Starting phenix.real_space_refine on Thu Mar 5 18:41:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6f_23694/03_2026/7m6f_23694_neut.cif" } resolution = 3.9 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= 0.000 sd= 0.016 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 106 5.16 5 C 15415 2.51 5 N 4144 2.21 5 O 4639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24304 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 7026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7026 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 788 Unresolved non-hydrogen angles: 1010 Unresolved non-hydrogen dihedrals: 620 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 18, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 10, 'ARG:plan': 10, 'TYR:plan': 10, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "C" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 197 Conformer: "B" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 197 bond proxies already assigned to first conformer: 589 Chain: "D" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 7, 'HIS:plan': 2, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 7, 'HIS:plan': 2, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 518 Chain: "E" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASP:plan': 25, 'GLU:plan': 17, 'ASN:plan1': 29, 'GLN:plan1': 9, 'PHE:plan': 8, 'ARG:plan': 10, 'TYR:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 437 Chain: "H" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 197 Conformer: "B" Number of residues, atoms: 118, 591 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 6, 'TRP:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 197 bond proxies already assigned to first conformer: 589 Chain: "L" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 7, 'HIS:plan': 2, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 162 Conformer: "B" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'TYR:plan': 7, 'HIS:plan': 2, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 162 bond proxies already assigned to first conformer: 518 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASER C 17 " occ=0.35 ... (8 atoms not shown) pdb=" CB BSER C 17 " occ=0.65 residue: pdb=" N AARG D 54 " occ=0.46 ... (8 atoms not shown) pdb=" CB BARG D 54 " occ=0.54 residue: pdb=" N ASER H 17 " occ=0.35 ... (8 atoms not shown) pdb=" CB BSER H 17 " occ=0.65 residue: pdb=" N AARG L 54 " occ=0.46 ... (8 atoms not shown) pdb=" CB BARG L 54 " occ=0.54 Time building chain proxies: 6.13, per 1000 atoms: 0.25 Number of scatterers: 24304 At special positions: 0 Unit cell: (132.088, 134.695, 208.56, 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 106 16.00 O 4639 8.00 N 4144 7.00 C 15415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23574 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 282 " " NAG A1311 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 709 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 603 " " NAG E1303 " - " ASN E 657 " " NAG E1304 " - " ASN E1074 " " NAG E1305 " - " ASN E 61 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 331 " " NAG E1310 " - " ASN E 709 " " NAG E1311 " - " ASN E 616 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN E1098 " " NAG I 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN E 717 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 801 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6418 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 57 sheets defined 23.2% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.861A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.064A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.137A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.642A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.701A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.332A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.575A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.040A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.108A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.485A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.504A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.698A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.727A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.573A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.560A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.982A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.832A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.074A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.219A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.580A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 753 Processing helix chain 'E' and resid 754 through 757 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.644A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.376A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.518A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 967 Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.048A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.053A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27B through 31 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.514A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.547A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.377A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASN E 542 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.473A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.854A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.967A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.352A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.303A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.270A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.531A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.907A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.733A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.975A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.563A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.391A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.745A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.819A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.837A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.279A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.279A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.001A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.588A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.886A pdb=" N ALA B 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.541A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.514A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.440A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.223A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.565A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'C' and resid 57 through 58 removed outlier: 5.786A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 9 through 11 removed outlier: 7.083A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.882A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AE4, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.786A pdb=" N VAL E 62 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA E 93 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 273 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 271 " --> pdb=" O PHE E 55 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.454A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 120 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN E 122 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL E 126 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR E 170 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.649A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.067A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS E 356 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.609A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.683A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.880A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF9, first strand: chain 'H' and resid 57 through 58 removed outlier: 5.786A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 11 removed outlier: 7.082A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.883A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 89 through 90 1113 hydrogen bonds defined for protein. 3019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 2.37 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: 7542 1.33 - 1.46: 6324 1.46 - 1.59: 10797 1.59 - 1.72: 0 1.72 - 1.84: 130 Bond restraints: 24793 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.523 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.33e-02 5.65e+03 1.03e+01 bond pdb=" N GLN D 17 " pdb=" CA GLN D 17 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.88e+00 ... (remaining 24788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 33881 5.06 - 10.11: 112 10.11 - 15.17: 7 15.17 - 20.23: 0 20.23 - 25.29: 1 Bond angle restraints: 34001 Sorted by residual: angle pdb=" C ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 109.95 84.66 25.29 1.99e+00 2.53e-01 1.61e+02 angle pdb=" C ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 111.02 123.08 -12.06 1.61e+00 3.86e-01 5.61e+01 angle pdb=" N ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 110.41 120.86 -10.45 1.68e+00 3.54e-01 3.87e+01 angle pdb=" CG ARG B 273 " pdb=" CD ARG B 273 " pdb=" NE ARG B 273 " ideal model delta sigma weight residual 112.00 99.01 12.99 2.20e+00 2.07e-01 3.49e+01 angle pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " pdb=" CG ASN A 709 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.00e+00 1.00e+00 3.41e+01 ... (remaining 33996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 14960 24.23 - 48.47: 374 48.47 - 72.70: 86 72.70 - 96.94: 23 96.94 - 121.17: 4 Dihedral angle restraints: 15447 sinusoidal: 5493 harmonic: 9954 Sorted by residual: dihedral pdb=" C ASN A 709 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta harmonic sigma weight residual -122.60 -98.28 -24.32 0 2.50e+00 1.60e-01 9.47e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 175.66 -82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.16 66.16 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 15444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4183 0.264 - 0.528: 15 0.528 - 0.791: 3 0.791 - 1.055: 0 1.055 - 1.319: 2 Chirality restraints: 4203 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.52e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.82e+01 chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.21 -1.32 2.00e-01 2.50e+01 4.35e+01 ... (remaining 4200 not shown) Planarity restraints: 4487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.184 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG G 1 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.134 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.250 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.154 2.00e-02 2.50e+03 1.28e-01 2.05e+02 pdb=" C7 NAG F 1 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.207 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.145 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" C7 NAG G 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.108 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.191 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 4484 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 104 2.48 - 3.08: 16669 3.08 - 3.69: 35195 3.69 - 4.29: 49399 4.29 - 4.90: 82499 Nonbonded interactions: 183866 Sorted by model distance: nonbonded pdb=" OH TYR A 421 " pdb=" CG PRO H 53 " model vdw 1.869 3.440 nonbonded pdb=" OH TYR A 421 " pdb=" CD PRO H 53 " model vdw 1.875 3.440 nonbonded pdb=" OH TYR A 421 " pdb=" N GLY H 54 " model vdw 1.925 3.120 nonbonded pdb=" OH TYR A 421 " pdb=" CB PRO H 53 " model vdw 2.019 3.440 nonbonded pdb=" OD1 ASN B 122 " pdb=" N2 NAG B1307 " model vdw 2.079 3.120 ... (remaining 183861 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 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) selection = (chain 'B' and (resid 27 through 510 or (resid 511 through 512 and (name N or na \ me CA or name C or name O or name CB )) or resid 513 through 1311)) selection = (chain 'E' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 374 or \ (resid 375 through 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 920 or (resid 921 and (name N or name CA or name C or name \ O or name CB )) or resid 922 through 1311)) } ncs_group { reference = (chain 'C' and (resid 2 through 16 or resid 18 through 116)) selection = (chain 'H' and (resid 2 through 16 or resid 18 through 116)) } ncs_group { reference = (chain 'D' and (resid 3 through 9 or resid 12 through 19 or resid 21 through 53 \ or resid 55 through 106)) selection = (chain 'L' and (resid 3 through 9 or resid 12 through 19 or resid 21 through 53 \ or resid 55 through 106)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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=0.18 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: 5.450 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.810 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 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 : 0.006 0.117 24897 Z= 0.312 Angle : 1.152 28.521 34272 Z= 0.608 Chirality : 0.069 1.319 4203 Planarity : 0.006 0.153 4439 Dihedral : 11.514 121.170 8906 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.12 % 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: 0.42 (0.14), residues: 3402 helix: 0.98 (0.19), residues: 628 sheet: 0.62 (0.19), residues: 737 loop : 0.00 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG B 273 TYR 0.036 0.002 TYR A 707 PHE 0.039 0.003 PHE A1042 TRP 0.021 0.002 TRP B1102 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00611 (24793) covalent geometry : angle 1.00281 (34001) SS BOND : bond 0.00433 ( 41) SS BOND : angle 1.95951 ( 82) hydrogen bonds : bond 0.24510 ( 1111) hydrogen bonds : angle 10.05669 ( 3019) link_BETA1-4 : bond 0.01386 ( 15) link_BETA1-4 : angle 4.77999 ( 45) link_NAG-ASN : bond 0.01929 ( 48) link_NAG-ASN : angle 8.31581 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8267 (t80) cc_final: 0.7915 (t80) REVERT: A 1049 LEU cc_start: 0.8785 (mt) cc_final: 0.8475 (mp) REVERT: A 1081 ILE cc_start: 0.8212 (mm) cc_final: 0.7820 (mm) REVERT: E 592 PHE cc_start: 0.7183 (p90) cc_final: 0.6652 (p90) REVERT: E 759 PHE cc_start: 0.7544 (m-80) cc_final: 0.7342 (m-80) REVERT: E 1002 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8635 (tm-30) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1323 time to fit residues: 45.2022 Evaluate side-chains 97 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B1002 GLN B1135 ASN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 935 GLN E1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.096641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067320 restraints weight = 189574.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069803 restraints weight = 83788.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.070321 restraints weight = 46493.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071088 restraints weight = 35575.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070936 restraints weight = 35031.667| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24897 Z= 0.174 Angle : 0.746 17.335 34272 Z= 0.364 Chirality : 0.051 0.538 4203 Planarity : 0.005 0.060 4439 Dihedral : 8.052 114.814 4928 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 1.05 % Allowed : 6.05 % Favored : 92.90 % 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: 0.81 (0.14), residues: 3402 helix: 2.07 (0.19), residues: 658 sheet: 0.68 (0.18), residues: 779 loop : 0.01 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.026 0.002 TYR A 421 PHE 0.024 0.002 PHE B 238 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00374 (24793) covalent geometry : angle 0.67750 (34001) SS BOND : bond 0.00252 ( 41) SS BOND : angle 1.03956 ( 82) hydrogen bonds : bond 0.04939 ( 1111) hydrogen bonds : angle 7.32630 ( 3019) link_BETA1-4 : bond 0.00684 ( 15) link_BETA1-4 : angle 1.90691 ( 45) link_NAG-ASN : bond 0.00891 ( 48) link_NAG-ASN : angle 4.72807 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: A 925 ASN cc_start: 0.8562 (t0) cc_final: 0.8330 (t0) REVERT: B 740 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8337 (tpt) REVERT: E 592 PHE cc_start: 0.6908 (p90) cc_final: 0.6586 (p90) REVERT: E 740 MET cc_start: 0.8992 (tpp) cc_final: 0.8633 (tpp) REVERT: E 1002 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8200 (tm-30) outliers start: 20 outliers final: 9 residues processed: 134 average time/residue: 0.1245 time to fit residues: 29.9758 Evaluate side-chains 106 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 935 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 125 optimal weight: 40.0000 chunk 243 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 209 optimal weight: 40.0000 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 153 optimal weight: 6.9990 chunk 331 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1010 GLN B 901 GLN E 901 GLN ** E 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.086272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057274 restraints weight = 257280.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059741 restraints weight = 97603.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061356 restraints weight = 50745.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062288 restraints weight = 30113.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062333 restraints weight = 23968.204| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 24897 Z= 0.196 Angle : 0.714 27.955 34272 Z= 0.339 Chirality : 0.049 0.530 4203 Planarity : 0.004 0.050 4439 Dihedral : 7.136 106.059 4928 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.31 % Allowed : 7.94 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3402 helix: 2.13 (0.20), residues: 658 sheet: 0.29 (0.18), residues: 799 loop : -0.15 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 815 TYR 0.018 0.002 TYR A 204 PHE 0.022 0.002 PHE B 135 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00437 (24793) covalent geometry : angle 0.63552 (34001) SS BOND : bond 0.00232 ( 41) SS BOND : angle 1.06158 ( 82) hydrogen bonds : bond 0.04163 ( 1111) hydrogen bonds : angle 6.47373 ( 3019) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 1.52547 ( 45) link_NAG-ASN : bond 0.01231 ( 48) link_NAG-ASN : angle 4.95389 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8529 (t80) cc_final: 0.8149 (t80) REVERT: A 586 ASP cc_start: 0.7975 (m-30) cc_final: 0.7764 (m-30) REVERT: A 1031 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: B 819 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 592 PHE cc_start: 0.7346 (p90) cc_final: 0.7023 (p90) REVERT: E 740 MET cc_start: 0.8840 (tpp) cc_final: 0.8464 (tpp) REVERT: E 759 PHE cc_start: 0.8167 (m-80) cc_final: 0.7943 (m-80) REVERT: E 1002 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8447 (tm-30) outliers start: 25 outliers final: 14 residues processed: 114 average time/residue: 0.1287 time to fit residues: 26.5292 Evaluate side-chains 99 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 258 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 321 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1135 ASN E 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.090455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.061460 restraints weight = 232976.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063401 restraints weight = 99689.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064698 restraints weight = 58188.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065490 restraints weight = 40537.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066029 restraints weight = 32030.138| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24897 Z= 0.180 Angle : 0.660 18.608 34272 Z= 0.315 Chirality : 0.048 0.525 4203 Planarity : 0.004 0.059 4439 Dihedral : 6.244 101.520 4928 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.95 % Allowed : 8.41 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3402 helix: 2.21 (0.20), residues: 662 sheet: 0.26 (0.18), residues: 789 loop : -0.24 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.021 0.002 TYR B 741 PHE 0.021 0.002 PHE B 338 TRP 0.010 0.001 TRP A 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00400 (24793) covalent geometry : angle 0.59056 (34001) SS BOND : bond 0.00224 ( 41) SS BOND : angle 0.98782 ( 82) hydrogen bonds : bond 0.03706 ( 1111) hydrogen bonds : angle 6.09896 ( 3019) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.32524 ( 45) link_NAG-ASN : bond 0.00884 ( 48) link_NAG-ASN : angle 4.49506 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8599 (t80) cc_final: 0.8268 (t80) REVERT: A 925 ASN cc_start: 0.8916 (t0) cc_final: 0.8683 (t0) REVERT: E 592 PHE cc_start: 0.7477 (p90) cc_final: 0.7231 (p90) REVERT: E 740 MET cc_start: 0.8724 (tpp) cc_final: 0.8493 (tpp) REVERT: E 864 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9094 (mm) REVERT: E 1002 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8518 (tm-30) outliers start: 37 outliers final: 18 residues processed: 116 average time/residue: 0.1270 time to fit residues: 26.4182 Evaluate side-chains 92 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 208 optimal weight: 50.0000 chunk 59 optimal weight: 6.9990 chunk 168 optimal weight: 0.0170 chunk 197 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 141 optimal weight: 50.0000 chunk 65 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 337 optimal weight: 50.0000 chunk 147 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B1135 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.090723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066152 restraints weight = 250011.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066065 restraints weight = 114940.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066361 restraints weight = 83470.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066791 restraints weight = 71499.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066747 restraints weight = 62514.915| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24897 Z= 0.136 Angle : 0.611 21.305 34272 Z= 0.291 Chirality : 0.047 0.592 4203 Planarity : 0.004 0.044 4439 Dihedral : 5.856 99.113 4928 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 1.84 % Allowed : 9.04 % Favored : 89.12 % 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: 0.57 (0.14), residues: 3402 helix: 2.27 (0.20), residues: 668 sheet: 0.26 (0.18), residues: 797 loop : -0.20 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.013 0.001 TYR E1067 PHE 0.019 0.001 PHE E 374 TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00302 (24793) covalent geometry : angle 0.54176 (34001) SS BOND : bond 0.00167 ( 41) SS BOND : angle 0.90069 ( 82) hydrogen bonds : bond 0.03499 ( 1111) hydrogen bonds : angle 5.90983 ( 3019) link_BETA1-4 : bond 0.00421 ( 15) link_BETA1-4 : angle 1.23320 ( 45) link_NAG-ASN : bond 0.00802 ( 48) link_NAG-ASN : angle 4.32442 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 318 PHE cc_start: 0.8641 (t80) cc_final: 0.8255 (t80) REVERT: B 819 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: E 740 MET cc_start: 0.8794 (tpp) cc_final: 0.8536 (tpp) REVERT: E 864 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9060 (mm) REVERT: E 1002 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8376 (tm-30) outliers start: 35 outliers final: 22 residues processed: 105 average time/residue: 0.1296 time to fit residues: 24.3007 Evaluate side-chains 99 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 264 optimal weight: 2.9990 chunk 329 optimal weight: 0.0670 chunk 212 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 52 optimal weight: 0.0970 chunk 222 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 265 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.089759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061579 restraints weight = 237257.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064394 restraints weight = 108412.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064347 restraints weight = 61158.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.064983 restraints weight = 43977.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065210 restraints weight = 38598.916| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24897 Z= 0.168 Angle : 0.622 19.554 34272 Z= 0.298 Chirality : 0.048 0.636 4203 Planarity : 0.004 0.040 4439 Dihedral : 5.667 95.216 4928 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 1.95 % Allowed : 9.94 % Favored : 88.12 % 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: 0.49 (0.14), residues: 3402 helix: 2.22 (0.20), residues: 665 sheet: 0.20 (0.18), residues: 802 loop : -0.25 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 815 TYR 0.025 0.001 TYR A 421 PHE 0.030 0.002 PHE E 592 TRP 0.008 0.001 TRP E1102 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00375 (24793) covalent geometry : angle 0.55664 (34001) SS BOND : bond 0.00244 ( 41) SS BOND : angle 0.96569 ( 82) hydrogen bonds : bond 0.03524 ( 1111) hydrogen bonds : angle 5.86129 ( 3019) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.23100 ( 45) link_NAG-ASN : bond 0.00780 ( 48) link_NAG-ASN : angle 4.22139 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: B 819 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: E 740 MET cc_start: 0.8806 (tpp) cc_final: 0.8545 (tpp) REVERT: E 1002 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8759 (tp40) outliers start: 37 outliers final: 23 residues processed: 106 average time/residue: 0.1314 time to fit residues: 24.7184 Evaluate side-chains 96 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 125 optimal weight: 0.2980 chunk 109 optimal weight: 0.2980 chunk 256 optimal weight: 40.0000 chunk 307 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 255 optimal weight: 50.0000 chunk 103 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 334 optimal weight: 50.0000 chunk 226 optimal weight: 30.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1135 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.083863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.057585 restraints weight = 267699.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060129 restraints weight = 114762.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060241 restraints weight = 56861.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.060428 restraints weight = 44025.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060543 restraints weight = 39864.451| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24897 Z= 0.217 Angle : 0.655 18.708 34272 Z= 0.319 Chirality : 0.048 0.629 4203 Planarity : 0.004 0.056 4439 Dihedral : 5.834 89.627 4928 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.10 % Allowed : 10.46 % Favored : 87.43 % 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: 0.37 (0.14), residues: 3402 helix: 2.16 (0.20), residues: 664 sheet: 0.02 (0.17), residues: 810 loop : -0.29 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 328 TYR 0.035 0.002 TYR A 421 PHE 0.022 0.002 PHE E 592 TRP 0.012 0.001 TRP A 436 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00487 (24793) covalent geometry : angle 0.59462 (34001) SS BOND : bond 0.00269 ( 41) SS BOND : angle 1.04913 ( 82) hydrogen bonds : bond 0.03740 ( 1111) hydrogen bonds : angle 5.97812 ( 3019) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 1.24690 ( 45) link_NAG-ASN : bond 0.00811 ( 48) link_NAG-ASN : angle 4.19237 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8525 (mm) cc_final: 0.8053 (mm) REVERT: A 306 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 318 PHE cc_start: 0.8815 (t80) cc_final: 0.8507 (t80) REVERT: B 133 PHE cc_start: 0.6745 (m-80) cc_final: 0.6467 (m-80) REVERT: B 819 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: E 740 MET cc_start: 0.8789 (tpp) cc_final: 0.8539 (tpp) REVERT: E 1002 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8823 (tp40) outliers start: 40 outliers final: 30 residues processed: 103 average time/residue: 0.1242 time to fit residues: 22.7596 Evaluate side-chains 98 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 227 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 284 optimal weight: 0.8980 chunk 319 optimal weight: 50.0000 chunk 264 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 777 ASN B1108 ASN B1135 ASN ** E 965 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 = 0.3909 r_free = 0.3909 target = 0.089696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062154 restraints weight = 230342.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065382 restraints weight = 110246.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.065177 restraints weight = 52354.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065255 restraints weight = 44057.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.065445 restraints weight = 43639.811| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24897 Z= 0.115 Angle : 0.578 18.991 34272 Z= 0.277 Chirality : 0.047 0.538 4203 Planarity : 0.004 0.043 4439 Dihedral : 5.428 90.499 4928 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 11.62 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3402 helix: 2.37 (0.20), residues: 665 sheet: 0.10 (0.18), residues: 802 loop : -0.27 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.027 0.001 TYR A 421 PHE 0.021 0.001 PHE B 238 TRP 0.008 0.001 TRP A 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00255 (24793) covalent geometry : angle 0.51428 (34001) SS BOND : bond 0.00171 ( 41) SS BOND : angle 0.75621 ( 82) hydrogen bonds : bond 0.03272 ( 1111) hydrogen bonds : angle 5.66156 ( 3019) link_BETA1-4 : bond 0.00415 ( 15) link_BETA1-4 : angle 1.12888 ( 45) link_NAG-ASN : bond 0.00763 ( 48) link_NAG-ASN : angle 4.04072 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8663 (mm) cc_final: 0.8152 (mm) REVERT: A 306 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: B 819 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: E 740 MET cc_start: 0.8756 (tpp) cc_final: 0.8471 (tpp) REVERT: E 1002 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8764 (tp40) outliers start: 26 outliers final: 21 residues processed: 98 average time/residue: 0.1357 time to fit residues: 23.5945 Evaluate side-chains 95 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 111 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.083590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058241 restraints weight = 224347.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060321 restraints weight = 104906.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060117 restraints weight = 56662.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060337 restraints weight = 51666.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060706 restraints weight = 39482.037| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24897 Z= 0.214 Angle : 0.640 18.263 34272 Z= 0.310 Chirality : 0.048 0.525 4203 Planarity : 0.004 0.048 4439 Dihedral : 5.640 86.264 4928 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.68 % Allowed : 11.57 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3402 helix: 2.31 (0.20), residues: 661 sheet: -0.05 (0.17), residues: 802 loop : -0.35 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 815 TYR 0.026 0.001 TYR A 421 PHE 0.022 0.002 PHE E 92 TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00478 (24793) covalent geometry : angle 0.58067 (34001) SS BOND : bond 0.00241 ( 41) SS BOND : angle 0.94295 ( 82) hydrogen bonds : bond 0.03645 ( 1111) hydrogen bonds : angle 5.83092 ( 3019) link_BETA1-4 : bond 0.00284 ( 15) link_BETA1-4 : angle 1.27490 ( 45) link_NAG-ASN : bond 0.00802 ( 48) link_NAG-ASN : angle 4.10391 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8620 (mm) cc_final: 0.8170 (mm) REVERT: A 306 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: B 819 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: E 740 MET cc_start: 0.8779 (tpp) cc_final: 0.8341 (tpp) REVERT: E 1002 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8810 (tp40) outliers start: 32 outliers final: 24 residues processed: 95 average time/residue: 0.1305 time to fit residues: 21.8259 Evaluate side-chains 92 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 116 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 201 optimal weight: 30.0000 chunk 167 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1071 GLN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.087155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061614 restraints weight = 308515.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061560 restraints weight = 150915.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062317 restraints weight = 100383.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062206 restraints weight = 91464.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.062775 restraints weight = 70596.199| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 24897 Z= 0.238 Angle : 0.661 18.480 34272 Z= 0.322 Chirality : 0.048 0.511 4203 Planarity : 0.004 0.054 4439 Dihedral : 5.861 83.901 4928 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.68 % Allowed : 11.72 % Favored : 86.59 % 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: 0.20 (0.14), residues: 3402 helix: 2.17 (0.20), residues: 664 sheet: -0.14 (0.17), residues: 804 loop : -0.44 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 815 TYR 0.026 0.002 TYR A 421 PHE 0.024 0.002 PHE B 238 TRP 0.013 0.002 TRP A 436 HIS 0.006 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00531 (24793) covalent geometry : angle 0.60197 (34001) SS BOND : bond 0.00269 ( 41) SS BOND : angle 0.95514 ( 82) hydrogen bonds : bond 0.03740 ( 1111) hydrogen bonds : angle 5.94078 ( 3019) link_BETA1-4 : bond 0.00268 ( 15) link_BETA1-4 : angle 1.24431 ( 45) link_NAG-ASN : bond 0.00813 ( 48) link_NAG-ASN : angle 4.17128 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8599 (mm) cc_final: 0.8192 (mm) REVERT: A 306 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: B 819 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: E 740 MET cc_start: 0.8822 (tpp) cc_final: 0.8398 (tpp) REVERT: E 1002 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8842 (tp40) outliers start: 32 outliers final: 25 residues processed: 97 average time/residue: 0.1340 time to fit residues: 22.8646 Evaluate side-chains 93 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 864 LEU Chi-restraints excluded: chain E residue 915 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 997 ILE Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 153 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 0.0670 chunk 334 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 323 optimal weight: 0.4980 chunk 228 optimal weight: 9.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B1135 ASN ** E 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.084673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059327 restraints weight = 254144.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061727 restraints weight = 109799.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061510 restraints weight = 55108.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061820 restraints weight = 45348.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.061926 restraints weight = 37566.851| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24897 Z= 0.112 Angle : 0.579 18.439 34272 Z= 0.279 Chirality : 0.047 0.501 4203 Planarity : 0.004 0.053 4439 Dihedral : 5.419 85.712 4928 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.16 % Allowed : 12.41 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3402 helix: 2.36 (0.20), residues: 664 sheet: -0.03 (0.18), residues: 773 loop : -0.36 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.025 0.001 TYR A 421 PHE 0.027 0.001 PHE B 238 TRP 0.010 0.001 TRP A1102 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00246 (24793) covalent geometry : angle 0.51735 (34001) SS BOND : bond 0.00119 ( 41) SS BOND : angle 0.74745 ( 82) hydrogen bonds : bond 0.03260 ( 1111) hydrogen bonds : angle 5.59445 ( 3019) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 1.14804 ( 45) link_NAG-ASN : bond 0.00763 ( 48) link_NAG-ASN : angle 3.97633 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.02 seconds wall clock time: 72 minutes 4.64 seconds (4324.64 seconds total)