 0.9659 (m-80) cc_final: 0.9375 (t80) REVERT: B 229 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9191 (mm) REVERT: B 544 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.8788 (m-40) REVERT: B 869 MET cc_start: 0.9205 (mtt) cc_final: 0.8775 (mtt) REVERT: B 1010 GLN cc_start: 0.9414 (mm-40) cc_final: 0.9193 (mm-40) REVERT: B 1111 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8496 (tm-30) REVERT: C 298 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: C 1029 MET cc_start: 0.9178 (tpp) cc_final: 0.8900 (tpp) REVERT: F 376 MET cc_start: -0.3815 (tpp) cc_final: -0.4451 (mmt) REVERT: F 408 MET cc_start: 0.1009 (mtp) cc_final: 0.0298 (ppp) REVERT: F 474 MET cc_start: -0.2198 (tpp) cc_final: -0.2771 (tpp) REVERT: H 190 MET cc_start: 0.0477 (mmp) cc_final: -0.0643 (tmm) REVERT: H 213 ASP cc_start: 0.6273 (m-30) cc_final: 0.5633 (t70) REVERT: H 360 MET cc_start: -0.0943 (mtp) cc_final: -0.1467 (mtp) REVERT: H 408 MET cc_start: 0.5806 (pmm) cc_final: 0.5568 (pmm) REVERT: H 455 MET cc_start: 0.0501 (ppp) cc_final: -0.0007 (ttp) REVERT: H 480 MET cc_start: 0.1480 (ptt) cc_final: 0.1230 (ptt) outliers start: 74 outliers final: 41 residues processed: 162 average time/residue: 0.1701 time to fit residues: 49.6531 Evaluate side-chains 139 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 169 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN F 137 ASN H 96 GLN H 417 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.113171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070778 restraints weight = 165706.764| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 9.10 r_work: 0.2901 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36052 Z= 0.192 Angle : 0.626 14.928 49195 Z= 0.308 Chirality : 0.046 0.511 5645 Planarity : 0.004 0.058 6228 Dihedral : 6.412 59.680 6196 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 1.80 % Allowed : 12.96 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4254 helix: 1.32 (0.14), residues: 1366 sheet: -0.26 (0.19), residues: 717 loop : -1.82 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.023 0.001 TYR F 243 PHE 0.024 0.001 PHE C1121 TRP 0.026 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00441 (35933) covalent geometry : angle 0.59905 (48882) SS BOND : bond 0.00333 ( 44) SS BOND : angle 1.62371 ( 88) hydrogen bonds : bond 0.04349 ( 1450) hydrogen bonds : angle 4.93543 ( 4098) link_BETA1-4 : bond 0.00266 ( 31) link_BETA1-4 : angle 1.53687 ( 93) link_NAG-ASN : bond 0.00310 ( 44) link_NAG-ASN : angle 3.08359 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 93 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 873 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: A 984 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8778 (tt) REVERT: B 117 LEU cc_start: 0.9479 (mp) cc_final: 0.9214 (tp) REVERT: B 200 TYR cc_start: 0.9617 (m-80) cc_final: 0.9328 (t80) REVERT: B 869 MET cc_start: 0.9159 (mtt) cc_final: 0.8742 (mtt) REVERT: B 1010 GLN cc_start: 0.9449 (mm-40) cc_final: 0.9232 (mm-40) REVERT: B 1111 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 298 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: C 788 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8452 (mp) REVERT: C 1029 MET cc_start: 0.9111 (tpp) cc_final: 0.8851 (tpp) REVERT: C 1072 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: F 376 MET cc_start: -0.3387 (tpp) cc_final: -0.4100 (mmt) REVERT: F 408 MET cc_start: 0.0402 (mtp) cc_final: 0.0114 (ppp) REVERT: H 190 MET cc_start: 0.0379 (mmp) cc_final: -0.0715 (tmm) REVERT: H 213 ASP cc_start: 0.6170 (m-30) cc_final: 0.5707 (t70) REVERT: H 360 MET cc_start: -0.0381 (mtp) cc_final: -0.0892 (mtp) REVERT: H 408 MET cc_start: 0.6659 (pmm) cc_final: 0.6386 (pmm) REVERT: H 455 MET cc_start: 0.0588 (ppp) cc_final: 0.0020 (ttp) REVERT: H 480 MET cc_start: 0.2876 (ptt) cc_final: 0.2352 (ptt) outliers start: 68 outliers final: 39 residues processed: 156 average time/residue: 0.1803 time to fit residues: 50.6685 Evaluate side-chains 133 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 331 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 380 optimal weight: 30.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN F 137 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.113529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.071829 restraints weight = 166353.096| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 8.15 r_work: 0.2933 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36052 Z= 0.159 Angle : 0.600 14.693 49195 Z= 0.295 Chirality : 0.045 0.500 5645 Planarity : 0.004 0.062 6228 Dihedral : 6.219 59.993 6196 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 1.54 % Allowed : 13.60 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4254 helix: 1.40 (0.14), residues: 1367 sheet: -0.19 (0.19), residues: 708 loop : -1.77 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.018 0.001 TYR C1067 PHE 0.020 0.001 PHE C1121 TRP 0.034 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00364 (35933) covalent geometry : angle 0.57375 (48882) SS BOND : bond 0.00289 ( 44) SS BOND : angle 1.45956 ( 88) hydrogen bonds : bond 0.04132 ( 1450) hydrogen bonds : angle 4.82195 ( 4098) link_BETA1-4 : bond 0.00281 ( 31) link_BETA1-4 : angle 1.52729 ( 93) link_NAG-ASN : bond 0.00306 ( 44) link_NAG-ASN : angle 3.00482 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 92 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9203 (pp) REVERT: A 873 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: A 984 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8849 (tt) REVERT: B 117 LEU cc_start: 0.9432 (mp) cc_final: 0.9131 (tp) REVERT: B 200 TYR cc_start: 0.9523 (m-80) cc_final: 0.9245 (t80) REVERT: B 869 MET cc_start: 0.9290 (mtt) cc_final: 0.8891 (mtt) REVERT: B 1010 GLN cc_start: 0.9488 (mm-40) cc_final: 0.9247 (mm-40) REVERT: B 1111 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 298 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: C 788 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 1029 MET cc_start: 0.9100 (tpp) cc_final: 0.8826 (tpp) REVERT: C 1050 MET cc_start: 0.8801 (ptm) cc_final: 0.8313 (ptt) REVERT: C 1072 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: F 376 MET cc_start: -0.3399 (tpp) cc_final: -0.4128 (mmt) REVERT: F 408 MET cc_start: 0.0418 (mtp) cc_final: 0.0149 (ppp) REVERT: F 474 MET cc_start: -0.2595 (tpp) cc_final: -0.2897 (mmp) REVERT: H 190 MET cc_start: 0.0010 (mmp) cc_final: -0.1017 (tmm) REVERT: H 213 ASP cc_start: 0.6140 (m-30) cc_final: 0.5619 (t70) REVERT: H 360 MET cc_start: -0.0763 (mtp) cc_final: -0.1246 (mtp) REVERT: H 366 MET cc_start: 0.3411 (mmt) cc_final: 0.3124 (mmt) REVERT: H 408 MET cc_start: 0.6707 (pmm) cc_final: 0.6420 (pmm) REVERT: H 455 MET cc_start: 0.0672 (ppp) cc_final: 0.0221 (ttp) REVERT: H 480 MET cc_start: 0.2978 (ptt) cc_final: 0.2496 (ptt) outliers start: 58 outliers final: 42 residues processed: 147 average time/residue: 0.1916 time to fit residues: 50.7247 Evaluate side-chains 138 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 201 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 chunk 379 optimal weight: 50.0000 chunk 21 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 289 optimal weight: 0.0010 chunk 82 optimal weight: 3.9990 chunk 213 optimal weight: 0.5980 chunk 208 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 overall best weight: 0.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 901 GLN B 501 ASN B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS F 137 ASN H 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.114916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.070918 restraints weight = 166150.352| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 8.08 r_work: 0.2980 rms_B_bonded: 5.96 restraints_weight: 2.0000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36052 Z= 0.101 Angle : 0.564 14.218 49195 Z= 0.276 Chirality : 0.044 0.478 5645 Planarity : 0.004 0.066 6228 Dihedral : 5.777 59.860 6196 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 1.30 % Allowed : 14.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 4254 helix: 1.66 (0.14), residues: 1361 sheet: -0.07 (0.19), residues: 717 loop : -1.65 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.016 0.001 TYR C1067 PHE 0.010 0.001 PHE B1075 TRP 0.040 0.001 TRP H 610 HIS 0.014 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00214 (35933) covalent geometry : angle 0.53907 (48882) SS BOND : bond 0.00230 ( 44) SS BOND : angle 1.15622 ( 88) hydrogen bonds : bond 0.03662 ( 1450) hydrogen bonds : angle 4.56585 ( 4098) link_BETA1-4 : bond 0.00386 ( 31) link_BETA1-4 : angle 1.53557 ( 93) link_NAG-ASN : bond 0.00410 ( 44) link_NAG-ASN : angle 2.86087 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 775 ASP cc_start: 0.9050 (t0) cc_final: 0.8587 (m-30) REVERT: B 200 TYR cc_start: 0.9655 (m-80) cc_final: 0.9393 (t80) REVERT: B 936 ASP cc_start: 0.9616 (t0) cc_final: 0.9413 (m-30) REVERT: B 1111 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 298 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: C 1005 GLN cc_start: 0.9231 (tp40) cc_final: 0.8925 (tp-100) REVERT: C 1029 MET cc_start: 0.8899 (tpp) cc_final: 0.8696 (tpp) REVERT: F 376 MET cc_start: -0.3265 (tpp) cc_final: -0.3908 (mmt) REVERT: F 474 MET cc_start: -0.0559 (tpp) cc_final: -0.1065 (mmp) REVERT: H 190 MET cc_start: -0.0583 (mmp) cc_final: -0.1459 (tmm) REVERT: H 213 ASP cc_start: 0.5990 (m-30) cc_final: 0.5586 (t70) REVERT: H 360 MET cc_start: 0.1120 (mtp) cc_final: 0.0394 (mtp) REVERT: H 408 MET cc_start: 0.6530 (pmm) cc_final: 0.6249 (pmm) REVERT: H 455 MET cc_start: 0.0008 (ppp) cc_final: -0.0430 (ttp) REVERT: H 480 MET cc_start: 0.3674 (ptt) cc_final: 0.3282 (ptt) outliers start: 49 outliers final: 38 residues processed: 145 average time/residue: 0.1845 time to fit residues: 47.9912 Evaluate side-chains 130 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 315 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 402 optimal weight: 30.0000 chunk 266 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 363 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1048 HIS C 901 GLN F 137 ASN H 96 GLN H 417 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.111516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071149 restraints weight = 166217.718| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 7.99 r_work: 0.2858 rms_B_bonded: 6.70 restraints_weight: 2.0000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 36052 Z= 0.360 Angle : 0.768 14.706 49195 Z= 0.382 Chirality : 0.050 0.541 5645 Planarity : 0.005 0.064 6228 Dihedral : 6.401 58.363 6196 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.64 % Rotamer: Outliers : 1.51 % Allowed : 14.58 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4254 helix: 1.12 (0.14), residues: 1372 sheet: -0.58 (0.20), residues: 693 loop : -1.83 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 408 TYR 0.028 0.002 TYR C1067 PHE 0.036 0.002 PHE C1121 TRP 0.041 0.002 TRP H 610 HIS 0.015 0.002 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00818 (35933) covalent geometry : angle 0.74444 (48882) SS BOND : bond 0.00484 ( 44) SS BOND : angle 1.75246 ( 88) hydrogen bonds : bond 0.05026 ( 1450) hydrogen bonds : angle 5.18479 ( 4098) link_BETA1-4 : bond 0.00265 ( 31) link_BETA1-4 : angle 1.68687 ( 93) link_NAG-ASN : bond 0.00609 ( 44) link_NAG-ASN : angle 3.21508 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 1.320 Fit side-chains REVERT: A 873 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: A 1029 MET cc_start: 0.9284 (tpp) cc_final: 0.9029 (tpp) REVERT: B 200 TYR cc_start: 0.9665 (m-80) cc_final: 0.9415 (t80) REVERT: B 1111 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8587 (tm-30) REVERT: C 788 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8378 (mp) REVERT: C 1029 MET cc_start: 0.9220 (tpp) cc_final: 0.8893 (tpp) REVERT: C 1072 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: F 474 MET cc_start: -0.0743 (tpp) cc_final: -0.1266 (mmp) REVERT: H 190 MET cc_start: -0.0794 (mmp) cc_final: -0.1783 (tmm) REVERT: H 360 MET cc_start: 0.0134 (mtp) cc_final: -0.0481 (mtt) REVERT: H 408 MET cc_start: 0.6390 (pmm) cc_final: 0.6047 (pmm) REVERT: H 455 MET cc_start: 0.0360 (ppp) cc_final: -0.0038 (ttp) REVERT: H 480 MET cc_start: 0.4013 (ptt) cc_final: 0.3624 (ptt) outliers start: 57 outliers final: 44 residues processed: 140 average time/residue: 0.1852 time to fit residues: 46.6975 Evaluate side-chains 133 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 86 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 220 optimal weight: 4.9990 chunk 405 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 125 optimal weight: 1.9990 chunk 379 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN H 96 GLN H 417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.113322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071277 restraints weight = 164103.480| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 8.58 r_work: 0.2908 rms_B_bonded: 6.44 restraints_weight: 2.0000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36052 Z= 0.146 Angle : 0.608 14.601 49195 Z= 0.299 Chirality : 0.045 0.479 5645 Planarity : 0.004 0.067 6228 Dihedral : 6.098 59.886 6196 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 1.27 % Allowed : 14.79 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4254 helix: 1.46 (0.14), residues: 1348 sheet: -0.19 (0.19), residues: 703 loop : -1.74 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.020 0.001 TYR A 508 PHE 0.017 0.001 PHE C1121 TRP 0.044 0.001 TRP H 610 HIS 0.016 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00331 (35933) covalent geometry : angle 0.58325 (48882) SS BOND : bond 0.00361 ( 44) SS BOND : angle 1.53408 ( 88) hydrogen bonds : bond 0.04128 ( 1450) hydrogen bonds : angle 4.79595 ( 4098) link_BETA1-4 : bond 0.00306 ( 31) link_BETA1-4 : angle 1.48967 ( 93) link_NAG-ASN : bond 0.00302 ( 44) link_NAG-ASN : angle 2.96637 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 89 time to evaluate : 1.295 Fit side-chains REVERT: A 153 MET cc_start: 0.7555 (ppp) cc_final: 0.7316 (ppp) REVERT: A 775 ASP cc_start: 0.9177 (t0) cc_final: 0.8757 (m-30) REVERT: A 1029 MET cc_start: 0.9192 (tpp) cc_final: 0.8938 (tpp) REVERT: B 200 TYR cc_start: 0.9675 (m-80) cc_final: 0.9423 (t80) REVERT: B 1111 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 1005 GLN cc_start: 0.9388 (tp40) cc_final: 0.9140 (tp-100) REVERT: C 1029 MET cc_start: 0.9056 (tpp) cc_final: 0.8807 (tpp) REVERT: F 474 MET cc_start: -0.1336 (tpp) cc_final: -0.1793 (mmp) REVERT: H 190 MET cc_start: -0.0601 (mmp) cc_final: -0.1646 (tmm) REVERT: H 360 MET cc_start: 0.0222 (mtp) cc_final: -0.0522 (mtp) REVERT: H 408 MET cc_start: 0.6334 (pmm) cc_final: 0.5974 (pmm) REVERT: H 455 MET cc_start: 0.0076 (ppp) cc_final: -0.0258 (ttp) REVERT: H 480 MET cc_start: 0.3553 (ptt) cc_final: 0.3055 (ptt) outliers start: 48 outliers final: 39 residues processed: 133 average time/residue: 0.1878 time to fit residues: 45.2058 Evaluate side-chains 127 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 420 optimal weight: 30.0000 chunk 352 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 376 optimal weight: 50.0000 chunk 299 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 327 optimal weight: 50.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.112287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.071333 restraints weight = 165643.180| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 9.35 r_work: 0.2938 rms_B_bonded: 5.83 restraints_weight: 2.0000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 36052 Z= 0.265 Angle : 0.681 14.506 49195 Z= 0.335 Chirality : 0.047 0.501 5645 Planarity : 0.004 0.065 6228 Dihedral : 6.250 59.996 6196 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 1.38 % Allowed : 14.90 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.13), residues: 4254 helix: 1.32 (0.14), residues: 1348 sheet: -0.47 (0.20), residues: 674 loop : -1.78 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.024 0.001 TYR A1067 PHE 0.031 0.002 PHE C1121 TRP 0.042 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00607 (35933) covalent geometry : angle 0.65752 (48882) SS BOND : bond 0.00418 ( 44) SS BOND : angle 1.63636 ( 88) hydrogen bonds : bond 0.04527 ( 1450) hydrogen bonds : angle 4.97454 ( 4098) link_BETA1-4 : bond 0.00240 ( 31) link_BETA1-4 : angle 1.53197 ( 93) link_NAG-ASN : bond 0.00397 ( 44) link_NAG-ASN : angle 3.05355 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17497.12 seconds wall clock time: 297 minutes 11.80 seconds (17831.80 seconds total)