Starting phenix.real_space_refine on Sun Jul 5 10:13:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ybh_33721/07_2026/7ybh_33721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybh_33721/07_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_33721/07_2026/7ybh_33721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybh_33721/07_2026/7ybh_33721.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ybh_33721/07_2026/7ybh_33721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ybh_33721/07_2026/7ybh_33721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ybh_33721/07_2026/7ybh_33721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybh_33721/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 5 Time building chain proxies: 5.84, per 1000 atoms: 0.22 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: 2.66 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: 0.83 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: 6.39 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 - 18.00: 14234 18.00 - 35.99: 1166 35.99 - 53.99: 214 53.99 - 71.99: 53 71.99 - 89.98: 45 Dihedral angle restraints: 15712 sinusoidal: 6111 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 15709 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.170 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 14.363 89.983 9410 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/Z covalent geometry : bond 0.00480 / 0.24 (27564) covalent geometry : angle 0.77421 / 0.40 (37531) SS BOND : bond 0.00692 / 0.36 ( 42) SS BOND : angle 1.58785 / 1.05 ( 84) hydrogen bonds : bond 0.14661 / 9.83 ( 1002) hydrogen bonds : angle 6.72420 / 4.54 ( 2727) link_ALPHA1-3 : bond 0.00434 / 0.23 ( 1) link_ALPHA1-3 : angle 1.54093 / 0.85 ( 3) link_BETA1-4 : bond 0.00607 / 0.39 ( 47) link_BETA1-4 : angle 1.77232 / 1.23 ( 141) link_NAG-ASN : bond 0.00350 / 0.22 ( 45) link_NAG-ASN : angle 2.55455 / 1.93 ( 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 : 0.966 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: 0.1728 time to fit residues: 137.5375 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 : 1.052 ------------------------------------------------------------------------------- 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... ** 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 = 0.4220 r_free = 0.4220 target = 0.135385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097291 restraints weight = 72981.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100183 restraints weight = 39052.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.101376 restraints weight = 21894.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.101479 restraints weight = 21670.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101428 restraints weight = 18141.875| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27699 Z= 0.212 Angle : 0.770 12.307 37894 Z= 0.386 Chirality : 0.049 0.390 4529 Planarity : 0.005 0.086 4744 Dihedral : 5.239 45.480 3540 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 1.75 % Allowed : 11.54 % Favored : 86.71 % 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: -1.09 (0.14), residues: 3271 helix: 0.98 (0.19), residues: 749 sheet: -0.14 (0.21), residues: 580 loop : -1.68 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 21 TYR 0.029 0.002 TYR B 362 PHE 0.032 0.002 PHE A1141 TRP 0.017 0.002 TRP B 64 HIS 0.005 0.001 HIS C 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (27564) covalent geometry : angle 0.74805 / 0.38 (37531) SS BOND : bond 0.00477 / 0.30 ( 42) SS BOND : angle 1.88670 / 1.24 ( 84) hydrogen bonds : bond 0.05765 / 3.80 ( 1002) hydrogen bonds : angle 5.66651 / 3.83 ( 2727) link_ALPHA1-3 : bond 0.00262 / 0.14 ( 1) link_ALPHA1-3 : angle 2.30855 / 1.21 ( 3) link_BETA1-4 : bond 0.00487 / 0.31 ( 47) link_BETA1-4 : angle 1.70570 / 1.20 ( 141) link_NAG-ASN : bond 0.00460 / 0.27 ( 45) link_NAG-ASN : angle 2.32418 / 1.67 ( 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 308 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 0.745 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 577 ILE cc_start: 0.8312 (mm) cc_final: 0.7722 (mt) REVERT: A 895 MET cc_start: 0.8792 (mmt) cc_final: 0.8591 (tpt) REVERT: B 21 ARG cc_start: 0.5831 (mtt180) cc_final: 0.4839 (mmm160) REVERT: B 177 MET cc_start: 0.7266 (pmm) cc_final: 0.4548 (tpt) REVERT: B 385 PHE cc_start: 0.8011 (m-80) cc_final: 0.7685 (m-80) REVERT: B 449 PHE cc_start: 0.8148 (m-80) cc_final: 0.7676 (m-80) REVERT: B 466 TYR cc_start: 0.7825 (t80) cc_final: 0.7397 (t80) REVERT: B 972 ASP cc_start: 0.8071 (t0) cc_final: 0.7581 (t0) REVERT: C 168 PHE cc_start: 0.7405 (t80) cc_final: 0.7188 (t80) REVERT: C 449 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8226 (t80) REVERT: C 769 LYS cc_start: 0.9158 (tppp) cc_final: 0.8732 (tptm) outliers start: 50 outliers final: 32 residues processed: 298 average time/residue: 0.1470 time to fit residues: 72.5150 Evaluate side-chains 227 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL 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 295 THR 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 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 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: 20.0000 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 234 optimal weight: 10.0000 chunk 188 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 259 optimal weight: 0.0470 chunk 110 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 263 optimal weight: 6.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 962 ASN A 985 GLN B 245 HIS B 637 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.139462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.100500 restraints weight = 71117.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.104415 restraints weight = 36606.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.104955 restraints weight = 20562.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.105633 restraints weight = 16463.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.105566 restraints weight = 15899.374| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27699 Z= 0.118 Angle : 0.629 10.250 37894 Z= 0.311 Chirality : 0.045 0.367 4529 Planarity : 0.004 0.048 4744 Dihedral : 4.718 35.718 3534 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % Favored : 84.62 % 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: 1.36 (0.19), residues: 752 sheet: -0.11 (0.21), residues: 591 loop : -1.58 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 758 TYR 0.020 0.001 TYR C 170 PHE 0.020 0.001 PHE A1141 TRP 0.038 0.002 TRP C 626 HIS 0.018 0.001 HIS C 512 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27564) covalent geometry : angle 0.60838 / 0.31 (37531) SS BOND : bond 0.00448 / 0.29 ( 42) SS BOND : angle 1.51739 / 1.05 ( 84) hydrogen bonds : bond 0.04904 / 3.26 ( 1002) hydrogen bonds : angle 5.30540 / 3.59 ( 2727) link_ALPHA1-3 : bond 0.00607 / 0.32 ( 1) link_ALPHA1-3 : angle 1.44459 / 0.80 ( 3) link_BETA1-4 : bond 0.00530 / 0.34 ( 47) link_BETA1-4 : angle 1.45696 / 1.02 ( 141) link_NAG-ASN : bond 0.00359 / 0.23 ( 45) link_NAG-ASN : angle 2.07459 / 1.53 ( 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 278 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ILE cc_start: 0.8398 (mm) cc_final: 0.7734 (mt) REVERT: A 1024 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: B 21 ARG cc_start: 0.5800 (mtt180) cc_final: 0.5304 (mmm-85) REVERT: B 177 MET cc_start: 0.6948 (pmm) cc_final: 0.4286 (tpt) REVERT: B 449 PHE cc_start: 0.8121 (m-80) cc_final: 0.7650 (m-80) REVERT: B 466 TYR cc_start: 0.7927 (t80) cc_final: 0.7497 (t80) REVERT: B 893 MET cc_start: 0.7942 (mtt) cc_final: 0.7700 (mtp) REVERT: B 958 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 972 ASP cc_start: 0.7953 (t0) cc_final: 0.7559 (t0) REVERT: C 168 PHE cc_start: 0.7373 (t80) cc_final: 0.6656 (t80) REVERT: C 449 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 728 SER cc_start: 0.9262 (t) cc_final: 0.8776 (m) REVERT: C 769 LYS cc_start: 0.9146 (tppp) cc_final: 0.8728 (tptm) REVERT: C 1131 TYR cc_start: 0.7903 (t80) cc_final: 0.7635 (t80) outliers start: 55 outliers final: 29 residues processed: 264 average time/residue: 0.1408 time to fit residues: 62.0267 Evaluate side-chains 221 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 588 VAL Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 1030 SER 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 376 SER 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 581 THR 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: 0.2980 chunk 158 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 326 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 305 optimal weight: 3.9990 chunk 247 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 232 optimal weight: 30.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 ASN ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.139053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.099753 restraints weight = 70811.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.103486 restraints weight = 36795.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.104113 restraints weight = 20322.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.104606 restraints weight = 17246.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104638 restraints weight = 16736.460| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 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 = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27699 Z= 0.117 Angle : 0.615 9.367 37894 Z= 0.303 Chirality : 0.044 0.363 4529 Planarity : 0.004 0.044 4744 Dihedral : 4.557 28.500 3534 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 2.27 % Allowed : 14.90 % Favored : 82.83 % 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: -0.71 (0.14), residues: 3271 helix: 1.53 (0.20), residues: 747 sheet: 0.02 (0.21), residues: 609 loop : -1.54 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 758 TYR 0.017 0.001 TYR B 501 PHE 0.022 0.001 PHE A 826 TRP 0.037 0.001 TRP C 626 HIS 0.003 0.001 HIS B1081 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (27564) covalent geometry : angle 0.59631 / 0.30 (37531) SS BOND : bond 0.00368 / 0.23 ( 42) SS BOND : angle 1.31854 / 0.93 ( 84) hydrogen bonds : bond 0.04492 / 2.99 ( 1002) hydrogen bonds : angle 5.17235 / 3.50 ( 2727) link_ALPHA1-3 : bond 0.00553 / 0.29 ( 1) link_ALPHA1-3 : angle 1.49689 / 0.82 ( 3) link_BETA1-4 : bond 0.00470 / 0.30 ( 47) link_BETA1-4 : angle 1.43909 / 1.00 ( 141) link_NAG-ASN : bond 0.00334 / 0.21 ( 45) link_NAG-ASN : angle 1.98340 / 1.45 ( 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 282 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 1.174 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: 0.8377 (mm) cc_final: 0.7716 (mt) REVERT: A 1022 MET cc_start: 0.8844 (tpp) cc_final: 0.8078 (ttm) REVERT: A 1024 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: B 21 ARG cc_start: 0.5983 (mtt180) cc_final: 0.5458 (mmm-85) REVERT: B 52 GLN cc_start: 0.8529 (tm-30) cc_final: 0.7962 (pp30) REVERT: B 177 MET cc_start: 0.6923 (pmm) cc_final: 0.4467 (tpt) REVERT: B 396 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7509 (tpp80) REVERT: B 417 LYS cc_start: 0.7485 (tppt) cc_final: 0.7206 (tppt) REVERT: B 449 PHE cc_start: 0.8115 (m-80) cc_final: 0.7588 (m-80) REVERT: B 466 TYR cc_start: 0.7867 (t80) cc_final: 0.7455 (t80) REVERT: B 874 THR cc_start: 0.8154 (m) cc_final: 0.7897 (m) REVERT: B 946 ASN cc_start: 0.8775 (m-40) cc_final: 0.8572 (m-40) REVERT: B 972 ASP cc_start: 0.8060 (t0) cc_final: 0.7696 (t0) REVERT: C 449 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8219 (t80) REVERT: C 769 LYS cc_start: 0.9140 (tppp) cc_final: 0.8784 (tptm) REVERT: C 866 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8944 (m-10) REVERT: C 1131 TYR cc_start: 0.7890 (t80) cc_final: 0.7618 (t80) outliers start: 65 outliers final: 34 residues processed: 268 average time/residue: 0.1519 time to fit residues: 68.7614 Evaluate side-chains 235 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 685 ILE 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 189 LEU 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 608 VAL Chi-restraints excluded: chain B residue 647 GLU 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 120 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 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 1010 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 49 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 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 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN C 770 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.127697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086828 restraints weight = 72079.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089834 restraints weight = 35016.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091805 restraints weight = 23222.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092972 restraints weight = 18242.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.093491 restraints weight = 15877.889| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27699 Z= 0.250 Angle : 0.787 10.798 37894 Z= 0.390 Chirality : 0.049 0.390 4529 Planarity : 0.005 0.047 4744 Dihedral : 5.125 29.793 3534 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.48 % Rotamer: Outliers : 3.36 % Allowed : 15.70 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3271 helix: 1.12 (0.19), residues: 738 sheet: -0.39 (0.20), residues: 681 loop : -1.80 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 758 TYR 0.030 0.002 TYR B1040 PHE 0.024 0.002 PHE C 508 TRP 0.021 0.002 TRP A 64 HIS 0.007 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (27564) covalent geometry : angle 0.76385 / 0.38 (37531) SS BOND : bond 0.00911 / 0.60 ( 42) SS BOND : angle 2.00128 / 1.48 ( 84) hydrogen bonds : bond 0.06687 / 4.45 ( 1002) hydrogen bonds : angle 5.65973 / 3.83 ( 2727) link_ALPHA1-3 : bond 0.00678 / 0.36 ( 1) link_ALPHA1-3 : angle 1.56724 / 0.85 ( 3) link_BETA1-4 : bond 0.00506 / 0.32 ( 47) link_BETA1-4 : angle 1.71522 / 1.20 ( 141) link_NAG-ASN : bond 0.00503 / 0.30 ( 45) link_NAG-ASN : angle 2.42296 / 1.70 ( 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 297 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 201 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8694 (t) REVERT: A 577 ILE cc_start: 0.8622 (mm) cc_final: 0.8026 (mt) REVERT: A 812 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 842 LEU cc_start: 0.8932 (tp) cc_final: 0.8710 (tp) REVERT: A 895 MET cc_start: 0.9038 (tpt) cc_final: 0.8749 (tpt) REVERT: A 1022 MET cc_start: 0.8812 (tpp) cc_final: 0.8272 (ttm) REVERT: A 1024 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6632 (mp0) REVERT: B 21 ARG cc_start: 0.5441 (mtt180) cc_final: 0.4853 (ttm170) REVERT: B 177 MET cc_start: 0.6839 (pmm) cc_final: 0.4472 (tpt) REVERT: B 417 LYS cc_start: 0.7789 (tppt) cc_final: 0.7471 (tppt) REVERT: B 426 VAL cc_start: 0.8627 (t) cc_final: 0.8344 (p) REVERT: B 446 TYR cc_start: 0.8481 (p90) cc_final: 0.7908 (p90) REVERT: B 449 PHE cc_start: 0.8446 (m-80) cc_final: 0.7920 (m-80) REVERT: B 466 TYR cc_start: 0.7894 (t80) cc_final: 0.7468 (t80) REVERT: B 972 ASP cc_start: 0.8322 (t0) cc_final: 0.8065 (t0) REVERT: C 54 LEU cc_start: 0.9202 (mp) cc_final: 0.9000 (pt) REVERT: C 449 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 461 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7376 (mt) REVERT: C 555 PHE cc_start: 0.7895 (p90) cc_final: 0.7411 (p90) REVERT: C 769 LYS cc_start: 0.9185 (tppp) cc_final: 0.8834 (tptm) REVERT: C 866 TYR cc_start: 0.9335 (OUTLIER) cc_final: 0.8967 (m-10) REVERT: C 950 GLN cc_start: 0.8539 (tm130) cc_final: 0.8310 (tm-30) REVERT: C 1131 TYR cc_start: 0.7875 (t80) cc_final: 0.7522 (t80) outliers start: 96 outliers final: 55 residues processed: 277 average time/residue: 0.1538 time to fit residues: 72.0478 Evaluate side-chains 238 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 518 CYS 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 875 ILE Chi-restraints excluded: chain A residue 931 LEU 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 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 226 LEU Chi-restraints excluded: chain B residue 278 ILE 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 508 PHE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 ASP 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 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 954 THR Chi-restraints excluded: chain B residue 969 VAL 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 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 316 THR Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 414 TYR 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 581 THR 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 1109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 228 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 212 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 995 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 HIS ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 947 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 = 0.4121 r_free = 0.4121 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087479 restraints weight = 72078.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090592 restraints weight = 34421.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092572 restraints weight = 22547.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093633 restraints weight = 17629.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094400 restraints weight = 15355.001| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27699 Z= 0.188 Angle : 0.698 12.266 37894 Z= 0.345 Chirality : 0.046 0.392 4529 Planarity : 0.004 0.064 4744 Dihedral : 4.936 29.265 3534 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 2.83 % Allowed : 17.45 % Favored : 79.72 % 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: -1.06 (0.14), residues: 3271 helix: 1.37 (0.19), residues: 743 sheet: -0.30 (0.20), residues: 639 loop : -1.80 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 758 TYR 0.019 0.001 TYR C1060 PHE 0.020 0.002 PHE A 32 TRP 0.053 0.002 TRP C 626 HIS 0.003 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (27564) covalent geometry : angle 0.67659 / 0.34 (37531) SS BOND : bond 0.00392 / 0.23 ( 42) SS BOND : angle 1.67066 / 1.23 ( 84) hydrogen bonds : bond 0.05694 / 3.80 ( 1002) hydrogen bonds : angle 5.38959 / 3.66 ( 2727) link_ALPHA1-3 : bond 0.00622 / 0.33 ( 1) link_ALPHA1-3 : angle 1.65830 / 0.90 ( 3) link_BETA1-4 : bond 0.00487 / 0.32 ( 47) link_BETA1-4 : angle 1.52845 / 1.07 ( 141) link_NAG-ASN : bond 0.00341 / 0.21 ( 45) link_NAG-ASN : angle 2.26110 / 1.61 ( 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 272 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 191 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.3583 (OUTLIER) cc_final: 0.3325 (pt) REVERT: A 577 ILE cc_start: 0.8684 (mm) cc_final: 0.8115 (mt) REVERT: A 812 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 1022 MET cc_start: 0.8795 (tpp) cc_final: 0.8183 (ttm) REVERT: A 1024 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: B 21 ARG cc_start: 0.5448 (mtt180) cc_final: 0.4713 (ttm170) REVERT: B 177 MET cc_start: 0.6387 (pmm) cc_final: 0.4285 (tpt) REVERT: B 373 TYR cc_start: 0.7459 (m-10) cc_final: 0.7257 (m-10) REVERT: B 417 LYS cc_start: 0.7920 (tppt) cc_final: 0.7636 (tppt) REVERT: B 426 VAL cc_start: 0.8612 (t) cc_final: 0.8361 (p) REVERT: B 449 PHE cc_start: 0.8409 (m-80) cc_final: 0.7908 (m-80) REVERT: B 466 TYR cc_start: 0.7799 (t80) cc_final: 0.7407 (t80) REVERT: B 972 ASP cc_start: 0.8204 (t0) cc_final: 0.7991 (t0) REVERT: B 1085 GLU cc_start: 0.8182 (tp30) cc_final: 0.7974 (tp30) REVERT: C 54 LEU cc_start: 0.9265 (mp) cc_final: 0.9044 (pt) REVERT: C 224 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 555 PHE cc_start: 0.7818 (p90) cc_final: 0.7399 (p90) REVERT: C 769 LYS cc_start: 0.9177 (tppp) cc_final: 0.8830 (tptm) REVERT: C 866 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.9056 (m-10) outliers start: 81 outliers final: 57 residues processed: 259 average time/residue: 0.1508 time to fit residues: 65.5411 Evaluate side-chains 234 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 924 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 1024 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 239 GLN 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 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 608 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 VAL 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 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL 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 510 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 728 SER 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 973 ILE 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: 8.9990 chunk 201 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 127 optimal weight: 0.0770 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN B 66 HIS ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.128837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088223 restraints weight = 67038.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090897 restraints weight = 35218.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092679 restraints weight = 23981.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093748 restraints weight = 19020.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094285 restraints weight = 16602.191| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 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 = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27699 Z= 0.175 Angle : 0.693 15.602 37894 Z= 0.341 Chirality : 0.046 0.386 4529 Planarity : 0.004 0.042 4744 Dihedral : 4.887 28.919 3534 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.83 % Allowed : 18.29 % Favored : 78.88 % 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: -1.03 (0.14), residues: 3271 helix: 1.41 (0.19), residues: 745 sheet: -0.30 (0.20), residues: 662 loop : -1.80 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 758 TYR 0.033 0.001 TYR A 416 PHE 0.024 0.002 PHE A 186 TRP 0.014 0.001 TRP C 626 HIS 0.004 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (27564) covalent geometry : angle 0.67325 / 0.34 (37531) SS BOND : bond 0.00382 / 0.22 ( 42) SS BOND : angle 1.53353 / 1.10 ( 84) hydrogen bonds : bond 0.05572 / 3.73 ( 1002) hydrogen bonds : angle 5.35110 / 3.64 ( 2727) link_ALPHA1-3 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-3 : angle 1.63909 / 0.88 ( 3) link_BETA1-4 : bond 0.00465 / 0.30 ( 47) link_BETA1-4 : angle 1.50735 / 1.05 ( 141) link_NAG-ASN : bond 0.00349 / 0.21 ( 45) link_NAG-ASN : angle 2.24268 / 1.59 ( 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 270 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 189 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3877 (t80) REVERT: A 228 ASP cc_start: 0.8056 (p0) cc_final: 0.7810 (p0) REVERT: A 461 ILE cc_start: 0.3753 (OUTLIER) cc_final: 0.3465 (pt) REVERT: A 812 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: A 895 MET cc_start: 0.8899 (tpt) cc_final: 0.8519 (tpt) REVERT: A 1024 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: B 21 ARG cc_start: 0.5400 (mtt180) cc_final: 0.4608 (ttm170) REVERT: B 177 MET cc_start: 0.6365 (pmm) cc_final: 0.4323 (tpt) REVERT: B 373 TYR cc_start: 0.7440 (m-10) cc_final: 0.7217 (m-10) REVERT: B 426 VAL cc_start: 0.8765 (t) cc_final: 0.8555 (p) REVERT: B 446 TYR cc_start: 0.8408 (p90) cc_final: 0.7789 (p90) REVERT: B 449 PHE cc_start: 0.8277 (m-80) cc_final: 0.7792 (m-80) REVERT: B 466 TYR cc_start: 0.7678 (t80) cc_final: 0.7270 (t80) REVERT: B 1085 GLU cc_start: 0.8073 (tp30) cc_final: 0.7840 (tp30) REVERT: C 224 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: C 234 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6885 (p0) REVERT: C 449 PHE cc_start: 0.7904 (t80) cc_final: 0.7223 (t80) REVERT: C 461 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7461 (mt) REVERT: C 466 TYR cc_start: 0.7256 (t80) cc_final: 0.6193 (t80) REVERT: C 477 GLU cc_start: 0.6147 (tp30) cc_final: 0.5781 (pp20) REVERT: C 555 PHE cc_start: 0.7759 (p90) cc_final: 0.7402 (p90) REVERT: C 769 LYS cc_start: 0.9129 (tppp) cc_final: 0.8836 (tptm) REVERT: C 866 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8982 (m-10) outliers start: 81 outliers final: 59 residues processed: 254 average time/residue: 0.1615 time to fit residues: 69.0055 Evaluate side-chains 240 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 186 PHE 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 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 685 ILE Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 924 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 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 239 GLN 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 360 VAL Chi-restraints excluded: chain B residue 498 TYR 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 960 SER Chi-restraints excluded: chain B residue 969 VAL 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 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 234 ASN 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 461 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 746 LEU 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 968 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE 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: 9.9990 chunk 146 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 273 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 245 HIS A 995 GLN A1003 GLN ** B1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 GLN ** C 947 GLN ** 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 = 0.4040 r_free = 0.4040 target = 0.126202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085549 restraints weight = 67785.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088215 restraints weight = 35258.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.089992 restraints weight = 23957.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090966 restraints weight = 18984.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091670 restraints weight = 16644.087| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27699 Z= 0.209 Angle : 0.729 14.490 37894 Z= 0.358 Chirality : 0.047 0.390 4529 Planarity : 0.004 0.046 4744 Dihedral : 5.035 29.640 3534 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.88 % Favored : 93.09 % Rotamer: Outliers : 3.43 % Allowed : 18.22 % Favored : 78.36 % 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: -1.12 (0.14), residues: 3271 helix: 1.36 (0.19), residues: 750 sheet: -0.31 (0.20), residues: 648 loop : -1.89 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 758 TYR 0.034 0.002 TYR A 416 PHE 0.038 0.002 PHE B 186 TRP 0.022 0.001 TRP C 251 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (27564) covalent geometry : angle 0.70881 / 0.35 (37531) SS BOND : bond 0.00399 / 0.24 ( 42) SS BOND : angle 1.65391 / 1.19 ( 84) hydrogen bonds : bond 0.05928 / 3.95 ( 1002) hydrogen bonds : angle 5.43286 / 3.70 ( 2727) link_ALPHA1-3 : bond 0.00730 / 0.38 ( 1) link_ALPHA1-3 : angle 1.69346 / 0.91 ( 3) link_BETA1-4 : bond 0.00478 / 0.31 ( 47) link_BETA1-4 : angle 1.55431 / 1.08 ( 141) link_NAG-ASN : bond 0.00370 / 0.23 ( 45) link_NAG-ASN : angle 2.31041 / 1.62 ( 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 276 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 178 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.4230 (t80) REVERT: A 228 ASP cc_start: 0.8115 (p0) cc_final: 0.7896 (p0) REVERT: A 416 TYR cc_start: 0.5187 (t80) cc_final: 0.4938 (t80) REVERT: A 461 ILE cc_start: 0.3928 (OUTLIER) cc_final: 0.3608 (pt) REVERT: A 812 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: A 895 MET cc_start: 0.8883 (tpt) cc_final: 0.8480 (tpt) REVERT: A 1024 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 21 ARG cc_start: 0.5527 (mtt180) cc_final: 0.4955 (ttm170) REVERT: B 52 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 177 MET cc_start: 0.6196 (pmm) cc_final: 0.4367 (tpt) REVERT: B 239 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: B 385 PHE cc_start: 0.8126 (m-10) cc_final: 0.7843 (m-10) REVERT: B 395 ILE cc_start: 0.7693 (tp) cc_final: 0.7359 (tt) REVERT: B 446 TYR cc_start: 0.8427 (p90) cc_final: 0.7837 (p90) REVERT: B 449 PHE cc_start: 0.8259 (m-80) cc_final: 0.7787 (m-80) REVERT: B 466 TYR cc_start: 0.7736 (t80) cc_final: 0.7304 (t80) REVERT: B 508 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7609 (p90) REVERT: C 224 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: C 234 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6678 (p0) REVERT: C 449 PHE cc_start: 0.8166 (t80) cc_final: 0.7761 (t80) REVERT: C 477 GLU cc_start: 0.6141 (tp30) cc_final: 0.5779 (pp20) REVERT: C 555 PHE cc_start: 0.7761 (p90) cc_final: 0.7384 (p90) REVERT: C 769 LYS cc_start: 0.9173 (tppp) cc_final: 0.8927 (tptm) REVERT: C 866 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.9030 (m-10) outliers start: 98 outliers final: 72 residues processed: 257 average time/residue: 0.1514 time to fit residues: 65.3911 Evaluate side-chains 247 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 166 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 186 PHE 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 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 902 ILE Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 LEU 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 239 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 VAL 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 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 766 GLU 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 42 VAL Chi-restraints excluded: chain C residue 110 LEU 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 234 ASN Chi-restraints excluded: chain C residue 236 THR 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 690 MET Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 746 LEU 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 968 SER Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 973 ILE 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: 0.9980 chunk 312 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 328 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 772 GLN ** A 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 950 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.127457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087089 restraints weight = 67459.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089775 restraints weight = 35330.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091536 restraints weight = 23981.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092517 restraints weight = 18986.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093030 restraints weight = 16634.553| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 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 = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27699 Z= 0.175 Angle : 0.707 14.804 37894 Z= 0.344 Chirality : 0.046 0.385 4529 Planarity : 0.004 0.047 4744 Dihedral : 4.951 29.764 3534 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 2.90 % Allowed : 19.02 % Favored : 78.08 % 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: -1.06 (0.14), residues: 3271 helix: 1.51 (0.19), residues: 741 sheet: -0.36 (0.21), residues: 631 loop : -1.84 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 758 TYR 0.025 0.001 TYR A 416 PHE 0.031 0.002 PHE C 168 TRP 0.016 0.001 TRP C 251 HIS 0.004 0.001 HIS B 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (27564) covalent geometry : angle 0.68801 / 0.34 (37531) SS BOND : bond 0.00361 / 0.22 ( 42) SS BOND : angle 1.49304 / 1.06 ( 84) hydrogen bonds : bond 0.05595 / 3.73 ( 1002) hydrogen bonds : angle 5.31893 / 3.62 ( 2727) link_ALPHA1-3 : bond 0.00756 / 0.40 ( 1) link_ALPHA1-3 : angle 1.74877 / 0.94 ( 3) link_BETA1-4 : bond 0.00466 / 0.30 ( 47) link_BETA1-4 : angle 1.50604 / 1.04 ( 141) link_NAG-ASN : bond 0.00326 / 0.20 ( 45) link_NAG-ASN : angle 2.24937 / 1.59 ( 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 265 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 182 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4539 (OUTLIER) cc_final: 0.4307 (t80) REVERT: A 416 TYR cc_start: 0.5248 (t80) cc_final: 0.4864 (t80) REVERT: A 461 ILE cc_start: 0.4193 (OUTLIER) cc_final: 0.3816 (pt) REVERT: A 812 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: A 895 MET cc_start: 0.8872 (tpt) cc_final: 0.8475 (tpt) REVERT: A 962 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8311 (t0) REVERT: A 1024 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: B 21 ARG cc_start: 0.5322 (mtt180) cc_final: 0.5002 (tpp80) REVERT: B 52 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 177 MET cc_start: 0.6048 (pmm) cc_final: 0.4315 (tpt) REVERT: B 417 LYS cc_start: 0.7519 (tttt) cc_final: 0.7301 (tptt) REVERT: B 446 TYR cc_start: 0.8446 (p90) cc_final: 0.7815 (p90) REVERT: B 466 TYR cc_start: 0.7630 (t80) cc_final: 0.7174 (t80) REVERT: B 1085 GLU cc_start: 0.8130 (tp30) cc_final: 0.7888 (tp30) REVERT: C 234 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6795 (p0) REVERT: C 449 PHE cc_start: 0.8093 (t80) cc_final: 0.7580 (t80) REVERT: C 466 TYR cc_start: 0.7481 (t80) cc_final: 0.6373 (t80) REVERT: C 477 GLU cc_start: 0.6120 (tp30) cc_final: 0.5734 (pp20) REVERT: C 555 PHE cc_start: 0.7715 (p90) cc_final: 0.7381 (p90) REVERT: C 769 LYS cc_start: 0.9150 (tppp) cc_final: 0.8916 (tptm) REVERT: C 866 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8984 (m-10) outliers start: 83 outliers final: 62 residues processed: 245 average time/residue: 0.1459 time to fit residues: 60.4165 Evaluate side-chains 233 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 186 PHE 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 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 902 ILE Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 962 ASN 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 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 546 THR 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 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 766 GLU 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 42 VAL Chi-restraints excluded: chain C residue 88 ASP 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 234 ASN Chi-restraints excluded: chain C residue 236 THR 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 736 CYS Chi-restraints excluded: chain C residue 746 LEU 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 968 SER 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: 5.9990 chunk 61 optimal weight: 0.9980 chunk 321 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 780 GLN A 829 GLN A 962 ASN ** 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** ** 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 = 0.4047 r_free = 0.4047 target = 0.126996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086691 restraints weight = 68438.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089406 restraints weight = 35253.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.091197 restraints weight = 23797.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092135 restraints weight = 18813.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092855 restraints weight = 16504.182| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27699 Z= 0.139 Angle : 0.688 14.885 37894 Z= 0.334 Chirality : 0.045 0.373 4529 Planarity : 0.004 0.055 4744 Dihedral : 4.821 30.155 3534 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 2.45 % Allowed : 19.51 % Favored : 78.04 % 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: -0.96 (0.14), residues: 3271 helix: 1.53 (0.19), residues: 752 sheet: -0.25 (0.20), residues: 667 loop : -1.80 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 758 TYR 0.024 0.001 TYR A 416 PHE 0.024 0.001 PHE A 133 TRP 0.018 0.001 TRP C 251 HIS 0.009 0.001 HIS C 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (27564) covalent geometry : angle 0.67014 / 0.33 (37531) SS BOND : bond 0.00338 / 0.20 ( 42) SS BOND : angle 1.38094 / 1.01 ( 84) hydrogen bonds : bond 0.05107 / 3.41 ( 1002) hydrogen bonds : angle 5.20562 / 3.54 ( 2727) link_ALPHA1-3 : bond 0.00718 / 0.38 ( 1) link_ALPHA1-3 : angle 1.64510 / 0.89 ( 3) link_BETA1-4 : bond 0.00458 / 0.30 ( 47) link_BETA1-4 : angle 1.45894 / 1.01 ( 141) link_NAG-ASN : bond 0.00317 / 0.20 ( 45) link_NAG-ASN : angle 2.14801 / 1.53 ( 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 246 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.4685 (OUTLIER) cc_final: 0.4421 (t80) REVERT: A 416 TYR cc_start: 0.5202 (t80) cc_final: 0.4785 (t80) REVERT: A 461 ILE cc_start: 0.4130 (OUTLIER) cc_final: 0.3731 (pt) REVERT: A 812 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 895 MET cc_start: 0.8836 (tpt) cc_final: 0.8433 (tpt) REVERT: A 1024 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6107 (mp0) REVERT: B 21 ARG cc_start: 0.5825 (mtt180) cc_final: 0.5071 (tpp80) REVERT: B 52 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 177 MET cc_start: 0.6143 (pmm) cc_final: 0.4409 (tpt) REVERT: B 446 TYR cc_start: 0.8422 (p90) cc_final: 0.7760 (p90) REVERT: B 466 TYR cc_start: 0.7566 (t80) cc_final: 0.7163 (t80) REVERT: B 874 THR cc_start: 0.8389 (m) cc_final: 0.8104 (m) REVERT: B 1085 GLU cc_start: 0.8201 (tp30) cc_final: 0.7941 (tp30) REVERT: C 234 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6799 (p0) REVERT: C 449 PHE cc_start: 0.8103 (t80) cc_final: 0.7562 (t80) REVERT: C 466 TYR cc_start: 0.7431 (t80) cc_final: 0.6426 (t80) REVERT: C 477 GLU cc_start: 0.6003 (tp30) cc_final: 0.5660 (pp20) REVERT: C 555 PHE cc_start: 0.7682 (p90) cc_final: 0.7315 (p90) REVERT: C 769 LYS cc_start: 0.9148 (tppp) cc_final: 0.8827 (tptp) REVERT: C 866 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8944 (m-10) outliers start: 70 outliers final: 60 residues processed: 230 average time/residue: 0.1601 time to fit residues: 61.8945 Evaluate side-chains 231 residues out of total 2889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 186 PHE 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 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 902 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 239 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 546 THR 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 623 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 766 GLU 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 42 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR 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 581 THR 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 746 LEU 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 24 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 184 optimal weight: 0.0050 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.125531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084818 restraints weight = 67846.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087534 restraints weight = 34926.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089328 restraints weight = 23607.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090420 restraints weight = 18690.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090963 restraints weight = 16289.226| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27699 Z= 0.199 Angle : 0.731 14.602 37894 Z= 0.356 Chirality : 0.046 0.382 4529 Planarity : 0.004 0.047 4744 Dihedral : 4.946 30.270 3534 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.34 % Allowed : 19.79 % Favored : 77.87 % 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: -1.08 (0.14), residues: 3271 helix: 1.46 (0.19), residues: 752 sheet: -0.36 (0.21), residues: 626 loop : -1.85 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 758 TYR 0.023 0.001 TYR C1060 PHE 0.034 0.002 PHE C 168 TRP 0.016 0.001 TRP A 64 HIS 0.010 0.001 HIS C 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (27564) covalent geometry : angle 0.71155 / 0.35 (37531) SS BOND : bond 0.00388 / 0.24 ( 42) SS BOND : angle 1.55898 / 1.12 ( 84) hydrogen bonds : bond 0.05741 / 3.83 ( 1002) hydrogen bonds : angle 5.34622 / 3.64 ( 2727) link_ALPHA1-3 : bond 0.00826 / 0.43 ( 1) link_ALPHA1-3 : angle 1.75695 / 0.95 ( 3) link_BETA1-4 : bond 0.00463 / 0.30 ( 47) link_BETA1-4 : angle 1.53320 / 1.05 ( 141) link_NAG-ASN : bond 0.00356 / 0.21 ( 45) link_NAG-ASN : angle 2.28952 / 1.61 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5718.41 seconds wall clock time: 99 minutes 9.93 seconds (5949.93 seconds total)