Starting phenix.real_space_refine on Fri Mar 6 02:03:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybh_33721/03_2026/7ybh_33721.map" } resolution = 3.5 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= 0.067 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 114 5.16 5 C 17099 2.51 5 N 4366 2.21 5 O 5385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 26964 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8596 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1046} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 8578 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 1101, 8578 Classifications: {'peptide': 1101} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 8497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8497 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 58, 'TRANS': 1032} Chain breaks: 4 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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: 6.22, per 1000 atoms: 0.23 Number of scatterers: 26964 At special positions: 0 Unit cell: (157.29, 147.66, 219.35, 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 114 16.00 O 5385 8.00 N 4366 7.00 C 17099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.04 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 583 " distance=2.04 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 642 " distance=2.02 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.04 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 833 " - pdb=" SG CYS A 844 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " 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 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 642 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " 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 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 583 " distance=2.07 Simple disulfide: pdb=" SG CYS C 610 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 655 " - pdb=" SG CYS C 664 " distance=2.04 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.04 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 275 " " NAG A1306 " - " ASN A 596 " " NAG A1307 " - " ASN A 650 " " NAG A1308 " - " ASN A 609 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 336 " " NAG B1303 " - " ASN B 596 " " NAG B1304 " - " ASN B 650 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 324 " " NAG C1304 " - " ASN C 596 " " NAG C1305 " - " ASN C 650 " " NAG D 1 " - " ASN A 336 " " NAG E 1 " - " ASN A 702 " " NAG G 1 " - " ASN A 710 " " NAG H 1 " - " ASN A 794 " " NAG I 1 " - " ASN A1067 " " NAG J 1 " - " ASN A1091 " " NAG K 1 " - " ASN A1127 " " NAG L 1 " - " ASN B 324 " " NAG M 1 " - " ASN B 702 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 275 " " NAG R 1 " - " ASN B 609 " " NAG S 1 " - " ASN B 710 " " NAG T 1 " - " ASN B 794 " " NAG U 1 " - " ASN B1067 " " NAG V 1 " - " ASN B1091 " " NAG W 1 " - " ASN B1127 " " NAG X 1 " - " ASN C 275 " " NAG Y 1 " - " ASN C 336 " " NAG Z 1 " - " ASN C 702 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 609 " " NAG d 1 " - " ASN C 710 " " NAG e 1 " - " ASN C 794 " " NAG f 1 " - " ASN C1067 " " NAG g 1 " - " ASN C1091 " " NAG h 1 " - " ASN C1127 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 43 sheets defined 26.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 376 through 383 removed outlier: 5.095A pdb=" N ASN A 381 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 5.334A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 404 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.655A pdb=" N VAL A 613 " --> pdb=" O CYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 747 Processing helix chain 'A' and resid 752 through 776 removed outlier: 3.697A pdb=" N ASP A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 Processing helix chain 'A' and resid 823 through 828 removed outlier: 4.057A pdb=" N ILE A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 829 through 835 Processing helix chain 'A' and resid 843 through 849 removed outlier: 3.615A pdb=" N ASN A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.536A pdb=" N GLY A 882 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 removed outlier: 3.600A pdb=" N GLN A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 934 removed outlier: 3.731A pdb=" N TYR A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 922 " --> pdb=" O ASN A 918 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 926 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.452A pdb=" N VAL A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 976 removed outlier: 3.633A pdb=" N ILE A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1026 removed outlier: 4.026A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1154 removed outlier: 4.156A pdb=" N GLU A1137 " --> pdb=" O PRO A1133 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A1154 " --> pdb=" O LYS A1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.818A pdb=" N VAL B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.632A pdb=" N TRP B 346 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.867A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.542A pdb=" N ASN B 381 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 4.573A pdb=" N ARG B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.568A pdb=" N ASN B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 619 through 622 Processing helix chain 'B' and resid 623 through 632 removed outlier: 3.935A pdb=" N TYR B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'B' and resid 751 through 776 removed outlier: 3.680A pdb=" N GLN B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 859 through 878 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.095A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.578A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 3.614A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 959 removed outlier: 4.393A pdb=" N VAL B 944 " --> pdb=" O LYS B 940 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 977 removed outlier: 3.794A pdb=" N ILE B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.918A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1111 No H-bonds generated for 'chain 'B' and resid 1109 through 1111' Processing helix chain 'B' and resid 1133 through 1154 removed outlier: 4.024A pdb=" N SER B1154 " --> pdb=" O LYS B1150 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.680A pdb=" N LEU C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 342 through 346 removed outlier: 3.621A pdb=" N TRP C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 removed outlier: 4.380A pdb=" N LEU C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 4.151A pdb=" N ASN C 381 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 4.424A pdb=" N ARG C 401 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 404 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 415 Processing helix chain 'C' and resid 611 through 616 Processing helix chain 'C' and resid 731 through 737 Processing helix chain 'C' and resid 740 through 746 Processing helix chain 'C' and resid 747 through 749 No H-bonds generated for 'chain 'C' and resid 747 through 749' Processing helix chain 'C' and resid 751 through 776 removed outlier: 3.949A pdb=" N ASN C 757 " --> pdb=" O CYS C 753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 758 " --> pdb=" O THR C 754 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 768 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 819 Processing helix chain 'C' and resid 859 through 878 removed outlier: 3.580A pdb=" N GLY C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 883 removed outlier: 3.920A pdb=" N GLY C 882 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 removed outlier: 3.781A pdb=" N ILE C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.517A pdb=" N TYR C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 934 removed outlier: 3.686A pdb=" N ILE C 927 " --> pdb=" O ALA C 923 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 932 " --> pdb=" O GLN C 928 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 934 " --> pdb=" O SER C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.090A pdb=" N VAL C 944 " --> pdb=" O LYS C 940 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 961 No H-bonds generated for 'chain 'C' and resid 959 through 961' Processing helix chain 'C' and resid 969 through 975 removed outlier: 3.603A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 984 through 1026 removed outlier: 3.674A pdb=" N VAL C1026 " --> pdb=" O MET C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1154 removed outlier: 4.304A pdb=" N SER C1154 " --> pdb=" O LYS C1150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.033A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 257 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 95 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.074A pdb=" N ASP A 280 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.935A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.355A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 312 removed outlier: 5.323A pdb=" N ASN A 310 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 586 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY A 587 " --> pdb=" O GLN A 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 606 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 321 removed outlier: 5.680A pdb=" N ASP A 567 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 558 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 351 removed outlier: 4.146A pdb=" N ASN A 387 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 425 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA9, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AB1, first strand: chain 'A' and resid 647 through 648 removed outlier: 3.660A pdb=" N GLU A 647 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 695 removed outlier: 6.524A pdb=" N ALA A 694 " --> pdb=" O ILE C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 704 through 708 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 721 removed outlier: 6.940A pdb=" N GLY A1052 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER A1048 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1054 " --> pdb=" O PRO A1046 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A1056 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER A1044 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A1058 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1113 through 1118 removed outlier: 5.487A pdb=" N VAL A1115 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A1082 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLY A1117 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1074 " --> pdb=" O HIS A1081 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.241A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR B 262 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 257 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 95 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.970A pdb=" N ASP B 280 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.114A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 141 through 144 removed outlier: 6.722A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.832A pdb=" N GLY B 304 " --> pdb=" O THR B 592 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 592 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 317 through 321 removed outlier: 4.038A pdb=" N VAL B 532 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY B 543 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 347 through 351 Processing sheet with id=AC5, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AC6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'B' and resid 647 through 648 removed outlier: 5.726A pdb=" N GLU B 647 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR B 689 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA B 665 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 704 through 721 removed outlier: 6.454A pdb=" N SER B 704 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B1069 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 706 " --> pdb=" O ASN B1067 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B1067 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B1065 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLY B1052 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SER B1048 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1054 " --> pdb=" O PRO B1046 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1056 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER B1044 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B1058 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AD1, first strand: chain 'B' and resid 1080 through 1083 removed outlier: 3.800A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1087 through 1090 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.516A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA C 257 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 95 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 280 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.605A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 140 through 143 Processing sheet with id=AD7, first strand: chain 'C' and resid 306 through 312 removed outlier: 4.436A pdb=" N VAL C 588 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN C 310 " --> pdb=" O GLY C 586 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY C 586 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY C 587 " --> pdb=" O GLN C 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 318 through 321 Processing sheet with id=AD9, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.656A pdb=" N VAL C 388 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 355 removed outlier: 6.824A pdb=" N CYS C 354 " --> pdb=" O CYS C 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 445 through 447 Processing sheet with id=AE3, first strand: chain 'C' and resid 657 through 660 removed outlier: 6.498A pdb=" N ILE C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 721 removed outlier: 6.012A pdb=" N TYR C1060 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS C1041 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1069 through 1070 Processing sheet with id=AE7, first strand: chain 'C' and resid 1113 through 1118 removed outlier: 4.825A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C1074 " --> pdb=" O HIS C1081 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2727 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: 5.93 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6897 1.33 - 1.46: 6893 1.46 - 1.58: 13633 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 27564 Sorted by residual: bond pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 ... (remaining 27559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 36959 2.62 - 5.24: 503 5.24 - 7.85: 48 7.85 - 10.47: 7 10.47 - 13.09: 14 Bond angle restraints: 37531 Sorted by residual: angle pdb=" CA PRO C 935 " pdb=" N PRO C 935 " pdb=" CD PRO C 935 " ideal model delta sigma weight residual 112.00 99.11 12.89 1.40e+00 5.10e-01 8.48e+01 angle pdb=" CA PRO B 935 " pdb=" N PRO B 935 " pdb=" CD PRO B 935 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" CA PRO B 810 " pdb=" N PRO B 810 " pdb=" CD PRO B 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO A 810 " pdb=" N PRO A 810 " pdb=" CD PRO A 810 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.16e+01 angle pdb=" CA PRO A 892 " pdb=" N PRO A 892 " pdb=" CD PRO A 892 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 ... (remaining 37526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 16165 22.08 - 44.17: 1104 44.17 - 66.25: 158 66.25 - 88.33: 169 88.33 - 110.42: 98 Dihedral angle restraints: 17694 sinusoidal: 8093 harmonic: 9601 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 1.98 -87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA CYS C 583 " pdb=" C CYS C 583 " pdb=" N SER C 584 " pdb=" CA SER C 584 " ideal model delta harmonic sigma weight residual -180.00 -137.49 -42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 20.07 72.93 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 17691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4386 0.112 - 0.224: 121 0.224 - 0.336: 20 0.336 - 0.447: 1 0.447 - 0.559: 1 Chirality restraints: 4529 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 324 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 324 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 702 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 4526 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " 1.009 9.50e-02 1.11e+02 4.52e-01 1.24e+02 pdb=" NE ARG C 312 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.971 9.50e-02 1.11e+02 4.35e-01 1.14e+02 pdb=" NE ARG A 321 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 891 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO B 892 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 892 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO B 892 " 0.080 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 168 2.51 - 3.11: 20298 3.11 - 3.70: 39300 3.70 - 4.30: 53018 4.30 - 4.90: 88947 Nonbonded interactions: 201731 Sorted by model distance: nonbonded pdb=" OG SER C 809 " pdb=" CD PRO C 810 " model vdw 1.909 3.440 nonbonded pdb=" O ASP C 283 " pdb=" OG SER C 290 " model vdw 2.064 3.040 nonbonded pdb=" OG SER A 809 " pdb=" OE1 GLU A 812 " model vdw 2.119 3.040 nonbonded pdb=" OG SER B 462 " pdb=" OE1 GLU B 464 " model vdw 2.147 3.040 nonbonded pdb=" O TYR C1040 " pdb=" OG1 THR C1059 " model vdw 2.149 3.040 ... (remaining 201726 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' and (resid 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 821 or (resid 846 and (name N o \ r name CA or name C or name O or name CB )) or resid 847 through 1304)) selection = (chain 'B' and (resid 14 through 546 or (resid 547 and (name N or name CA or nam \ e C or name O or name CB )) or resid 548 through 616 or resid 634 through 842 or \ (resid 846 and (name N or name CA or name C or name O or name CB )) or resid 84 \ 7 through 1304)) selection = (chain 'C' and (resid 14 through 616 or resid 634 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.330 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.062 27699 Z= 0.242 Angle : 0.796 13.088 37894 Z= 0.409 Chirality : 0.051 0.559 4529 Planarity : 0.012 0.452 4744 Dihedral : 18.854 110.416 11392 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 0.42 % Allowed : 0.45 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.97 (0.14), residues: 3271 helix: 0.98 (0.20), residues: 736 sheet: -0.04 (0.20), residues: 649 loop : -1.60 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 102 TYR 0.016 0.001 TYR A1060 PHE 0.030 0.002 PHE A 157 TRP 0.018 0.001 TRP C 429 HIS 0.007 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00480 (27564) covalent geometry : angle 0.77421 (37531) SS BOND : bond 0.00692 ( 42) SS BOND : angle 1.58785 ( 84) hydrogen bonds : bond 0.14661 ( 1002) hydrogen bonds : angle 6.72420 ( 2727) link_ALPHA1-3 : bond 0.00434 ( 1) link_ALPHA1-3 : angle 1.54093 ( 3) link_BETA1-4 : bond 0.00607 ( 47) link_BETA1-4 : angle 1.77232 ( 141) link_NAG-ASN : bond 0.00350 ( 45) link_NAG-ASN : angle 2.55455 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 482 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6831 (t0) cc_final: 0.6598 (t0) REVERT: A 577 ILE cc_start: 0.8285 (mm) cc_final: 0.7741 (mt) REVERT: B 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7746 (pp30) REVERT: B 177 MET cc_start: 0.7083 (pmm) cc_final: 0.4405 (mmm) REVERT: B 335 PHE cc_start: 0.8024 (m-80) cc_final: 0.7752 (m-80) REVERT: B 385 PHE cc_start: 0.6832 (m-80) cc_final: 0.5795 (m-80) REVERT: C 313 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8625 (t) REVERT: C 490 PHE cc_start: 0.4148 (m-80) cc_final: 0.3196 (m-80) REVERT: C 733 MET cc_start: 0.7906 (ttt) cc_final: 0.7699 (ttm) REVERT: C 769 LYS cc_start: 0.8948 (tppp) cc_final: 0.8712 (tptm) outliers start: 12 outliers final: 5 residues processed: 494 average time/residue: 0.1643 time to fit residues: 130.5534 Evaluate side-chains 233 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 227 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN A 668 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN B 948 ASN B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 121 ASN C 310 ASN C 491 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104369 restraints weight = 72567.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107577 restraints weight = 34676.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109624 restraints weight = 22609.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.110846 restraints weight = 17565.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.111465 restraints weight = 15202.099| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27699 Z= 0.213 Angle : 0.819 11.173 37894 Z= 0.397 Chirality : 0.052 0.419 4529 Planarity : 0.006 0.115 4744 Dihedral : 12.031 92.044 5522 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 1.75 % Allowed : 11.82 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.12 (0.14), residues: 3271 helix: 0.97 (0.19), residues: 742 sheet: -0.14 (0.21), residues: 580 loop : -1.71 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 21 TYR 0.027 0.002 TYR C 170 PHE 0.031 0.002 PHE A1141 TRP 0.012 0.002 TRP B 64 HIS 0.007 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00485 (27564) covalent geometry : angle 0.78757 (37531) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.85754 ( 84) hydrogen bonds : bond 0.05731 ( 1002) hydrogen bonds : angle 5.67799 ( 2727) link_ALPHA1-3 : bond 0.00802 ( 1) link_ALPHA1-3 : angle 4.04840 ( 3) link_BETA1-4 : bond 0.00606 ( 47) link_BETA1-4 : angle 2.70230 ( 141) link_NAG-ASN : bond 0.00484 ( 45) link_NAG-ASN : angle 2.40619 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8334 (mm) cc_final: 0.7770 (mt) REVERT: A 971 ASN cc_start: 0.8796 (p0) cc_final: 0.8568 (p0) REVERT: B 177 MET cc_start: 0.7285 (pmm) cc_final: 0.4594 (tpt) REVERT: B 385 PHE cc_start: 0.8077 (m-80) cc_final: 0.7795 (m-80) REVERT: B 449 PHE cc_start: 0.8176 (m-80) cc_final: 0.7700 (m-80) REVERT: B 466 TYR cc_start: 0.7758 (t80) cc_final: 0.7323 (t80) REVERT: B 972 ASP cc_start: 0.8147 (t0) cc_final: 0.7655 (t0) REVERT: C 168 PHE cc_start: 0.7426 (t80) cc_final: 0.7207 (t80) REVERT: C 449 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8099 (t80) REVERT: C 769 LYS cc_start: 0.9181 (tppp) cc_final: 0.8725 (tptm) outliers start: 50 outliers final: 30 residues processed: 302 average time/residue: 0.1542 time to fit residues: 76.7970 Evaluate side-chains 225 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 47 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 188 optimal weight: 0.4980 chunk 36 optimal weight: 8.9990 chunk 259 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 962 ASN A 985 GLN B 245 HIS B 637 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097385 restraints weight = 70568.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.101916 restraints weight = 35567.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.102170 restraints weight = 19801.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.102482 restraints weight = 16215.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102599 restraints weight = 16952.194| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27699 Z= 0.127 Angle : 0.670 9.603 37894 Z= 0.322 Chirality : 0.047 0.379 4529 Planarity : 0.004 0.049 4744 Dihedral : 9.848 91.324 5516 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 1.99 % Allowed : 13.67 % Favored : 84.34 % 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: -0.88 (0.14), residues: 3271 helix: 1.36 (0.19), residues: 750 sheet: -0.11 (0.21), residues: 591 loop : -1.61 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 758 TYR 0.019 0.001 TYR A1060 PHE 0.019 0.001 PHE A 32 TRP 0.030 0.002 TRP C 626 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00284 (27564) covalent geometry : angle 0.64091 (37531) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.54164 ( 84) hydrogen bonds : bond 0.04995 ( 1002) hydrogen bonds : angle 5.32057 ( 2727) link_ALPHA1-3 : bond 0.01263 ( 1) link_ALPHA1-3 : angle 2.25575 ( 3) link_BETA1-4 : bond 0.00602 ( 47) link_BETA1-4 : angle 2.24477 ( 141) link_NAG-ASN : bond 0.00370 ( 45) link_NAG-ASN : angle 2.18646 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 577 ILE cc_start: 0.8411 (mm) cc_final: 0.7799 (mt) REVERT: A 1024 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: B 177 MET cc_start: 0.6949 (pmm) cc_final: 0.4287 (tpt) REVERT: B 331 PHE cc_start: 0.8602 (m-80) cc_final: 0.8387 (m-80) REVERT: B 449 PHE cc_start: 0.8166 (m-80) cc_final: 0.7609 (m-80) REVERT: B 466 TYR cc_start: 0.7917 (t80) cc_final: 0.7497 (t80) REVERT: B 972 ASP cc_start: 0.7994 (t0) cc_final: 0.7596 (t0) REVERT: C 168 PHE cc_start: 0.7369 (t80) cc_final: 0.6650 (t80) REVERT: C 449 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8246 (t80) REVERT: C 728 SER cc_start: 0.9281 (t) cc_final: 0.8781 (m) REVERT: C 769 LYS cc_start: 0.9160 (tppp) cc_final: 0.8786 (tptm) REVERT: C 1131 TYR cc_start: 0.7956 (t80) cc_final: 0.7670 (t80) outliers start: 57 outliers final: 32 residues processed: 257 average time/residue: 0.1413 time to fit residues: 61.3052 Evaluate side-chains 218 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 83 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 310 optimal weight: 0.0030 chunk 326 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 232 optimal weight: 8.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.142417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103620 restraints weight = 72236.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108188 restraints weight = 36921.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.108348 restraints weight = 20726.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108716 restraints weight = 17648.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108948 restraints weight = 17505.204| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27699 Z= 0.132 Angle : 0.653 11.559 37894 Z= 0.316 Chirality : 0.046 0.380 4529 Planarity : 0.004 0.047 4744 Dihedral : 8.149 84.817 5516 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 3.11 % Allowed : 14.51 % Favored : 82.38 % 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 (0.14), residues: 3271 helix: 1.53 (0.19), residues: 741 sheet: -0.12 (0.21), residues: 593 loop : -1.62 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 758 TYR 0.020 0.001 TYR B 501 PHE 0.031 0.001 PHE A 826 TRP 0.044 0.001 TRP C 626 HIS 0.003 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00305 (27564) covalent geometry : angle 0.62747 (37531) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.36413 ( 84) hydrogen bonds : bond 0.04702 ( 1002) hydrogen bonds : angle 5.19932 ( 2727) link_ALPHA1-3 : bond 0.01251 ( 1) link_ALPHA1-3 : angle 2.66209 ( 3) link_BETA1-4 : bond 0.00529 ( 47) link_BETA1-4 : angle 2.05080 ( 141) link_NAG-ASN : bond 0.00348 ( 45) link_NAG-ASN : angle 2.15296 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 219 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8501 (mm) cc_final: 0.7889 (mt) REVERT: A 812 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 1024 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: A 1137 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6714 (mm-30) REVERT: B 177 MET cc_start: 0.6693 (pmm) cc_final: 0.4366 (tpt) REVERT: B 396 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7727 (tpp80) REVERT: B 417 LYS cc_start: 0.7456 (tppt) cc_final: 0.7228 (tppt) REVERT: B 449 PHE cc_start: 0.8189 (m-80) cc_final: 0.7642 (m-80) REVERT: B 466 TYR cc_start: 0.7828 (t80) cc_final: 0.7389 (t80) REVERT: B 972 ASP cc_start: 0.8108 (t0) cc_final: 0.7749 (t0) REVERT: C 449 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8239 (t80) REVERT: C 555 PHE cc_start: 0.7762 (p90) cc_final: 0.7306 (p90) REVERT: C 769 LYS cc_start: 0.9206 (tppp) cc_final: 0.8808 (tptm) REVERT: C 866 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8871 (m-10) REVERT: C 1131 TYR cc_start: 0.7999 (t80) cc_final: 0.7724 (t80) outliers start: 89 outliers final: 40 residues processed: 289 average time/residue: 0.1510 time to fit residues: 73.4983 Evaluate side-chains 236 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 212 optimal weight: 0.3980 chunk 222 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 66 HIS ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.140351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100374 restraints weight = 69446.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103489 restraints weight = 33183.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105505 restraints weight = 21686.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106562 restraints weight = 16900.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.107304 restraints weight = 14679.143| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27699 Z= 0.151 Angle : 0.666 9.466 37894 Z= 0.323 Chirality : 0.046 0.380 4529 Planarity : 0.004 0.063 4744 Dihedral : 7.708 80.853 5516 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.01 % Rotamer: Outliers : 2.41 % Allowed : 16.33 % Favored : 81.26 % 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: -0.78 (0.14), residues: 3271 helix: 1.59 (0.19), residues: 737 sheet: -0.16 (0.20), residues: 665 loop : -1.60 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 758 TYR 0.022 0.001 TYR A 416 PHE 0.017 0.001 PHE C 385 TRP 0.018 0.001 TRP C 251 HIS 0.003 0.001 HIS B1051 Details of bonding type rmsd covalent geometry : bond 0.00355 (27564) covalent geometry : angle 0.64137 (37531) SS BOND : bond 0.00312 ( 42) SS BOND : angle 1.41152 ( 84) hydrogen bonds : bond 0.04953 ( 1002) hydrogen bonds : angle 5.18184 ( 2727) link_ALPHA1-3 : bond 0.01220 ( 1) link_ALPHA1-3 : angle 2.34843 ( 3) link_BETA1-4 : bond 0.00554 ( 47) link_BETA1-4 : angle 1.91727 ( 141) link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.19350 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 TYR cc_start: 0.5096 (t80) cc_final: 0.4808 (t80) REVERT: A 577 ILE cc_start: 0.8572 (mm) cc_final: 0.7988 (mt) REVERT: A 1024 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: B 177 MET cc_start: 0.6747 (pmm) cc_final: 0.4412 (tpt) REVERT: B 417 LYS cc_start: 0.7667 (tppt) cc_final: 0.7366 (tppt) REVERT: B 449 PHE cc_start: 0.8297 (m-80) cc_final: 0.7776 (m-80) REVERT: B 466 TYR cc_start: 0.7723 (t80) cc_final: 0.7246 (t80) REVERT: B 972 ASP cc_start: 0.8204 (t0) cc_final: 0.7908 (t0) REVERT: C 449 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8193 (t80) REVERT: C 461 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7388 (mt) REVERT: C 555 PHE cc_start: 0.7766 (p90) cc_final: 0.7336 (p90) REVERT: C 769 LYS cc_start: 0.9191 (tppp) cc_final: 0.8819 (tptm) REVERT: C 866 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.9027 (m-10) REVERT: C 950 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 1131 TYR cc_start: 0.7928 (t80) cc_final: 0.7578 (t80) outliers start: 69 outliers final: 50 residues processed: 258 average time/residue: 0.1526 time to fit residues: 66.0229 Evaluate side-chains 242 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 449 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 228 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 0.0970 chunk 21 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 995 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 GLN B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 950 GLN ** 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 = 0.4084 r_free = 0.4084 target = 0.129294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088324 restraints weight = 67745.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091093 restraints weight = 35168.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092878 restraints weight = 23856.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093993 restraints weight = 18968.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094628 restraints weight = 16567.807| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27699 Z= 0.167 Angle : 0.681 9.585 37894 Z= 0.333 Chirality : 0.046 0.390 4529 Planarity : 0.004 0.046 4744 Dihedral : 7.196 72.684 5516 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 3.08 % Allowed : 16.82 % Favored : 80.10 % 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 (0.14), residues: 3271 helix: 1.54 (0.19), residues: 741 sheet: -0.19 (0.20), residues: 645 loop : -1.62 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.020 0.001 TYR C1060 PHE 0.026 0.002 PHE C 508 TRP 0.017 0.001 TRP C 251 HIS 0.003 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00391 (27564) covalent geometry : angle 0.65579 (37531) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.58604 ( 84) hydrogen bonds : bond 0.05318 ( 1002) hydrogen bonds : angle 5.21486 ( 2727) link_ALPHA1-3 : bond 0.00958 ( 1) link_ALPHA1-3 : angle 2.16538 ( 3) link_BETA1-4 : bond 0.00541 ( 47) link_BETA1-4 : angle 1.89801 ( 141) link_NAG-ASN : bond 0.00358 ( 45) link_NAG-ASN : angle 2.26206 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 199 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 TYR cc_start: 0.5324 (t80) cc_final: 0.5083 (t80) REVERT: A 461 ILE cc_start: 0.3971 (OUTLIER) cc_final: 0.3705 (pt) REVERT: A 577 ILE cc_start: 0.8640 (mm) cc_final: 0.8026 (mt) REVERT: A 812 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: A 842 LEU cc_start: 0.8923 (tp) cc_final: 0.8651 (tp) REVERT: A 1024 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: A 1137 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6601 (mm-30) REVERT: B 177 MET cc_start: 0.6423 (pmm) cc_final: 0.4388 (tpt) REVERT: B 361 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7915 (pp) REVERT: B 449 PHE cc_start: 0.8404 (m-80) cc_final: 0.7953 (m-80) REVERT: B 466 TYR cc_start: 0.7686 (t80) cc_final: 0.7254 (t80) REVERT: C 224 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: C 461 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7481 (mt) REVERT: C 555 PHE cc_start: 0.7730 (p90) cc_final: 0.7366 (p90) REVERT: C 769 LYS cc_start: 0.9138 (tppp) cc_final: 0.8828 (tptm) REVERT: C 866 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8839 (m-10) outliers start: 88 outliers final: 61 residues processed: 270 average time/residue: 0.1425 time to fit residues: 64.8908 Evaluate side-chains 247 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 690 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 249 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 772 GLN A 995 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 950 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.124518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083799 restraints weight = 68742.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086382 restraints weight = 36323.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088101 restraints weight = 24988.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089035 restraints weight = 20017.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089523 restraints weight = 17629.341| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27699 Z= 0.238 Angle : 0.758 10.079 37894 Z= 0.373 Chirality : 0.048 0.407 4529 Planarity : 0.005 0.057 4744 Dihedral : 7.441 65.217 5516 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 3.71 % Allowed : 17.59 % Favored : 78.71 % 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: -1.08 (0.14), residues: 3271 helix: 1.27 (0.19), residues: 751 sheet: -0.30 (0.20), residues: 643 loop : -1.80 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 627 TYR 0.025 0.002 TYR C1060 PHE 0.027 0.002 PHE B 385 TRP 0.048 0.002 TRP C 626 HIS 0.005 0.001 HIS B1051 Details of bonding type rmsd covalent geometry : bond 0.00563 (27564) covalent geometry : angle 0.73308 (37531) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.70113 ( 84) hydrogen bonds : bond 0.06218 ( 1002) hydrogen bonds : angle 5.49233 ( 2727) link_ALPHA1-3 : bond 0.00938 ( 1) link_ALPHA1-3 : angle 2.24568 ( 3) link_BETA1-4 : bond 0.00552 ( 47) link_BETA1-4 : angle 1.94711 ( 141) link_NAG-ASN : bond 0.00436 ( 45) link_NAG-ASN : angle 2.45955 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 182 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8061 (p0) cc_final: 0.7841 (p0) REVERT: A 461 ILE cc_start: 0.3914 (OUTLIER) cc_final: 0.3676 (pt) REVERT: A 812 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 1024 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: A 1137 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6655 (mm-30) REVERT: B 21 ARG cc_start: 0.3453 (mmt180) cc_final: 0.3015 (tpp80) REVERT: B 56 LEU cc_start: 0.7838 (tt) cc_final: 0.7384 (tt) REVERT: B 177 MET cc_start: 0.6389 (pmm) cc_final: 0.4348 (tpt) REVERT: B 373 TYR cc_start: 0.7658 (m-10) cc_final: 0.7400 (m-10) REVERT: B 446 TYR cc_start: 0.8405 (p90) cc_final: 0.7748 (p90) REVERT: B 449 PHE cc_start: 0.8399 (m-80) cc_final: 0.7903 (m-80) REVERT: B 466 TYR cc_start: 0.7800 (t80) cc_final: 0.7408 (t80) REVERT: B 1085 GLU cc_start: 0.8024 (tp30) cc_final: 0.7786 (tp30) REVERT: C 224 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: C 449 PHE cc_start: 0.8039 (t80) cc_final: 0.7599 (t80) REVERT: C 466 TYR cc_start: 0.7407 (t80) cc_final: 0.6654 (t80) REVERT: C 477 GLU cc_start: 0.6129 (tp30) cc_final: 0.5755 (pp20) REVERT: C 555 PHE cc_start: 0.7798 (p90) cc_final: 0.7412 (p90) REVERT: C 769 LYS cc_start: 0.9176 (tppp) cc_final: 0.8932 (tptm) REVERT: C 866 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.9079 (m-10) outliers start: 106 outliers final: 70 residues processed: 264 average time/residue: 0.1446 time to fit residues: 64.0449 Evaluate side-chains 243 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 826 PHE Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 583 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 829 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.125565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085061 restraints weight = 68075.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087729 restraints weight = 35468.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089489 restraints weight = 24081.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.090474 restraints weight = 19131.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091200 restraints weight = 16789.392| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27699 Z= 0.174 Angle : 0.703 14.258 37894 Z= 0.342 Chirality : 0.046 0.397 4529 Planarity : 0.004 0.053 4744 Dihedral : 7.095 60.359 5516 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.39 % Favored : 93.58 % Rotamer: Outliers : 2.90 % Allowed : 18.60 % Favored : 78.50 % 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: -1.00 (0.14), residues: 3271 helix: 1.42 (0.19), residues: 748 sheet: -0.28 (0.20), residues: 653 loop : -1.77 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 758 TYR 0.020 0.001 TYR C1131 PHE 0.034 0.002 PHE A 186 TRP 0.037 0.001 TRP C 626 HIS 0.003 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00407 (27564) covalent geometry : angle 0.67835 (37531) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.70359 ( 84) hydrogen bonds : bond 0.05562 ( 1002) hydrogen bonds : angle 5.32327 ( 2727) link_ALPHA1-3 : bond 0.00954 ( 1) link_ALPHA1-3 : angle 2.15074 ( 3) link_BETA1-4 : bond 0.00564 ( 47) link_BETA1-4 : angle 1.85363 ( 141) link_NAG-ASN : bond 0.00329 ( 45) link_NAG-ASN : angle 2.31267 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 178 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.3802 (OUTLIER) cc_final: 0.3476 (pt) REVERT: A 812 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: A 1024 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: A 1137 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6679 (mm-30) REVERT: B 21 ARG cc_start: 0.3247 (mmt180) cc_final: 0.2867 (tpp80) REVERT: B 56 LEU cc_start: 0.7711 (tt) cc_final: 0.7336 (tt) REVERT: B 177 MET cc_start: 0.6083 (pmm) cc_final: 0.4336 (tpt) REVERT: B 446 TYR cc_start: 0.8452 (p90) cc_final: 0.7835 (p90) REVERT: B 449 PHE cc_start: 0.8266 (m-80) cc_final: 0.7789 (m-80) REVERT: B 466 TYR cc_start: 0.7676 (t80) cc_final: 0.7270 (t80) REVERT: B 1085 GLU cc_start: 0.8014 (tp30) cc_final: 0.7794 (tp30) REVERT: C 224 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: C 449 PHE cc_start: 0.8130 (t80) cc_final: 0.7645 (t80) REVERT: C 466 TYR cc_start: 0.7345 (t80) cc_final: 0.6358 (t80) REVERT: C 477 GLU cc_start: 0.6053 (tp30) cc_final: 0.5713 (pp20) REVERT: C 555 PHE cc_start: 0.7722 (p90) cc_final: 0.7358 (p90) REVERT: C 769 LYS cc_start: 0.9161 (tppp) cc_final: 0.8906 (tptm) REVERT: C 866 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.9047 (m-10) outliers start: 83 outliers final: 59 residues processed: 245 average time/residue: 0.1459 time to fit residues: 60.2805 Evaluate side-chains 232 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 690 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 55 optimal weight: 0.7980 chunk 312 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 744 ASN A 780 GLN A 995 GLN A1003 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.124713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084126 restraints weight = 68667.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086795 restraints weight = 35921.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088572 restraints weight = 24528.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089511 restraints weight = 19550.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090135 restraints weight = 17177.458| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27699 Z= 0.198 Angle : 0.728 13.312 37894 Z= 0.355 Chirality : 0.047 0.398 4529 Planarity : 0.004 0.057 4744 Dihedral : 7.028 59.363 5516 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.91 % Favored : 93.06 % Rotamer: Outliers : 2.73 % Allowed : 19.02 % Favored : 78.25 % 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: -1.04 (0.14), residues: 3271 helix: 1.43 (0.19), residues: 741 sheet: -0.30 (0.20), residues: 655 loop : -1.81 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 758 TYR 0.023 0.001 TYR C1060 PHE 0.022 0.002 PHE B 385 TRP 0.019 0.001 TRP C 251 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00469 (27564) covalent geometry : angle 0.70296 (37531) SS BOND : bond 0.00393 ( 42) SS BOND : angle 1.71903 ( 84) hydrogen bonds : bond 0.05804 ( 1002) hydrogen bonds : angle 5.37522 ( 2727) link_ALPHA1-3 : bond 0.00905 ( 1) link_ALPHA1-3 : angle 1.99652 ( 3) link_BETA1-4 : bond 0.00531 ( 47) link_BETA1-4 : angle 1.84045 ( 141) link_NAG-ASN : bond 0.00373 ( 45) link_NAG-ASN : angle 2.39620 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 170 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.4100 (OUTLIER) cc_final: 0.3738 (pt) REVERT: A 812 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 1024 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: A 1137 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6746 (mm-30) REVERT: B 21 ARG cc_start: 0.3000 (mmt180) cc_final: 0.2675 (tpp80) REVERT: B 56 LEU cc_start: 0.7774 (tt) cc_final: 0.7404 (tt) REVERT: B 177 MET cc_start: 0.6076 (pmm) cc_final: 0.4391 (tpt) REVERT: B 446 TYR cc_start: 0.8426 (p90) cc_final: 0.7763 (p90) REVERT: B 466 TYR cc_start: 0.7690 (t80) cc_final: 0.7198 (t80) REVERT: B 1085 GLU cc_start: 0.8010 (tp30) cc_final: 0.7749 (tp30) REVERT: C 224 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: C 449 PHE cc_start: 0.8206 (t80) cc_final: 0.7926 (t80) REVERT: C 477 GLU cc_start: 0.5915 (tp30) cc_final: 0.5595 (pp20) REVERT: C 511 LEU cc_start: 0.7585 (mm) cc_final: 0.7309 (mm) REVERT: C 555 PHE cc_start: 0.7720 (p90) cc_final: 0.7376 (p90) REVERT: C 769 LYS cc_start: 0.9163 (tppp) cc_final: 0.8910 (tptm) REVERT: C 866 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.9037 (m-10) outliers start: 78 outliers final: 63 residues processed: 235 average time/residue: 0.1474 time to fit residues: 58.4211 Evaluate side-chains 225 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1070 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1129 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Chi-restraints excluded: chain C residue 1011 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 231 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 950 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.086400 restraints weight = 67484.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.089127 restraints weight = 34686.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090903 restraints weight = 23390.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091875 restraints weight = 18508.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092599 restraints weight = 16214.907| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27699 Z= 0.131 Angle : 0.673 13.500 37894 Z= 0.327 Chirality : 0.045 0.385 4529 Planarity : 0.004 0.055 4744 Dihedral : 6.521 59.522 5516 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 2.20 % Allowed : 19.69 % Favored : 78.11 % 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 (0.14), residues: 3271 helix: 1.62 (0.19), residues: 735 sheet: -0.15 (0.20), residues: 683 loop : -1.75 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 758 TYR 0.019 0.001 TYR C1131 PHE 0.028 0.001 PHE A 133 TRP 0.019 0.001 TRP C 251 HIS 0.003 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00299 (27564) covalent geometry : angle 0.65033 (37531) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.47086 ( 84) hydrogen bonds : bond 0.05007 ( 1002) hydrogen bonds : angle 5.19759 ( 2727) link_ALPHA1-3 : bond 0.00865 ( 1) link_ALPHA1-3 : angle 1.82569 ( 3) link_BETA1-4 : bond 0.00561 ( 47) link_BETA1-4 : angle 1.74011 ( 141) link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.21761 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6542 Ramachandran restraints generated. 3271 Oldfield, 0 Emsley, 3271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.4179 (OUTLIER) cc_final: 0.3771 (pt) REVERT: A 812 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: A 1024 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: A 1137 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6820 (mm-30) REVERT: B 21 ARG cc_start: 0.3076 (mmt180) cc_final: 0.2626 (tpp80) REVERT: B 56 LEU cc_start: 0.7655 (tt) cc_final: 0.7294 (tt) REVERT: B 177 MET cc_start: 0.6108 (pmm) cc_final: 0.4435 (tpt) REVERT: B 446 TYR cc_start: 0.8418 (p90) cc_final: 0.7783 (p90) REVERT: B 466 TYR cc_start: 0.7589 (t80) cc_final: 0.7147 (t80) REVERT: B 874 THR cc_start: 0.8386 (m) cc_final: 0.8108 (m) REVERT: B 1085 GLU cc_start: 0.7930 (tp30) cc_final: 0.7687 (tp30) REVERT: C 449 PHE cc_start: 0.8070 (t80) cc_final: 0.7593 (t80) REVERT: C 466 TYR cc_start: 0.7519 (t80) cc_final: 0.6459 (t80) REVERT: C 477 GLU cc_start: 0.5794 (tp30) cc_final: 0.5555 (pp20) REVERT: C 555 PHE cc_start: 0.7663 (p90) cc_final: 0.7338 (p90) REVERT: C 769 LYS cc_start: 0.9153 (tppp) cc_final: 0.8907 (tptm) REVERT: C 866 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.9006 (m-10) outliers start: 63 outliers final: 55 residues processed: 238 average time/residue: 0.1393 time to fit residues: 56.0679 Evaluate side-chains 231 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 311 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 924 ILE Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 311 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 812 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 866 TYR Chi-restraints excluded: chain C residue 954 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1010 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 24 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 265 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 259 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086395 restraints weight = 67487.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089131 restraints weight = 34773.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090869 restraints weight = 23495.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091855 restraints weight = 18651.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092604 restraints weight = 16305.618| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27699 Z= 0.129 Angle : 0.670 13.529 37894 Z= 0.325 Chirality : 0.045 0.381 4529 Planarity : 0.004 0.055 4744 Dihedral : 6.326 59.945 5516 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 2.20 % Allowed : 20.00 % Favored : 77.80 % 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: -0.85 (0.14), residues: 3271 helix: 1.57 (0.19), residues: 746 sheet: -0.02 (0.21), residues: 634 loop : -1.74 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 758 TYR 0.018 0.001 TYR C1060 PHE 0.022 0.001 PHE B 816 TRP 0.017 0.001 TRP C 251 HIS 0.003 0.001 HIS B 648 Details of bonding type rmsd covalent geometry : bond 0.00295 (27564) covalent geometry : angle 0.64784 (37531) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.38973 ( 84) hydrogen bonds : bond 0.04898 ( 1002) hydrogen bonds : angle 5.17369 ( 2727) link_ALPHA1-3 : bond 0.00842 ( 1) link_ALPHA1-3 : angle 1.73128 ( 3) link_BETA1-4 : bond 0.00551 ( 47) link_BETA1-4 : angle 1.71678 ( 141) link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 2.21895 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5774.49 seconds wall clock time: 99 minutes 47.81 seconds (5987.81 seconds total)